Mercurial > repos > greg > snpeff_v2_from_pablo
changeset 0:f8eaa3f8194b default tip
Uploaded snpEff_v2_1a_core.tgz from Pablo Cingolani
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpEff.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,482 @@ +<tool id="snpEff" name="SnpEff" version="1.0"> + <description>Variant efefct and annotation</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used by snpEff, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + <command>java -Xmx6G -jar /path/to/your/snpEff/snpEff.jar eff -c /path/to/your/snpEff/snpEff/snpEff.config $inputFormat $offset -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> + --> + <command>java -Xmx6G -jar /Users/pablocingolani/snpEff/snpEff.jar eff -c /Users/pablocingolani/snpEff/snpEff.config -i $inputFormat -o $outputFormat -upDownStreamLen $udLength $filterIn $filterHomHet -no $filterOut -stats $statsFile $genomeVersion $input > $output </command> + <inputs> + <param format="Tabular" name="input" type="data" label="Sequence changes (SNPs, MNPs, InDels)"/> + + <param name="inputFormat" type="select" label="Input format"> + <option value="vcf">VCF</option> + <option value="txt">Tabular</option> + <option value="pileup">Pileup</option> + <option value="bed">BED</option> + </param> + + <param name="outputFormat" type="select" label="Output format"> + <option value="txt">Tabular</option> + <option value="vcf">VCF (only if input is VCF)</option> + <option value="bed">BED</option> + <option value="bedAnn">BED Annotations</option> + </param> + + <param name="genomeVersion" type="select" label="Genome"> + <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> + <option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option> + <option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option> + <option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option> + <option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option> + <option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option> + <option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option> + <option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option> + <option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option> + <option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option> + <option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option> + <option value="agam2.6">Anopheles gambiae : agam2.6</option> + <option value="agam">Anopheles gambiae : agam</option> + <option value="aquiCoer">Aquilegia coerulea : aquiCoer</option> + <option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option> + <option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option> + <option value="athaliana130">Arabidopsis Thaliana : athaliana130</option> + <option value="alyrata107">Arabidopsis lyrata : alyrata107</option> + <option value="alyrata1">Arabidopsis lyrata : alyrata1</option> + <option value="amel2">Bee : amel2</option> + <option value="btau4.0.61">Bos taurus : btau4.0.61</option> + <option value="btau4.0.60">Bos taurus : btau4.0.60</option> + <option value="btau4.0.59">Bos taurus : btau4.0.59</option> + <option value="UMD3_1">Bos taurus : UMD3_1</option> + <option value="UMD3.1.66">Bos taurus : UMD3.1.66</option> + <option value="UMD3.1.65">Bos taurus : UMD3.1.65</option> + <option value="UMD3.1.64">Bos taurus : UMD3.1.64</option> + <option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option> + <option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option> + <option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option> + <option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option> + <option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option> + <option value="WS220.66">Caenorhabditis elegans : WS220.66</option> + <option value="WS220.65">Caenorhabditis elegans : WS220.65</option> + <option value="WS220.64">Caenorhabditis elegans : WS220.64</option> + <option value="WS220.63">Caenorhabditis elegans : WS220.63</option> + <option value="calJac3.2.1.61">Callithrix jacchus : calJac3.2.1.61</option> + <option value="calJac3.2.1.60">Callithrix jacchus : calJac3.2.1.60</option> + <option value="C_jacchus3.2.1.66">Callithrix jacchus : C_jacchus3.2.1.66</option> + <option value="C_jacchus3.2.1.65">Callithrix jacchus : C_jacchus3.2.1.65</option> + <option value="C_jacchus3.2.1.64">Callithrix jacchus : C_jacchus3.2.1.64</option> + <option value="C_jacchus3.2.1.63">Callithrix jacchus : C_jacchus3.2.1.63</option> + <option value="cAlbicansv21">Candida albicans SC5314 : cAlbicansv21</option> + <option value="canFam2.61">Canis familiaris : canFam2.61</option> + <option value="canFam2.60">Canis familiaris : canFam2.60</option> + <option value="canFam2.59">Canis familiaris : canFam2.59</option> + <option value="BROADD2.66">Canis familiaris : BROADD2.66</option> + <option value="BROADD2.65">Canis familiaris : BROADD2.65</option> + <option value="BROADD2.64">Canis familiaris : BROADD2.64</option> + <option value="BROADD2.63">Canis familiaris : BROADD2.63</option> + <option value="crubella">Capsella rubella v1.0 : crubella</option> + <option value="cavPor3.66">Cavia porcellus : cavPor3.66</option> + <option value="cavPor3.65">Cavia porcellus : cavPor3.65</option> + <option value="cavPor3.64">Cavia porcellus : cavPor3.64</option> + <option value="cavPor3.63">Cavia porcellus : cavPor3.63</option> + <option value="cavPor3.61">Cavia porcellus : cavPor3.61</option> + <option value="cavPor3.60">Cavia porcellus : cavPor3.60</option> + <option value="choHof1.66">Choloepus hoffmanni : choHof1.66</option> + <option value="choHof1.65">Choloepus hoffmanni : choHof1.65</option> + <option value="choHof1.64">Choloepus hoffmanni : choHof1.64</option> + <option value="choHof1.63">Choloepus hoffmanni : choHof1.63</option> + <option value="choHof1.61">Choloepus hoffmanni : choHof1.61</option> + <option value="choHof1.60">Choloepus hoffmanni : choHof1.60</option> + <option value="cInt2.61">Ciona intestinalis : cInt2.61</option> + <option value="cInt2.60">Ciona intestinalis : cInt2.60</option> + <option value="KH.66">Ciona intestinalis : KH.66</option> + <option value="JGI2.65">Ciona intestinalis : JGI2.65</option> + <option value="JGI2.64">Ciona intestinalis : JGI2.64</option> + <option value="JGI2.63">Ciona intestinalis : JGI2.63</option> + <option value="cSav2.0.61">Ciona savignyi : cSav2.0.61</option> + <option value="cSav2.0.60">Ciona savignyi : cSav2.0.60</option> + <option value="CSAV2.0.66">Ciona savignyi : CSAV2.0.66</option> + <option value="CSAV2.0.65">Ciona savignyi : CSAV2.0.65</option> + <option value="CSAV2.0.64">Ciona savignyi : CSAV2.0.64</option> + <option value="CSAV2.0.63">Ciona savignyi : CSAV2.0.63</option> + <option value="NC_009089.1">Clostridium difficile : NC_009089.1</option> + <option value="c_neoformans">Cryptococcus neoformans : c_neoformans</option> + <option value="danRer9.61">Danio rerio : danRer9.61</option> + <option value="danRer9.60">Danio rerio : danRer9.60</option> + <option value="danRer8.59">Danio rerio : danRer8.59</option> + <option value="Zv9.66">Danio rerio : Zv9.66</option> + <option value="Zv9.65">Danio rerio : Zv9.65</option> + <option value="Zv9.64">Danio rerio : Zv9.64</option> + <option value="Zv9.63">Danio rerio : Zv9.63</option> + <option value="dasNov2.66">Dasypus novemcinctus : dasNov2.66</option> + <option value="dasNov2.65">Dasypus novemcinctus : dasNov2.65</option> + <option value="dasNov2.64">Dasypus novemcinctus : dasNov2.64</option> + <option value="dasNov2.63">Dasypus novemcinctus : dasNov2.63</option> + <option value="dasNov2.61">Dasypus novemcinctus : dasNov2.61</option> + <option value="dasNov2.60">Dasypus novemcinctus : dasNov2.60</option> + <option value="dipOrd1.66">Dipodomys ordii : dipOrd1.66</option> + <option value="dipOrd1.65">Dipodomys ordii : dipOrd1.65</option> + <option value="dipOrd1.64">Dipodomys ordii : dipOrd1.64</option> + <option value="dipOrd1.63">Dipodomys ordii : dipOrd1.63</option> + <option value="dipOrd1.61">Dipodomys ordii : dipOrd1.61</option> + <option value="dipOrd1.60">Dipodomys ordii : dipOrd1.60</option> + <option value="dm5.42">Drosophila melanogaster : dm5.42</option> + <option value="dm5.40">Drosophila melanogaster : dm5.40</option> + <option value="dm5.34">Drosophila melanogaster : dm5.34</option> + <option value="dm5.32">Drosophila melanogaster : dm5.32</option> + <option value="dm5.31">Drosophila melanogaster : dm5.31</option> + <option value="dm5.30">Drosophila melanogaster : dm5.30</option> + <option value="dm5.25.63">Drosophila melanogaster : dm5.25.63</option> + <option value="dm5.25.61">Drosophila melanogaster : dm5.25.61</option> + <option value="dm5.25.60">Drosophila melanogaster : dm5.25.60</option> + <option value="dm5.25.59">Drosophila melanogaster : dm5.25.59</option> + <option value="dm5.22">Drosophila melanogaster : dm5.22</option> + <option value="dm5.12">Drosophila melanogaster : dm5.12</option> + <option value="BDGP5.66">Drosophila melanogaster : BDGP5.66</option> + <option value="BDGP5.25.65">Drosophila melanogaster : BDGP5.25.65</option> + <option value="BDGP5.25.64">Drosophila melanogaster : BDGP5.25.64</option> + <option value="BDGP5.25.63">Drosophila melanogaster : BDGP5.25.63</option> + <option value="tenrec1.61">Echinops telfairi : tenrec1.61</option> + <option value="tenrec1.60">Echinops telfairi : tenrec1.60</option> + <option value="TENREC.66">Echinops telfairi : TENREC.66</option> + <option value="TENREC.65">Echinops telfairi : TENREC.65</option> + <option value="TENREC.64">Echinops telfairi : TENREC.64</option> + <option value="TENREC.63">Echinops telfairi : TENREC.63</option> + <option value="equCab2.61">Equus caballus : equCab2.61</option> + <option value="equCab2.60">Equus caballus : equCab2.60</option> + <option value="EquCab2.66">Equus caballus : EquCab2.66</option> + <option value="EquCab2.65">Equus caballus : EquCab2.65</option> + <option value="EquCab2.64">Equus caballus : EquCab2.64</option> + <option value="EquCab2.63">Equus caballus : EquCab2.63</option> + <option value="eriEur1.61">Erinaceus europaeus : eriEur1.61</option> + <option value="eriEur1.60">Erinaceus europaeus : eriEur1.60</option> + <option value="HEDGEHOG.66">Erinaceus europaeus : HEDGEHOG.66</option> + <option value="HEDGEHOG.65">Erinaceus europaeus : HEDGEHOG.65</option> + <option value="HEDGEHOG.64">Erinaceus europaeus : HEDGEHOG.64</option> + <option value="HEDGEHOG.63">Erinaceus europaeus : HEDGEHOG.63</option> + <option value="NC_000913">Escherichia coli : NC_000913</option> + <option value="cat1.61">Felis catus : cat1.61</option> + <option value="cat1.60">Felis catus : cat1.60</option> + <option value="CAT.66">Felis catus : CAT.66</option> + <option value="CAT.65">Felis catus : CAT.65</option> + <option value="CAT.64">Felis catus : CAT.64</option> + <option value="CAT.63">Felis catus : CAT.63</option> + <option value="gadMor1.66">Gadus morhua : gadMor1.66</option> + <option value="ggallus2.61">Gallus gallus : ggallus2.61</option> + <option value="ggallus2.60">Gallus gallus : ggallus2.60</option> + <option value="ggallus2.59">Gallus gallus : ggallus2.59</option> + <option value="WASHUC2.66">Gallus gallus : WASHUC2.66</option> + <option value="WASHUC2.65">Gallus gallus : WASHUC2.65</option> + <option value="WASHUC2.64">Gallus gallus : WASHUC2.64</option> + <option value="WASHUC2.63">Gallus gallus : WASHUC2.63</option> + <option value="gacu1.61">Gasterosteus aculeatus : gacu1.61</option> + <option value="gacu1.60">Gasterosteus aculeatus : gacu1.60</option> + <option value="BROADS1.66">Gasterosteus aculeatus : BROADS1.66</option> + <option value="BROADS1.65">Gasterosteus aculeatus : BROADS1.65</option> + <option value="BROADS1.64">Gasterosteus aculeatus : BROADS1.64</option> + <option value="BROADS1.63">Gasterosteus aculeatus : BROADS1.63</option> + <option value="gmax1.09v8">Glycine Max : gmax1.09v8</option> + <option value="gmax1.09">Glycine Max : gmax1.09</option> + <option value="gorGor3.63">Gorilla gorilla : gorGor3.63</option> + <option value="gorGor3.61">Gorilla gorilla : gorGor3.61</option> + <option value="gorGor3.60">Gorilla gorilla : gorGor3.60</option> + <option value="gorGor3.1.66">Gorilla gorilla : gorGor3.1.66</option> + <option value="gorGor3.1.65">Gorilla gorilla : gorGor3.1.65</option> + <option value="gorGor3.1.64">Gorilla gorilla : gorGor3.1.64</option> + <option value="kw1407.2012">Grosmannia clavigera : kw1407.2012</option> + <option value="hiv">HIV : hiv</option> + <option value="SIVmac239">HIV : SIVmac239</option> + <option value="herpesvirus1">Herpesvirus : herpesvirus1</option> + <option value="hg37.63">Homo sapiens : hg37.63</option> + <option value="hg37.61">Homo sapiens : hg37.61</option> + <option value="hg37.60">Homo sapiens : hg37.60</option> + <option value="hg37.59">Homo sapiens : hg37.59</option> + <option value="hg36.54">Homo sapiens : hg36.54</option> + <option value="hg19">Homo sapiens : hg19</option> + <option value="GRCh37.66">Homo sapiens : GRCh37.66</option> + <option value="GRCh37.65">Homo sapiens : GRCh37.65</option> + <option value="GRCh37.64">Homo sapiens : GRCh37.64</option> + <option value="GRCh37.63">Homo sapiens : GRCh37.63</option> + <option value="LatCha1.66">Latimeria chalumnae : LatCha1.66</option> + <option value="lmjf4">LmajorFriedlin : lmjf4</option> + <option value="loxAfr3.66">Loxodonta africana : loxAfr3.66</option> + <option value="loxAfr3.65">Loxodonta africana : loxAfr3.65</option> + <option value="loxAfr3.64">Loxodonta africana : loxAfr3.64</option> + <option value="loxAfr3.63">Loxodonta africana : loxAfr3.63</option> + <option value="loxAfr3.61">Loxodonta africana : loxAfr3.61</option> + <option value="loxAfr3.60">Loxodonta africana : loxAfr3.60</option> + <option value="mmul1.61">Macaca mulatta : mmul1.61</option> + <option value="mmul1.60">Macaca mulatta : mmul1.60</option> + <option value="MMUL_1.66">Macaca mulatta : MMUL_1.66</option> + <option value="MMUL_1.65">Macaca mulatta : MMUL_1.65</option> + <option value="MMUL_1.64">Macaca mulatta : MMUL_1.64</option> + <option value="MMUL_1.63">Macaca mulatta : MMUL_1.63</option> + <option value="meug1.0.61">Macropus eugenii : meug1.0.61</option> + <option value="meug1.0.60">Macropus eugenii : meug1.0.60</option> + <option value="Meug_1.0.66">Macropus eugenii : Meug_1.0.66</option> + <option value="Meug_1.0.65">Macropus eugenii : Meug_1.0.65</option> + <option value="Meug_1.0.64">Macropus eugenii : Meug_1.0.64</option> + <option value="Meug_1.0.63">Macropus eugenii : Meug_1.0.63</option> + <option value="maizeZmB73">Maize ZmB73 : maizeZmB73</option> + <option value="turkey.UMD2.61">Meleagris gallopavo : turkey.UMD2.61</option> + <option value="UMD2.66">Meleagris gallopavo : UMD2.66</option> + <option value="UMD2.65">Meleagris gallopavo : UMD2.65</option> + <option value="UMD2.64">Meleagris gallopavo : UMD2.64</option> + <option value="UMD2.63">Meleagris gallopavo : UMD2.63</option> + <option value="micMur1.66">Microcebus murinus : micMur1.66</option> + <option value="micMur1.65">Microcebus murinus : micMur1.65</option> + <option value="micMur1.64">Microcebus murinus : micMur1.64</option> + <option value="micMur1.63">Microcebus murinus : micMur1.63</option> + <option value="micMur1.61">Microcebus murinus : micMur1.61</option> + <option value="micMur1.60">Microcebus murinus : micMur1.60</option> + <option value="monDom5.61">Monodelphis domestica : monDom5.61</option> + <option value="monDom5.60">Monodelphis domestica : monDom5.60</option> + <option value="BROADO5.66">Monodelphis domestica : BROADO5.66</option> + <option value="BROADO5.65">Monodelphis domestica : BROADO5.65</option> + <option value="BROADO5.64">Monodelphis domestica : BROADO5.64</option> + <option value="BROADO5.63">Monodelphis domestica : BROADO5.63</option> + <option value="mm37.61">Mus musculus : mm37.61</option> + <option value="mm37.60">Mus musculus : mm37.60</option> + <option value="mm37.59">Mus musculus : mm37.59</option> + <option value="mm37">Mus musculus : mm37</option> + <option value="NCBIM37.66">Mus musculus : NCBIM37.66</option> + <option value="NCBIM37.65">Mus musculus : NCBIM37.65</option> + <option value="NCBIM37.64">Mus musculus : NCBIM37.64</option> + <option value="NCBIM37.63">Mus musculus : NCBIM37.63</option> + <option value="mmm.2012">Mycobacterium marinum M : mmm.2012</option> + <option value="m_tuberculosis">Mycobacterium tuberculosis : m_tuberculosis</option> + <option value="myco_fh">Mycoplasma pneumoninae FH : myco_fh</option> + <option value="myco_m129">Mycoplasma pneumoninae M129 : myco_m129</option> + <option value="myoLuc1.61">Myotis lucifugus : myoLuc1.61</option> + <option value="myoLuc1.60">Myotis lucifugus : myoLuc1.60</option> + <option value="Myoluc2.0.66">Myotis lucifugus : Myoluc2.0.66</option> + <option value="Myoluc2.0.65">Myotis lucifugus : Myoluc2.0.65</option> + <option value="Myoluc2.0.64">Myotis lucifugus : Myoluc2.0.64</option> + <option value="Myoluc2.0.63">Myotis lucifugus : Myoluc2.0.63</option> + <option value="ncrassa">Neurospora Crassa : ncrassa</option> + <option value="Nleu1.0.66">Nomascus leucogenys : Nleu1.0.66</option> + <option value="Nleu1.0.65">Nomascus leucogenys : Nleu1.0.65</option> + <option value="Nleu1.0.64">Nomascus leucogenys : Nleu1.0.64</option> + <option value="Nleu1.0.63">Nomascus leucogenys : Nleu1.0.63</option> + <option value="pika.66">Ochotona princeps : pika.66</option> + <option value="pika.65">Ochotona princeps : pika.65</option> + <option value="pika.64">Ochotona princeps : pika.64</option> + <option value="pika.63">Ochotona princeps : pika.63</option> + <option value="ochPri2.61">Ochotona princeps : ochPri2.61</option> + <option value="ochPri2.60">Ochotona princeps : ochPri2.60</option> + <option value="oana5.61">Ornithorhynchus anatinus : oana5.61</option> + <option value="oana5.60">Ornithorhynchus anatinus : oana5.60</option> + <option value="OANA5.66">Ornithorhynchus anatinus : OANA5.66</option> + <option value="OANA5.65">Ornithorhynchus anatinus : OANA5.65</option> + <option value="OANA5.64">Ornithorhynchus anatinus : OANA5.64</option> + <option value="OANA5.63">Ornithorhynchus anatinus : OANA5.63</option> + <option value="oryCun2.66">Oryctolagus cuniculus : oryCun2.66</option> + <option value="oryCun2.65">Oryctolagus cuniculus : oryCun2.65</option> + <option value="oryCun2.64">Oryctolagus cuniculus : oryCun2.64</option> + <option value="oryCun2.63">Oryctolagus cuniculus : oryCun2.63</option> + <option value="oryCun2.61">Oryctolagus cuniculus : oryCun2.61</option> + <option value="oryCun2.60">Oryctolagus cuniculus : oryCun2.60</option> + <option value="medaka1.61">Oryzias latipes : medaka1.61</option> + <option value="medaka1.60">Oryzias latipes : medaka1.60</option> + <option value="MEDAKA1.66">Oryzias latipes : MEDAKA1.66</option> + <option value="MEDAKA1.65">Oryzias latipes : MEDAKA1.65</option> + <option value="MEDAKA1.64">Oryzias latipes : MEDAKA1.64</option> + <option value="MEDAKA1.63">Oryzias latipes : MEDAKA1.63</option> + <option value="bushBaby1.61">Otolemur garnettii : bushBaby1.61</option> + <option value="bushBaby1.60">Otolemur garnettii : bushBaby1.60</option> + <option value="OtoGar3.66">Otolemur garnettii : OtoGar3.66</option> + <option value="BUSHBABY1.65">Otolemur garnettii : BUSHBABY1.65</option> + <option value="BUSHBABY1.64">Otolemur garnettii : BUSHBABY1.64</option> + <option value="BUSHBABY1.63">Otolemur garnettii : BUSHBABY1.63</option> + <option value="chimp2.1.61">Pan troglodytes : chimp2.1.61</option> + <option value="chimp2.1.60">Pan troglodytes : chimp2.1.60</option> + <option value="chimp2.1.59">Pan troglodytes : chimp2.1.59</option> + <option value="CHIMP2.1.65">Pan troglodytes : CHIMP2.1.65</option> + <option value="CHIMP2.1.64">Pan troglodytes : CHIMP2.1.64</option> + <option value="CHIMP2.1.63">Pan troglodytes : CHIMP2.1.63</option> + <option value="CHIMP2.1.4.66">Pan troglodytes : CHIMP2.1.4.66</option> + <option value="ppersica139">Peach : ppersica139</option> + <option value="peromyscus">Peromyscus leucopus : peromyscus</option> + <option value="Pmarinus_7.0.66">Petromyzon marinus : Pmarinus_7.0.66</option> + <option value="Petromyzon_marinus_7.0.65">Petromyzon marinus : Petromyzon_marinus_7.0.65</option> + <option value="Petromyzon_marinus_7.0.64">Petromyzon marinus : Petromyzon_marinus_7.0.64</option> + <option value="plasmo72">Plasmodium falciparum : plasmo72</option> + <option value="PPYG2.66">Pongo abelii : PPYG2.66</option> + <option value="PPYG2.65">Pongo abelii : PPYG2.65</option> + <option value="PPYG2.64">Pongo abelii : PPYG2.64</option> + <option value="PPYG2.63">Pongo abelii : PPYG2.63</option> + <option value="ppyg2.61">Pongo pygmaeus : ppyg2.61</option> + <option value="ppyg2.60">Pongo pygmaeus : ppyg2.60</option> + <option value="proCap1.66">Procavia capensis : proCap1.66</option> + <option value="proCap1.65">Procavia capensis : proCap1.65</option> + <option value="proCap1.64">Procavia capensis : proCap1.64</option> + <option value="proCap1.63">Procavia capensis : proCap1.63</option> + <option value="proCap1.61">Procavia capensis : proCap1.61</option> + <option value="proCap1.60">Procavia capensis : proCap1.60</option> + <option value="paeru.PA14">Pseudomonas aeruginosa : paeru.PA14</option> + <option value="paeru.PA01">Pseudomonas aeruginosa : paeru.PA01</option> + <option value="pfluo.SBW25.NC_012660">Pseudomonas fluorescens : pfluo.SBW25.NC_012660</option> + <option value="pfluo.SBW25.NC_009444">Pseudomonas fluorescens : pfluo.SBW25.NC_009444</option> + <option value="pteVam1.66">Pteropus vampyrus : pteVam1.66</option> + <option value="pteVam1.65">Pteropus vampyrus : pteVam1.65</option> + <option value="pteVam1.64">Pteropus vampyrus : pteVam1.64</option> + <option value="pteVam1.63">Pteropus vampyrus : pteVam1.63</option> + <option value="pteVam1.61">Pteropus vampyrus : pteVam1.61</option> + <option value="pteVam1.60">Pteropus vampyrus : pteVam1.60</option> + <option value="rat3.4.61">Rattus norvegicus : rat3.4.61</option> + <option value="rat3.4.60">Rattus norvegicus : rat3.4.60</option> + <option value="rat3.4.59">Rattus norvegicus : rat3.4.59</option> + <option value="RGSC3.4.66">Rattus norvegicus : RGSC3.4.66</option> + <option value="RGSC3.4.65">Rattus norvegicus : RGSC3.4.65</option> + <option value="RGSC3.4.64">Rattus norvegicus : RGSC3.4.64</option> + <option value="RGSC3.4.63">Rattus norvegicus : RGSC3.4.63</option> + <option value="rice6.1">Rice : rice6.1</option> + <option value="rice5">Rice : rice5</option> + <option value="SCU49845">SCU49845 : SCU49845</option> + <option value="sacCer2.61">Saccharomyces cerevisiae : sacCer2.61</option> + <option value="sacCer2.60">Saccharomyces cerevisiae : sacCer2.60</option> + <option value="sacCer2.59">Saccharomyces cerevisiae : sacCer2.59</option> + <option value="sacCer2">Saccharomyces cerevisiae : sacCer2</option> + <option value="EF4.66">Saccharomyces cerevisiae : EF4.66</option> + <option value="EF4.65">Saccharomyces cerevisiae : EF4.65</option> + <option value="EF3.64">Saccharomyces cerevisiae : EF3.64</option> + <option value="EF3.63">Saccharomyces cerevisiae : EF3.63</option> + <option value="DEVIL7.0.66">Sarcophilus harrisii : DEVIL7.0.66</option> + <option value="DEVIL7.0.65">Sarcophilus harrisii : DEVIL7.0.65</option> + <option value="DEVIL7.0.64">Sarcophilus harrisii : DEVIL7.0.64</option> + <option value="spombe">Schizosaccharomyces pombe : spombe</option> + <option value="sorAra1.61">Sorex araneus : sorAra1.61</option> + <option value="sorAra1.60">Sorex araneus : sorAra1.60</option> + <option value="COMMON_SHREW1.66">Sorex araneus : COMMON_SHREW1.66</option> + <option value="COMMON_SHREW1.65">Sorex araneus : COMMON_SHREW1.65</option> + <option value="COMMON_SHREW1.64">Sorex araneus : COMMON_SHREW1.64</option> + <option value="COMMON_SHREW1.63">Sorex araneus : COMMON_SHREW1.63</option> + <option value="speTri1.61">Spermophilus tridecemlineatus : speTri1.61</option> + <option value="speTri1.60">Spermophilus tridecemlineatus : speTri1.60</option> + <option value="SQUIRREL.66">Spermophilus tridecemlineatus : SQUIRREL.66</option> + <option value="SQUIRREL.65">Spermophilus tridecemlineatus : SQUIRREL.65</option> + <option value="SQUIRREL.64">Spermophilus tridecemlineatus : SQUIRREL.64</option> + <option value="SQUIRREL.63">Spermophilus tridecemlineatus : SQUIRREL.63</option> + <option value="CP000730">Staphylococcus aureus : CP000730</option> + <option value="sScrofa9.61">Sus scrofa : sScrofa9.61</option> + <option value="sScrofa9.60">Sus scrofa : sScrofa9.60</option> + <option value="Sscrofa9.66">Sus scrofa : Sscrofa9.66</option> + <option value="Sscrofa9.65">Sus scrofa : Sscrofa9.65</option> + <option value="Sscrofa9.64">Sus scrofa : Sscrofa9.64</option> + <option value="Sscrofa9.63">Sus scrofa : Sscrofa9.63</option> + <option value="taeGut3.2.4.66">Taeniopygia guttata : taeGut3.2.4.66</option> + <option value="taeGut3.2.4.65">Taeniopygia guttata : taeGut3.2.4.65</option> + <option value="taeGut3.2.4.64">Taeniopygia guttata : taeGut3.2.4.64</option> + <option value="taeGut3.2.4.63">Taeniopygia guttata : taeGut3.2.4.63</option> + <option value="taeGut3.2.4.61">Taeniopygia guttata : taeGut3.2.4.61</option> + <option value="taeGut3.2.4.60">Taeniopygia guttata : taeGut3.2.4.60</option> + <option value="fugu4.61">Takifugu rubripes : fugu4.61</option> + <option value="fugu4.60">Takifugu rubripes : fugu4.60</option> + <option value="FUGU4.66">Takifugu rubripes : FUGU4.66</option> + <option value="FUGU4.65">Takifugu rubripes : FUGU4.65</option> + <option value="FUGU4.64">Takifugu rubripes : FUGU4.64</option> + <option value="FUGU4.63">Takifugu rubripes : FUGU4.63</option> + <option value="tarSyr1.66">Tarsius syrichta : tarSyr1.66</option> + <option value="tarSyr1.65">Tarsius syrichta : tarSyr1.65</option> + <option value="tarSyr1.64">Tarsius syrichta : tarSyr1.64</option> + <option value="tarSyr1.63">Tarsius syrichta : tarSyr1.63</option> + <option value="tarSyr1.61">Tarsius syrichta : tarSyr1.61</option> + <option value="tarSyr1.60">Tarsius syrichta : tarSyr1.60</option> + <option value="test_ENSG00000158062">TestCase : test_ENSG00000158062</option> + <option value="testHg3765Chr22">TestCase : testHg3765Chr22</option> + <option value="testHg3763ChrY">TestCase : testHg3763ChrY</option> + <option value="testHg3763Chr20">TestCase : testHg3763Chr20</option> + <option value="testHg3763Chr1">TestCase : testHg3763Chr1</option> + <option value="testHg3761Chr16">TestCase : testHg3761Chr16</option> + <option value="testHg3761Chr15">TestCase : testHg3761Chr15</option> + <option value="testCase">TestCase : testCase</option> + <option value="test">TestCase : test</option> + <option value="tetraodon8.61">Tetraodon nigroviridis : tetraodon8.61</option> + <option value="tetraodon8.60">Tetraodon nigroviridis : tetraodon8.60</option> + <option value="TETRAODON8.66">Tetraodon nigroviridis : TETRAODON8.66</option> + <option value="TETRAODON8.65">Tetraodon nigroviridis : TETRAODON8.65</option> + <option value="TETRAODON8.64">Tetraodon nigroviridis : TETRAODON8.64</option> + <option value="TETRAODON8.63">Tetraodon nigroviridis : TETRAODON8.63</option> + <option value="SL2.40">Tomato : SL2.40</option> + <option value="tupBel1.61">Tupaia belangeri : tupBel1.61</option> + <option value="tupBel1.60">Tupaia belangeri : tupBel1.60</option> + <option value="TREESHREW.66">Tupaia belangeri : TREESHREW.66</option> + <option value="TREESHREW.65">Tupaia belangeri : TREESHREW.65</option> + <option value="TREESHREW.64">Tupaia belangeri : TREESHREW.64</option> + <option value="TREESHREW.63">Tupaia belangeri : TREESHREW.63</option> + <option value="turTru1.66">Tursiops truncatus : turTru1.66</option> + <option value="turTru1.65">Tursiops truncatus : turTru1.65</option> + <option value="turTru1.64">Tursiops truncatus : turTru1.64</option> + <option value="turTru1.63">Tursiops truncatus : turTru1.63</option> + <option value="turTru1.61">Tursiops truncatus : turTru1.61</option> + <option value="turTru1.60">Tursiops truncatus : turTru1.60</option> + <option value="vacwr">Vaccinia Western Reserve : vacwr</option> + <option value="vibrio">Vibrio Cholerae : vibrio</option> + <option value="vicPac1.66">Vicugna pacos : vicPac1.66</option> + <option value="vicPac1.65">Vicugna pacos : vicPac1.65</option> + <option value="vicPac1.64">Vicugna pacos : vicPac1.64</option> + <option value="vicPac1.63">Vicugna pacos : vicPac1.63</option> + <option value="vicPac1.61">Vicugna pacos : vicPac1.61</option> + <option value="vicPac1.60">Vicugna pacos : vicPac1.60</option> + <option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option> + <option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option> + <option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option> + <option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option> + <option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option> + <option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option> + </param> + + <param name="udLength" type="select" label="Upstream / Downstream length"> + <option value="0">No upstream / downstream intervals (0 bases)</option> + <option value="200">200 bases</option> + <option value="500">500 bases</option> + <option value="1000">1000 bases</option> + <option value="2000">2000 bases</option> + <option value="5000" selected="true">5000 bases</option> + <option value="10000">10000 bases</option> + <option value="20000">20000 bases</option> + </param> + + <param name="filterHomHet" type="select" display="radio" label="Filter homozygous / heterozygous changes"> + <option value="">No filter (analyze everything)</option> + <option value="-hom">Analyze homozygous sequence changes only </option> + <option value="-het">Analyze heterozygous sequence changes only </option> + </param> + + <param name="filterIn" type="select" display="radio" label="Filter sequence changes"> + <option value="">No filter (analyze everything)</option> + <option value="-del">Analyze deletions only </option> + <option value="-ins">Analyze insertions only </option> + <option value="-nmp">Only MNPs (multiple nucleotide polymorphisms) </option> + <option value="-snp">Only SNPs (single nucleotide polymorphisms) </option> + </param> + + <param name="filterOut" type="select" display="checkboxes" multiple="true" optional="false" value="None" label="Filter output"> + <option value="None" selected="true">None</option> + <option value="downstream">Do not show DOWNSTREAM changes </option> + <option value="intergenic">Do not show INTERGENIC changes </option> + <option value="intron">Do not show INTRON changes </option> + <option value="upstream">Do not show UPSTREAM changes </option> + <option value="utr">Do not show 5_PRIME_UTR or 3_PRIME_UTR changes </option> + </param> + + <param name="offset" type="select" display="radio" optional="true" label="Chromosomal position"> + <option value="">Use default (based on input type)</option> + <option value="-0">Force zero-based positions (both input and output)</option> + <option value="-1">Force one-based positions (both input and output)</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" /> + <data format="html" name="statsFile" /> + </outputs> + + <help> + +This tool calculate the effect of variants (SNPs/MNPs/Insertions) and deletions. + +For details about this tool, please go to http://snpEff.sourceforge.net + + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpEff_download.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,421 @@ +<tool id="snpEff_download" name="SnpEff Download" version="1.0"> + <description>Download a new database</description> + <command>java -jar /Users/pablocingolani/snpEff/snpEff.jar download -c /Users/pablocingolani/snpEff/snpEff.config $genomeVersion > $logfile </command> + <inputs> + <param name="genomeVersion" type="select" label="Genome"> + <option value="ailmel1.61">Ailuropoda melanoleuca : ailmel1.61</option> + <option value="ailMel1.66">Ailuropoda melanoleuca : ailMel1.66</option> + <option value="ailMel1.65">Ailuropoda melanoleuca : ailMel1.65</option> + <option value="ailMel1.64">Ailuropoda melanoleuca : ailMel1.64</option> + <option value="ailMel1.63">Ailuropoda melanoleuca : ailMel1.63</option> + <option value="anoCar2.0.61">Anolis carolinensis : anoCar2.0.61</option> + <option value="anoCar1.0.60">Anolis carolinensis : anoCar1.0.60</option> + <option value="AnoCar2.0.66">Anolis carolinensis : AnoCar2.0.66</option> + <option value="AnoCar2.0.65">Anolis carolinensis : AnoCar2.0.65</option> + <option value="AnoCar2.0.64">Anolis carolinensis : AnoCar2.0.64</option> + <option value="AnoCar2.0.63">Anolis carolinensis : AnoCar2.0.63</option> + <option value="agam2.6">Anopheles gambiae : agam2.6</option> + <option value="agam">Anopheles gambiae : agam</option> + <option value="aquiCoer">Aquilegia coerulea : aquiCoer</option> + <option value="athalianaTair9">Arabidopsis Thaliana : athalianaTair9</option> + <option value="athalianaTair10">Arabidopsis Thaliana : athalianaTair10</option> + <option value="athaliana130">Arabidopsis Thaliana : athaliana130</option> + <option value="alyrata107">Arabidopsis lyrata : alyrata107</option> + <option value="alyrata1">Arabidopsis lyrata : alyrata1</option> + <option value="amel2">Bee : amel2</option> + <option value="btau4.0.61">Bos taurus : btau4.0.61</option> + <option value="btau4.0.60">Bos taurus : btau4.0.60</option> + <option value="btau4.0.59">Bos taurus : btau4.0.59</option> + <option value="UMD3_1">Bos taurus : UMD3_1</option> + <option value="UMD3.1.66">Bos taurus : UMD3.1.66</option> + <option value="UMD3.1.65">Bos taurus : UMD3.1.65</option> + <option value="UMD3.1.64">Bos taurus : UMD3.1.64</option> + <option value="Btau_4.0.63">Bos taurus : Btau_4.0.63</option> + <option value="c_briggsae_WS230">Caenorhabditis briggsae : c_briggsae_WS230</option> + <option value="ce.WS220.61">Caenorhabditis elegans : ce.WS220.61</option> + <option value="ce.WS210.60">Caenorhabditis elegans : ce.WS210.60</option> + <option value="ce.WS201">Caenorhabditis elegans : ce.WS201</option> + <option value="WS220.66">Caenorhabditis elegans : WS220.66</option> + <option value="WS220.65">Caenorhabditis elegans : WS220.65</option> + <option value="WS220.64">Caenorhabditis elegans : WS220.64</option> + <option value="WS220.63">Caenorhabditis elegans : WS220.63</option> + <option value="calJac3.2.1.61">Callithrix jacchus : calJac3.2.1.61</option> + <option value="calJac3.2.1.60">Callithrix jacchus : calJac3.2.1.60</option> + <option value="C_jacchus3.2.1.66">Callithrix jacchus : C_jacchus3.2.1.66</option> + <option value="C_jacchus3.2.1.65">Callithrix jacchus : C_jacchus3.2.1.65</option> + <option value="C_jacchus3.2.1.64">Callithrix jacchus : C_jacchus3.2.1.64</option> + <option value="C_jacchus3.2.1.63">Callithrix jacchus : C_jacchus3.2.1.63</option> + <option value="cAlbicansv21">Candida albicans SC5314 : cAlbicansv21</option> + <option value="canFam2.61">Canis familiaris : canFam2.61</option> + <option value="canFam2.60">Canis familiaris : canFam2.60</option> + <option value="canFam2.59">Canis familiaris : canFam2.59</option> + <option value="BROADD2.66">Canis familiaris : BROADD2.66</option> + <option value="BROADD2.65">Canis familiaris : BROADD2.65</option> + <option value="BROADD2.64">Canis familiaris : BROADD2.64</option> + <option value="BROADD2.63">Canis familiaris : BROADD2.63</option> + <option value="crubella">Capsella rubella v1.0 : crubella</option> + <option value="cavPor3.66">Cavia porcellus : cavPor3.66</option> + <option value="cavPor3.65">Cavia porcellus : cavPor3.65</option> + <option value="cavPor3.64">Cavia porcellus : cavPor3.64</option> + <option value="cavPor3.63">Cavia porcellus : cavPor3.63</option> + <option value="cavPor3.61">Cavia porcellus : cavPor3.61</option> + <option value="cavPor3.60">Cavia porcellus : cavPor3.60</option> + <option value="choHof1.66">Choloepus hoffmanni : choHof1.66</option> + <option value="choHof1.65">Choloepus hoffmanni : choHof1.65</option> + <option value="choHof1.64">Choloepus hoffmanni : choHof1.64</option> + <option value="choHof1.63">Choloepus hoffmanni : choHof1.63</option> + <option value="choHof1.61">Choloepus hoffmanni : choHof1.61</option> + <option value="choHof1.60">Choloepus hoffmanni : choHof1.60</option> + <option value="cInt2.61">Ciona intestinalis : cInt2.61</option> + <option value="cInt2.60">Ciona intestinalis : cInt2.60</option> + <option value="KH.66">Ciona intestinalis : KH.66</option> + <option value="JGI2.65">Ciona intestinalis : JGI2.65</option> + <option value="JGI2.64">Ciona intestinalis : JGI2.64</option> + <option value="JGI2.63">Ciona intestinalis : JGI2.63</option> + <option value="cSav2.0.61">Ciona savignyi : cSav2.0.61</option> + <option value="cSav2.0.60">Ciona savignyi : cSav2.0.60</option> + <option value="CSAV2.0.66">Ciona savignyi : CSAV2.0.66</option> + <option value="CSAV2.0.65">Ciona savignyi : CSAV2.0.65</option> + <option value="CSAV2.0.64">Ciona savignyi : CSAV2.0.64</option> + <option value="CSAV2.0.63">Ciona savignyi : CSAV2.0.63</option> + <option value="NC_009089.1">Clostridium difficile : NC_009089.1</option> + <option value="c_neoformans">Cryptococcus neoformans : c_neoformans</option> + <option value="danRer9.61">Danio rerio : danRer9.61</option> + <option value="danRer9.60">Danio rerio : danRer9.60</option> + <option value="danRer8.59">Danio rerio : danRer8.59</option> + <option value="Zv9.66">Danio rerio : Zv9.66</option> + <option value="Zv9.65">Danio rerio : Zv9.65</option> + <option value="Zv9.64">Danio rerio : Zv9.64</option> + <option value="Zv9.63">Danio rerio : Zv9.63</option> + <option value="dasNov2.66">Dasypus novemcinctus : dasNov2.66</option> + <option value="dasNov2.65">Dasypus novemcinctus : dasNov2.65</option> + <option value="dasNov2.64">Dasypus novemcinctus : dasNov2.64</option> + <option value="dasNov2.63">Dasypus novemcinctus : dasNov2.63</option> + <option value="dasNov2.61">Dasypus novemcinctus : dasNov2.61</option> + <option value="dasNov2.60">Dasypus novemcinctus : dasNov2.60</option> + <option value="dipOrd1.66">Dipodomys ordii : dipOrd1.66</option> + <option value="dipOrd1.65">Dipodomys ordii : dipOrd1.65</option> + <option value="dipOrd1.64">Dipodomys ordii : dipOrd1.64</option> + <option value="dipOrd1.63">Dipodomys ordii : dipOrd1.63</option> + <option value="dipOrd1.61">Dipodomys ordii : dipOrd1.61</option> + <option value="dipOrd1.60">Dipodomys ordii : dipOrd1.60</option> + <option value="dm5.42">Drosophila melanogaster : dm5.42</option> + <option value="dm5.40">Drosophila melanogaster : dm5.40</option> + <option value="dm5.34">Drosophila melanogaster : dm5.34</option> + <option value="dm5.32">Drosophila melanogaster : dm5.32</option> + <option value="dm5.31">Drosophila melanogaster : dm5.31</option> + <option value="dm5.30">Drosophila melanogaster : dm5.30</option> + <option value="dm5.25.63">Drosophila melanogaster : dm5.25.63</option> + <option value="dm5.25.61">Drosophila melanogaster : dm5.25.61</option> + <option value="dm5.25.60">Drosophila melanogaster : dm5.25.60</option> + <option value="dm5.25.59">Drosophila melanogaster : dm5.25.59</option> + <option value="dm5.22">Drosophila melanogaster : dm5.22</option> + <option value="dm5.12">Drosophila melanogaster : dm5.12</option> + <option value="BDGP5.66">Drosophila melanogaster : BDGP5.66</option> + <option value="BDGP5.25.65">Drosophila melanogaster : BDGP5.25.65</option> + <option value="BDGP5.25.64">Drosophila melanogaster : BDGP5.25.64</option> + <option value="BDGP5.25.63">Drosophila melanogaster : BDGP5.25.63</option> + <option value="tenrec1.61">Echinops telfairi : tenrec1.61</option> + <option value="tenrec1.60">Echinops telfairi : tenrec1.60</option> + <option value="TENREC.66">Echinops telfairi : TENREC.66</option> + <option value="TENREC.65">Echinops telfairi : TENREC.65</option> + <option value="TENREC.64">Echinops telfairi : TENREC.64</option> + <option value="TENREC.63">Echinops telfairi : TENREC.63</option> + <option value="equCab2.61">Equus caballus : equCab2.61</option> + <option value="equCab2.60">Equus caballus : equCab2.60</option> + <option value="EquCab2.66">Equus caballus : EquCab2.66</option> + <option value="EquCab2.65">Equus caballus : EquCab2.65</option> + <option value="EquCab2.64">Equus caballus : EquCab2.64</option> + <option value="EquCab2.63">Equus caballus : EquCab2.63</option> + <option value="eriEur1.61">Erinaceus europaeus : eriEur1.61</option> + <option value="eriEur1.60">Erinaceus europaeus : eriEur1.60</option> + <option value="HEDGEHOG.66">Erinaceus europaeus : HEDGEHOG.66</option> + <option value="HEDGEHOG.65">Erinaceus europaeus : HEDGEHOG.65</option> + <option value="HEDGEHOG.64">Erinaceus europaeus : HEDGEHOG.64</option> + <option value="HEDGEHOG.63">Erinaceus europaeus : HEDGEHOG.63</option> + <option value="NC_000913">Escherichia coli : NC_000913</option> + <option value="cat1.61">Felis catus : cat1.61</option> + <option value="cat1.60">Felis catus : cat1.60</option> + <option value="CAT.66">Felis catus : CAT.66</option> + <option value="CAT.65">Felis catus : CAT.65</option> + <option value="CAT.64">Felis catus : CAT.64</option> + <option value="CAT.63">Felis catus : CAT.63</option> + <option value="gadMor1.66">Gadus morhua : gadMor1.66</option> + <option value="ggallus2.61">Gallus gallus : ggallus2.61</option> + <option value="ggallus2.60">Gallus gallus : ggallus2.60</option> + <option value="ggallus2.59">Gallus gallus : ggallus2.59</option> + <option value="WASHUC2.66">Gallus gallus : WASHUC2.66</option> + <option value="WASHUC2.65">Gallus gallus : WASHUC2.65</option> + <option value="WASHUC2.64">Gallus gallus : WASHUC2.64</option> + <option value="WASHUC2.63">Gallus gallus : WASHUC2.63</option> + <option value="gacu1.61">Gasterosteus aculeatus : gacu1.61</option> + <option value="gacu1.60">Gasterosteus aculeatus : gacu1.60</option> + <option value="BROADS1.66">Gasterosteus aculeatus : BROADS1.66</option> + <option value="BROADS1.65">Gasterosteus aculeatus : BROADS1.65</option> + <option value="BROADS1.64">Gasterosteus aculeatus : BROADS1.64</option> + <option value="BROADS1.63">Gasterosteus aculeatus : BROADS1.63</option> + <option value="gmax1.09v8">Glycine Max : gmax1.09v8</option> + <option value="gmax1.09">Glycine Max : gmax1.09</option> + <option value="gorGor3.63">Gorilla gorilla : gorGor3.63</option> + <option value="gorGor3.61">Gorilla gorilla : gorGor3.61</option> + <option value="gorGor3.60">Gorilla gorilla : gorGor3.60</option> + <option value="gorGor3.1.66">Gorilla gorilla : gorGor3.1.66</option> + <option value="gorGor3.1.65">Gorilla gorilla : gorGor3.1.65</option> + <option value="gorGor3.1.64">Gorilla gorilla : gorGor3.1.64</option> + <option value="kw1407.2012">Grosmannia clavigera : kw1407.2012</option> + <option value="hiv">HIV : hiv</option> + <option value="SIVmac239">HIV : SIVmac239</option> + <option value="herpesvirus1">Herpesvirus : herpesvirus1</option> + <option value="hg37.63">Homo sapiens : hg37.63</option> + <option value="hg37.61">Homo sapiens : hg37.61</option> + <option value="hg37.60">Homo sapiens : hg37.60</option> + <option value="hg37.59">Homo sapiens : hg37.59</option> + <option value="hg36.54">Homo sapiens : hg36.54</option> + <option value="hg19">Homo sapiens : hg19</option> + <option value="GRCh37.66">Homo sapiens : GRCh37.66</option> + <option value="GRCh37.65">Homo sapiens : GRCh37.65</option> + <option value="GRCh37.64">Homo sapiens : GRCh37.64</option> + <option value="GRCh37.63">Homo sapiens : GRCh37.63</option> + <option value="LatCha1.66">Latimeria chalumnae : LatCha1.66</option> + <option value="lmjf4">LmajorFriedlin : lmjf4</option> + <option value="loxAfr3.66">Loxodonta africana : loxAfr3.66</option> + <option value="loxAfr3.65">Loxodonta africana : loxAfr3.65</option> + <option value="loxAfr3.64">Loxodonta africana : loxAfr3.64</option> + <option value="loxAfr3.63">Loxodonta africana : loxAfr3.63</option> + <option value="loxAfr3.61">Loxodonta africana : loxAfr3.61</option> + <option value="loxAfr3.60">Loxodonta africana : loxAfr3.60</option> + <option value="mmul1.61">Macaca mulatta : mmul1.61</option> + <option value="mmul1.60">Macaca mulatta : mmul1.60</option> + <option value="MMUL_1.66">Macaca mulatta : MMUL_1.66</option> + <option value="MMUL_1.65">Macaca mulatta : MMUL_1.65</option> + <option value="MMUL_1.64">Macaca mulatta : MMUL_1.64</option> + <option value="MMUL_1.63">Macaca mulatta : MMUL_1.63</option> + <option value="meug1.0.61">Macropus eugenii : meug1.0.61</option> + <option value="meug1.0.60">Macropus eugenii : meug1.0.60</option> + <option value="Meug_1.0.66">Macropus eugenii : Meug_1.0.66</option> + <option value="Meug_1.0.65">Macropus eugenii : Meug_1.0.65</option> + <option value="Meug_1.0.64">Macropus eugenii : Meug_1.0.64</option> + <option value="Meug_1.0.63">Macropus eugenii : Meug_1.0.63</option> + <option value="maizeZmB73">Maize ZmB73 : maizeZmB73</option> + <option value="turkey.UMD2.61">Meleagris gallopavo : turkey.UMD2.61</option> + <option value="UMD2.66">Meleagris gallopavo : UMD2.66</option> + <option value="UMD2.65">Meleagris gallopavo : UMD2.65</option> + <option value="UMD2.64">Meleagris gallopavo : UMD2.64</option> + <option value="UMD2.63">Meleagris gallopavo : UMD2.63</option> + <option value="micMur1.66">Microcebus murinus : micMur1.66</option> + <option value="micMur1.65">Microcebus murinus : micMur1.65</option> + <option value="micMur1.64">Microcebus murinus : micMur1.64</option> + <option value="micMur1.63">Microcebus murinus : micMur1.63</option> + <option value="micMur1.61">Microcebus murinus : micMur1.61</option> + <option value="micMur1.60">Microcebus murinus : micMur1.60</option> + <option value="monDom5.61">Monodelphis domestica : monDom5.61</option> + <option value="monDom5.60">Monodelphis domestica : monDom5.60</option> + <option value="BROADO5.66">Monodelphis domestica : BROADO5.66</option> + <option value="BROADO5.65">Monodelphis domestica : BROADO5.65</option> + <option value="BROADO5.64">Monodelphis domestica : BROADO5.64</option> + <option value="BROADO5.63">Monodelphis domestica : BROADO5.63</option> + <option value="mm37.61">Mus musculus : mm37.61</option> + <option value="mm37.60">Mus musculus : mm37.60</option> + <option value="mm37.59">Mus musculus : mm37.59</option> + <option value="mm37">Mus musculus : mm37</option> + <option value="NCBIM37.66">Mus musculus : NCBIM37.66</option> + <option value="NCBIM37.65">Mus musculus : NCBIM37.65</option> + <option value="NCBIM37.64">Mus musculus : NCBIM37.64</option> + <option value="NCBIM37.63">Mus musculus : NCBIM37.63</option> + <option value="mmm.2012">Mycobacterium marinum M : mmm.2012</option> + <option value="m_tuberculosis">Mycobacterium tuberculosis : m_tuberculosis</option> + <option value="myco_fh">Mycoplasma pneumoninae FH : myco_fh</option> + <option value="myco_m129">Mycoplasma pneumoninae M129 : myco_m129</option> + <option value="myoLuc1.61">Myotis lucifugus : myoLuc1.61</option> + <option value="myoLuc1.60">Myotis lucifugus : myoLuc1.60</option> + <option value="Myoluc2.0.66">Myotis lucifugus : Myoluc2.0.66</option> + <option value="Myoluc2.0.65">Myotis lucifugus : Myoluc2.0.65</option> + <option value="Myoluc2.0.64">Myotis lucifugus : Myoluc2.0.64</option> + <option value="Myoluc2.0.63">Myotis lucifugus : Myoluc2.0.63</option> + <option value="ncrassa">Neurospora Crassa : ncrassa</option> + <option value="Nleu1.0.66">Nomascus leucogenys : Nleu1.0.66</option> + <option value="Nleu1.0.65">Nomascus leucogenys : Nleu1.0.65</option> + <option value="Nleu1.0.64">Nomascus leucogenys : Nleu1.0.64</option> + <option value="Nleu1.0.63">Nomascus leucogenys : Nleu1.0.63</option> + <option value="pika.66">Ochotona princeps : pika.66</option> + <option value="pika.65">Ochotona princeps : pika.65</option> + <option value="pika.64">Ochotona princeps : pika.64</option> + <option value="pika.63">Ochotona princeps : pika.63</option> + <option value="ochPri2.61">Ochotona princeps : ochPri2.61</option> + <option value="ochPri2.60">Ochotona princeps : ochPri2.60</option> + <option value="oana5.61">Ornithorhynchus anatinus : oana5.61</option> + <option value="oana5.60">Ornithorhynchus anatinus : oana5.60</option> + <option value="OANA5.66">Ornithorhynchus anatinus : OANA5.66</option> + <option value="OANA5.65">Ornithorhynchus anatinus : OANA5.65</option> + <option value="OANA5.64">Ornithorhynchus anatinus : OANA5.64</option> + <option value="OANA5.63">Ornithorhynchus anatinus : OANA5.63</option> + <option value="oryCun2.66">Oryctolagus cuniculus : oryCun2.66</option> + <option value="oryCun2.65">Oryctolagus cuniculus : oryCun2.65</option> + <option value="oryCun2.64">Oryctolagus cuniculus : oryCun2.64</option> + <option value="oryCun2.63">Oryctolagus cuniculus : oryCun2.63</option> + <option value="oryCun2.61">Oryctolagus cuniculus : oryCun2.61</option> + <option value="oryCun2.60">Oryctolagus cuniculus : oryCun2.60</option> + <option value="medaka1.61">Oryzias latipes : medaka1.61</option> + <option value="medaka1.60">Oryzias latipes : medaka1.60</option> + <option value="MEDAKA1.66">Oryzias latipes : MEDAKA1.66</option> + <option value="MEDAKA1.65">Oryzias latipes : MEDAKA1.65</option> + <option value="MEDAKA1.64">Oryzias latipes : MEDAKA1.64</option> + <option value="MEDAKA1.63">Oryzias latipes : MEDAKA1.63</option> + <option value="bushBaby1.61">Otolemur garnettii : bushBaby1.61</option> + <option value="bushBaby1.60">Otolemur garnettii : bushBaby1.60</option> + <option value="OtoGar3.66">Otolemur garnettii : OtoGar3.66</option> + <option value="BUSHBABY1.65">Otolemur garnettii : BUSHBABY1.65</option> + <option value="BUSHBABY1.64">Otolemur garnettii : BUSHBABY1.64</option> + <option value="BUSHBABY1.63">Otolemur garnettii : BUSHBABY1.63</option> + <option value="chimp2.1.61">Pan troglodytes : chimp2.1.61</option> + <option value="chimp2.1.60">Pan troglodytes : chimp2.1.60</option> + <option value="chimp2.1.59">Pan troglodytes : chimp2.1.59</option> + <option value="CHIMP2.1.65">Pan troglodytes : CHIMP2.1.65</option> + <option value="CHIMP2.1.64">Pan troglodytes : CHIMP2.1.64</option> + <option value="CHIMP2.1.63">Pan troglodytes : CHIMP2.1.63</option> + <option value="CHIMP2.1.4.66">Pan troglodytes : CHIMP2.1.4.66</option> + <option value="ppersica139">Peach : ppersica139</option> + <option value="peromyscus">Peromyscus leucopus : peromyscus</option> + <option value="Pmarinus_7.0.66">Petromyzon marinus : Pmarinus_7.0.66</option> + <option value="Petromyzon_marinus_7.0.65">Petromyzon marinus : Petromyzon_marinus_7.0.65</option> + <option value="Petromyzon_marinus_7.0.64">Petromyzon marinus : Petromyzon_marinus_7.0.64</option> + <option value="plasmo72">Plasmodium falciparum : plasmo72</option> + <option value="PPYG2.66">Pongo abelii : PPYG2.66</option> + <option value="PPYG2.65">Pongo abelii : PPYG2.65</option> + <option value="PPYG2.64">Pongo abelii : PPYG2.64</option> + <option value="PPYG2.63">Pongo abelii : PPYG2.63</option> + <option value="ppyg2.61">Pongo pygmaeus : ppyg2.61</option> + <option value="ppyg2.60">Pongo pygmaeus : ppyg2.60</option> + <option value="proCap1.66">Procavia capensis : proCap1.66</option> + <option value="proCap1.65">Procavia capensis : proCap1.65</option> + <option value="proCap1.64">Procavia capensis : proCap1.64</option> + <option value="proCap1.63">Procavia capensis : proCap1.63</option> + <option value="proCap1.61">Procavia capensis : proCap1.61</option> + <option value="proCap1.60">Procavia capensis : proCap1.60</option> + <option value="paeru.PA14">Pseudomonas aeruginosa : paeru.PA14</option> + <option value="paeru.PA01">Pseudomonas aeruginosa : paeru.PA01</option> + <option value="pfluo.SBW25.NC_012660">Pseudomonas fluorescens : pfluo.SBW25.NC_012660</option> + <option value="pfluo.SBW25.NC_009444">Pseudomonas fluorescens : pfluo.SBW25.NC_009444</option> + <option value="pteVam1.66">Pteropus vampyrus : pteVam1.66</option> + <option value="pteVam1.65">Pteropus vampyrus : pteVam1.65</option> + <option value="pteVam1.64">Pteropus vampyrus : pteVam1.64</option> + <option value="pteVam1.63">Pteropus vampyrus : pteVam1.63</option> + <option value="pteVam1.61">Pteropus vampyrus : pteVam1.61</option> + <option value="pteVam1.60">Pteropus vampyrus : pteVam1.60</option> + <option value="rat3.4.61">Rattus norvegicus : rat3.4.61</option> + <option value="rat3.4.60">Rattus norvegicus : rat3.4.60</option> + <option value="rat3.4.59">Rattus norvegicus : rat3.4.59</option> + <option value="RGSC3.4.66">Rattus norvegicus : RGSC3.4.66</option> + <option value="RGSC3.4.65">Rattus norvegicus : RGSC3.4.65</option> + <option value="RGSC3.4.64">Rattus norvegicus : RGSC3.4.64</option> + <option value="RGSC3.4.63">Rattus norvegicus : RGSC3.4.63</option> + <option value="rice6.1">Rice : rice6.1</option> + <option value="rice5">Rice : rice5</option> + <option value="SCU49845">SCU49845 : SCU49845</option> + <option value="sacCer2.61">Saccharomyces cerevisiae : sacCer2.61</option> + <option value="sacCer2.60">Saccharomyces cerevisiae : sacCer2.60</option> + <option value="sacCer2.59">Saccharomyces cerevisiae : sacCer2.59</option> + <option value="sacCer2">Saccharomyces cerevisiae : sacCer2</option> + <option value="EF4.66">Saccharomyces cerevisiae : EF4.66</option> + <option value="EF4.65">Saccharomyces cerevisiae : EF4.65</option> + <option value="EF3.64">Saccharomyces cerevisiae : EF3.64</option> + <option value="EF3.63">Saccharomyces cerevisiae : EF3.63</option> + <option value="DEVIL7.0.66">Sarcophilus harrisii : DEVIL7.0.66</option> + <option value="DEVIL7.0.65">Sarcophilus harrisii : DEVIL7.0.65</option> + <option value="DEVIL7.0.64">Sarcophilus harrisii : DEVIL7.0.64</option> + <option value="spombe">Schizosaccharomyces pombe : spombe</option> + <option value="sorAra1.61">Sorex araneus : sorAra1.61</option> + <option value="sorAra1.60">Sorex araneus : sorAra1.60</option> + <option value="COMMON_SHREW1.66">Sorex araneus : COMMON_SHREW1.66</option> + <option value="COMMON_SHREW1.65">Sorex araneus : COMMON_SHREW1.65</option> + <option value="COMMON_SHREW1.64">Sorex araneus : COMMON_SHREW1.64</option> + <option value="COMMON_SHREW1.63">Sorex araneus : COMMON_SHREW1.63</option> + <option value="speTri1.61">Spermophilus tridecemlineatus : speTri1.61</option> + <option value="speTri1.60">Spermophilus tridecemlineatus : speTri1.60</option> + <option value="SQUIRREL.66">Spermophilus tridecemlineatus : SQUIRREL.66</option> + <option value="SQUIRREL.65">Spermophilus tridecemlineatus : SQUIRREL.65</option> + <option value="SQUIRREL.64">Spermophilus tridecemlineatus : SQUIRREL.64</option> + <option value="SQUIRREL.63">Spermophilus tridecemlineatus : SQUIRREL.63</option> + <option value="CP000730">Staphylococcus aureus : CP000730</option> + <option value="sScrofa9.61">Sus scrofa : sScrofa9.61</option> + <option value="sScrofa9.60">Sus scrofa : sScrofa9.60</option> + <option value="Sscrofa9.66">Sus scrofa : Sscrofa9.66</option> + <option value="Sscrofa9.65">Sus scrofa : Sscrofa9.65</option> + <option value="Sscrofa9.64">Sus scrofa : Sscrofa9.64</option> + <option value="Sscrofa9.63">Sus scrofa : Sscrofa9.63</option> + <option value="taeGut3.2.4.66">Taeniopygia guttata : taeGut3.2.4.66</option> + <option value="taeGut3.2.4.65">Taeniopygia guttata : taeGut3.2.4.65</option> + <option value="taeGut3.2.4.64">Taeniopygia guttata : taeGut3.2.4.64</option> + <option value="taeGut3.2.4.63">Taeniopygia guttata : taeGut3.2.4.63</option> + <option value="taeGut3.2.4.61">Taeniopygia guttata : taeGut3.2.4.61</option> + <option value="taeGut3.2.4.60">Taeniopygia guttata : taeGut3.2.4.60</option> + <option value="fugu4.61">Takifugu rubripes : fugu4.61</option> + <option value="fugu4.60">Takifugu rubripes : fugu4.60</option> + <option value="FUGU4.66">Takifugu rubripes : FUGU4.66</option> + <option value="FUGU4.65">Takifugu rubripes : FUGU4.65</option> + <option value="FUGU4.64">Takifugu rubripes : FUGU4.64</option> + <option value="FUGU4.63">Takifugu rubripes : FUGU4.63</option> + <option value="tarSyr1.66">Tarsius syrichta : tarSyr1.66</option> + <option value="tarSyr1.65">Tarsius syrichta : tarSyr1.65</option> + <option value="tarSyr1.64">Tarsius syrichta : tarSyr1.64</option> + <option value="tarSyr1.63">Tarsius syrichta : tarSyr1.63</option> + <option value="tarSyr1.61">Tarsius syrichta : tarSyr1.61</option> + <option value="tarSyr1.60">Tarsius syrichta : tarSyr1.60</option> + <option value="test_ENSG00000158062">TestCase : test_ENSG00000158062</option> + <option value="testHg3765Chr22">TestCase : testHg3765Chr22</option> + <option value="testHg3763ChrY">TestCase : testHg3763ChrY</option> + <option value="testHg3763Chr20">TestCase : testHg3763Chr20</option> + <option value="testHg3763Chr1">TestCase : testHg3763Chr1</option> + <option value="testHg3761Chr16">TestCase : testHg3761Chr16</option> + <option value="testHg3761Chr15">TestCase : testHg3761Chr15</option> + <option value="testCase">TestCase : testCase</option> + <option value="test">TestCase : test</option> + <option value="tetraodon8.61">Tetraodon nigroviridis : tetraodon8.61</option> + <option value="tetraodon8.60">Tetraodon nigroviridis : tetraodon8.60</option> + <option value="TETRAODON8.66">Tetraodon nigroviridis : TETRAODON8.66</option> + <option value="TETRAODON8.65">Tetraodon nigroviridis : TETRAODON8.65</option> + <option value="TETRAODON8.64">Tetraodon nigroviridis : TETRAODON8.64</option> + <option value="TETRAODON8.63">Tetraodon nigroviridis : TETRAODON8.63</option> + <option value="SL2.40">Tomato : SL2.40</option> + <option value="tupBel1.61">Tupaia belangeri : tupBel1.61</option> + <option value="tupBel1.60">Tupaia belangeri : tupBel1.60</option> + <option value="TREESHREW.66">Tupaia belangeri : TREESHREW.66</option> + <option value="TREESHREW.65">Tupaia belangeri : TREESHREW.65</option> + <option value="TREESHREW.64">Tupaia belangeri : TREESHREW.64</option> + <option value="TREESHREW.63">Tupaia belangeri : TREESHREW.63</option> + <option value="turTru1.66">Tursiops truncatus : turTru1.66</option> + <option value="turTru1.65">Tursiops truncatus : turTru1.65</option> + <option value="turTru1.64">Tursiops truncatus : turTru1.64</option> + <option value="turTru1.63">Tursiops truncatus : turTru1.63</option> + <option value="turTru1.61">Tursiops truncatus : turTru1.61</option> + <option value="turTru1.60">Tursiops truncatus : turTru1.60</option> + <option value="vacwr">Vaccinia Western Reserve : vacwr</option> + <option value="vibrio">Vibrio Cholerae : vibrio</option> + <option value="vicPac1.66">Vicugna pacos : vicPac1.66</option> + <option value="vicPac1.65">Vicugna pacos : vicPac1.65</option> + <option value="vicPac1.64">Vicugna pacos : vicPac1.64</option> + <option value="vicPac1.63">Vicugna pacos : vicPac1.63</option> + <option value="vicPac1.61">Vicugna pacos : vicPac1.61</option> + <option value="vicPac1.60">Vicugna pacos : vicPac1.60</option> + <option value="xtrop7.1">Xenopus tropicalis : xtrop7.1</option> + <option value="xtrop4.1.61">Xenopus tropicalis : xtrop4.1.61</option> + <option value="xtrop4.1.60">Xenopus tropicalis : xtrop4.1.60</option> + <option value="JGI_4.2.66">Xenopus tropicalis : JGI_4.2.66</option> + <option value="JGI_4.2.64">Xenopus tropicalis : JGI_4.2.64</option> + <option value="JGI_4.2.63">Xenopus tropicalis : JGI_4.2.63</option> + </param> + </inputs> + + <outputs> + <data format="txt" name="logfile" /> + </outputs> + + <help> + +This tool downloads a SnpEff database. + +For details about this tool, please go to http://snpEff.sourceforge.net + + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpSift_annotate.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,24 @@ +<tool id="snpSift_annotate" name="SnpSift Annotate" version="1.0"> + <description>Annotate SNPs from dbSnp</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <command>java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar annotate -q $dbSnp $input > $output </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param format="Tabular" name="dbSnp" type="data" label="dbSnp in VCF format"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +This is typically used to annotate IDs from dbSnp. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#annotate + + </help> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpSift_caseControl.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,35 @@ +<tool id="snpSift_caseControl" name="SnpSift CaseControl" version="1.0"> + <description>Count samples are in 'case' and 'control' groups.</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <command> + java -Xmx1G -jar /home/pcingola/tools/SnpSift.jar casControl -q $hhCase $hhControl $caseControStr $input > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param name="hhCase" type="select" label="Hom/Het case"> + <option value="any">Any</option> + <option value="hom">Homozygous</option> + <option value="het">Heterozygous</option> + </param> + <param name="hhControl" type="select" label="Hom/Het control"> + <option value="any">Any</option> + <option value="hom">Homozygous</option> + <option value="het">Heterozygous</option> + </param> + <param name="caseControStr" type="text" label="Case / Control" size="50"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +Count samples are in 'case' and 'control' groups. You can count 'homozygous', 'heterozygous' or 'any' variants. Case and control are defined by a string containing plus and minus symbols ('+' and '-') where '+' is case and '-' is control. This command adds two annotations to the VCF file. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#casecontrol + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpSift_filter.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,33 @@ +<tool id="snpSift_filter" name="SnpSift Filter" version="1.0"> + <options sanitize="False" /> + <description>Filter variants using arbitrary expressions</description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar filter -f $input -e $exprFile > $output + --> + <command> + java -Xmx6G -jar /home/pcingola/tools/SnpSift.jar filter -f $input -e $exprFile > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param name="expr" type="text" label="Expression" size="50"/> + </inputs> + <configfiles> + <configfile name="exprFile"> + $expr + </configfile> + </configfiles> + + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +You can filter using arbitrary expressions. + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#filter + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/snpSift_int.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,25 @@ +<tool id="snpSift_int" name="SnpSift Intervals" version="1.0"> + <description>Filter variants using intervals </description> + <!-- + You will need to change the path to wherever your installation is. + You can change the amount of memory used, just change the -Xmx parameter (e.g. use -Xmx2G for 2Gb of memory) + --> + <command> + cat $input | java -Xmx2G -jar /home/pcingola/tools/SnpSift.jar int $bedFile > $output + </command> + <inputs> + <param format="Tabular" name="input" type="data" label="VCF input"/> + <param format="Tabular" name="bedFile" type="data" label="Intervals (BED file)"/> + </inputs> + <outputs> + <data format="tabular" name="output" /> + </outputs> + + <help> + +You can filter using intervals (BED file) + +For details about this tool, please go to http://snpeff.sourceforge.net/SnpSift.html#intervals + + </help> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/galaxy/tool_conf.xml Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,13 @@ + + <!-- + Add this section to tool_conf.xml file in your Galaxy distribution + --> + <section name="SnpEff tools" id="snpEff_tools"> + <tool file="snpEff/snpEff.xml" /> + <tool file="snpEff/snpEff_download.xml" /> + <tool file="snpEff/snpSift_annotate.xml" /> + <tool file="snpEff/snpSift_caseControl.xml" /> + <tool file="snpEff/snpSift_filter.xml" /> + <tool file="snpEff/snpSift_int.xml" /> + </section> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/bam2fastq.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,8 @@ +#!/usr/bin/perl + +while( $l = <STDIN> ) { + chomp $l; + @t = split /\t/, $l; + print "\@$t[0]\n$t[9]\n+\n$t[10]\n"; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/buildTestCases.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,16 @@ +#!/bin/sh + +# Test cases hg37 +./scripts/snpEffM.sh build -v -txt testCase + +# Test cases hg37.61 +./scripts/snpEffM.sh build -v -gtf22 testHg3761Chr15 +./scripts/snpEffM.sh build -v -gtf22 testHg3761Chr16 + +# Test cases hg37.63 +./scripts/snpEffM.sh build -v -gtf22 testHg3763Chr1 +./scripts/snpEffM.sh build -v -gtf22 testHg3763Chr20 +./scripts/snpEffM.sh build -v -gtf22 testHg3763ChrY + +# Test cases hg37.65 +./scripts/snpEffM.sh build -v -gtf22 testHg3765Chr22
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/build_regulation.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,5 @@ +#!/bin/sh + +./scripts/queue.pl 10 24 15 queue_build_regulation.txt + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/compareToEnsembl.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,8 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ + +java -Xmx3G \ + -classpath "$DIR/lib/charts4j-1.2.jar:$DIR/lib/flanagan.jar:$DIR/lib/freemarker.jar:$DIR/lib/junit.jar:$DIR/lib/trove-2.1.0.jar:$DIR" \ + ca.mcgill.mcb.pcingola.testCases.CompareToEnsembl \ + $*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/GRCh37.64/countBioTypes.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,71 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Count unmber of bioType for transcript (second column in GTF file) and +# for gene ('/gene_biotype' info field) +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +use strict; + +my($count, %count, $countMatch) = (0, 0); + +#--- +# Process input (GTF file) +#--- +my($l, $key, $field, @t, %bioType); +while( $l = <STDIN> ) { + chomp $l; + @t = split /\t/, $l; + + # Get transcript biotype + my($bioTypeTr) = $t[1]; + die "Cannot find biotype" if( $bioTypeTr eq '' ); + + # Get gene biotype + @t = split /;/, $t[8]; + my($bioTypeGene) = ''; + foreach $field ( @t ) { + # Parse 'name value' fields + if( $field =~/\s*(.*)\s\"(.*)\"/ ) { + my($name, $value) = ($1, $2); + if( $name eq 'gene_biotype' ) { $bioTypeGene = $value; } + } + } + die "Cannot find biotype" if($bioTypeGene eq ''); + + $bioType{$bioTypeTr} = 1; + $bioType{$bioTypeGene} = 1; + + $key = "$bioTypeTr\t$bioTypeGene"; + $count{$key}++; + + # Count + if( $bioTypeTr eq $bioTypeGene ) { $countMatch++; } + $count++; +} + +#--- +# Show results +#--- +foreach $key ( sort keys %count ) { print "$count{$key}\t$key\n"; } +print "Count\t$count\n"; +print "Count match\t$countMatch\n"; + +#--- +# Show as table +#--- +my($bt, $bg); +print "\t"; +foreach $bg ( sort keys %bioType ) { print "$bg\t"; } +print "\n"; +foreach $bt ( sort keys %bioType ) { + print "$bt\t"; + foreach $bg ( sort keys %bioType ) { + $key = "$bt\t$bg"; + print "$count{$key}\t"; + } + print "\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/SL2.40/create.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,26 @@ +#!/bin/sh + +# wget ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz + +# GFF has to be downloaded manually from +# +# http://solgenomics.net/itag/release/2.3/list_files# +# File ITAG2.3_gene_models.gff3 +# +# + +# Create genes.gff +echo Decompressing the file +cp ITAG2.3_gene_models.gff3.gz genes.gff.gz +rm -f genes.gff +gunzip genes.gff.gz + +echo Fixing start-end problem +cat genes.gff | ./fixStartEnd.pl > g +mv g genes.gff + +# Append FASTA Sequences +echo "###" >> genes.gff +echo "##FASTA" >> genes.gff +zcat S_lycopersicum_chromosomes.2.40.fa.gz >> genes.gff +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/SL2.40/fixStartEnd.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,19 @@ +#!/usr/bin/perl + +# +# If start > end swap values +# +while( $l = <STDIN> ) { + chomp $l; + @t = (); + @t = split /\t/, $l; + + ($start, $end) = ($t[3], $t[4]); + if( $start > $end ) { + #print STDERR "ERROR:\t$l\n"; + ($t[3], $t[4]) = ($t[4], $t[3]); + $l = join "\t", @t; + } + + print "$l\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/alyrata1/convert.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,56 @@ +#!/usr/bin/perl + + +# Parse command line argument +$gtfFile = $ARGV[0]; + +#--- +# Pass one: Get geneID -> transcriptID +# Note: It is assumed (and it is true for this particular file) that each genes has only one transcript +# This assumption os obviously not true for other files & other organisms +#---- +print STDERR "Pass 1: Read IDs\n"; +open GTF, $gtfFile or die "Cannot open file $gtfFile\n"; + +while( $l = <GTF> ) { + chomp $l; + ($seqname, $source, $feature, $start, $end, $score, $strand, $frame, $attr) = split /\t/, $l; + + $gid = $tid = ""; + if( $attr =~ /gene_id "(.*?)";/ ) { $gid = $1; } + if( $attr =~ /transcript_id "(.*?)";/ ) { $tid = $1; } + + if(( $gid ne '' ) && ( $tid ne '' )) { + # print "\tgid = $gid\n\ttid = $tid\n"; + + # Store transcriptId + if( $tbyg{$gid} eq '' ) { $tbyg{$gid} = $tid; } + + # Is there more than one transcript per gene? => Error + if( $tbyg{$gid} ne $tid ) { die "Error: More than one transcript per gene. We cannot map transcripts!\n\t$tid ne $tbyg{$gid}\n"; } + } +} + +close GTF; + +#--- +# Pass two: Fill in the missing transcript IDs +#--- +print STDERR "Pass 2: Add ID data\n"; +open GTF, $gtfFile or die "Cannot open file $gtfFile\n"; + +while( $l = <GTF> ) { + chomp $l; + ($seqname, $source, $feature, $start, $end, $score, $strand, $frame, $attr) = split /\t/, $l; + + $gid = ""; + if( $attr =~ /gene_id "(.*?)";/ ) { $gid = $1; } + elsif( $attr =~ /gene_id "(.*)"/ ) { $gid = $1; } + else { print STDERR "Cannot match '$attr'\n"; } + $tid = $tbyg{$gid}; + + if(( $gid ne '' ) && ( $tid ne '' )) { print "$seqname\t$source\t$feature\t$start\t$end\t$score\t$strand\t$frame\tgene_id \"$gid\"; transcript_id \"$tid\";\n"; } + else { print STDERR "Skipping line: $l\n\tgid = '$gid'\n\ttid = '$tid'\n"; } +} + +close GTF;
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/alyrata1/convert.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,11 @@ +#!/bin/sh + +zcat Araly1_GeneModels_FilteredModels6.gff.gz \ + | sed "s/name/gene_id/" \ + | sed "s/transcriptId \(.*\)/transcript_id \"\1\";/" \ + | sed "s/exonNumber \(.*\)/exon_number \"\1\";/" \ + > g1 + +./convert.pl g1 > genes.gtf +rm -vf g1 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/c_briggsae_WS230/create.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,15 @@ +#!/bin/sh -e + +zcat c_briggsae.WS230.annotations.gff3.gz \ + | grep -v SNP \ + | grep -v translated_nucleotide_match \ + | grep -v repeat_region \ + | grep -v inverted_repeat \ + | grep -v tandem_repeat \ + | grep -v nucleotide_match \ + > genes.gff + +# Add fasta sequence +echo "###" >> genes.gff +echo "##FASTA" >> genes.gff +zcat c_briggsae.WS230.genomic.fa.gz >> genes.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/genomes/x.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,8 @@ +#!/bin/sh + +for chr in chr10.fa chr11.fa chr12.fa chr13.fa chr14.fa chr15.fa chr16.fa chr17.fa chr18.fa chr19.fa chr1.fa chr20.fa chr21.fa chr22.fa chr2.fa chr3.fa chr4.fa chr5.fa chr6.fa chr7.fa chr8.fa chr9.fa chrMT.fa chrX.fa chrY.fa +do + MDGR=`cat GRCh37.65/$chr | grep -v "^>" | tr -d "\n" | tr "[a-z]" "[A-Z]" | md5sum` + MDHG=`cat hg19/chr$chr | grep -v "^>" | tr -d "\n" | tr "[a-z]" "[A-Z]" | md5sum` + echo -e "$chr\n\t$MDGR\n\t$MDHG" +done
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/gmax1.09v8/create.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,35 @@ +#!/bin/sh -e + +echo "Processing GFF file" +gunzip -c Gmax_109_gene.gff3.gz > genes.gff +# | sed "s/.five_prime_UTR.1//" \ +# | sed "s/.three_prime_UTR.1//" \ +# > genes.gff + +echo "Adding FASTA sequence" +( echo "###" ; echo "##FASTA" ; gunzip -c Gmax_109.fa.gz ) >> genes.gff + +ehco "Create CDS file" +gunzip -c Gmax_109_cds.fa.gz \ + | sed "s/|PACid:/|PAC:/" \ + | sed "s/Glyma.*|//" \ + > cds.fa + +echo "Create protein file" +gunzip -c Gmax_109_peptide.fa.gz \ + | sed "s/|PACid:/|PAC:/" \ + | sed "s/Glyma.*|//" \ + > protein.fa + +# Build databse +cd $HOME/snpEff + +./scripts/snpEffM.sh build -v -gff3 gmax1.09v8 2>&1 | tee gmax1.09v8.build + +# CDS test +./scripts/snpEffM.sh cds -v gmax1.09v8 data/gmax1.09v8/cds.fa 2>&1 | tee gmax1.09v8.cds + +cd - + +echo Done! +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/hg19/create.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,52 @@ +#!/bin/sh + +REF=hg19 + +#--- +# Download latest datasets +#--- + +# # Genome sequence +# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/bigZips/chromFa.tar.gz +# +# # Protein sequences +# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz +# +# # CDS sequences +# wget ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz +# +# # RefLink +# wget http://hgdownload.cse.ucsc.edu/goldenPath/$REF/database/refLink.txt.gz +# +# #--- +# # Create files +# #--- +# gunzip refLink.txt.gz +# +# # Protein fasta +# zcat human.protein.faa.gz | ../../scripts/proteinFasta2NM.pl refLink.txt > protein.fa +# gzip protein.fa +# +# # CDS fasta +# zcat human.rna.fna.gz | sed "s/^>gi|[0-9]*|ref|\(.*\)\..*|.*/>\1/" > cds.fa +# gzip cds.fa + +# Chromosome fasta +#rm -rvf chr +#mkdir chr +cd chr +#tar -xvzf ../chromFa.tar.gz + +FASTA=../$REF.fa +echo Creating FASTA file +rm -vf $FASTA +cat chr[1-9].fa >> $FASTA +cat chr??.fa >> $FASTA +cat chr[A-Z].fa >> $FASTA +cat chr???*.fa >> $FASTA + +cd - + +# # Compress genome file +# $HOME/tools/pigz/pigz hg19.fa +# cp hg19.fa.gz $HOME/snpEff/data/genomes/
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/paeru.PA01/genes.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_002516.2.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_002516.2.fna >> genes.gff +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/paeru.PA14/genes.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_008463.1.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_008463.1.fna >> genes.gff +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_009444/genes.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_009444.1.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_009444.1.fna >> genes.gff +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/pfluo.SBW25.NC_012660/genes.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,6 @@ +#!/bin/sh + +cat NC_012660.1.gff | sed "s/CDS/exon/" > genes.gff +echo "##FASTA" >> genes.gff +cat NC_012660.1.fna >> genes.gff +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/ppersica139/genes.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,8 @@ +#!/bin/sh + +# Download files +#wget ftp://ftp.plantgdb.org/download/Genomes/PeGDB/Ppersica_139.fa.gz +#wget ftp://ftp.plantgdb.org/download/Genomes/PeGDB/Ppersica_139_gene.gff3.gz + +( zcat Ppersica_139_gene.gff3.gz ; echo "###" ; echo "##FASTA" ; zcat Ppersica_139.fa.gz ) > genes.gff +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/rice5/genes.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,7 @@ +#!/bin/sh + +cat ORI/build5_locus.gff3 > genes.gff +cat ORI/build5_genes.gff3 | ./mRnaAddParent.pl >> genes.gff +echo "###" >> genes.gff +echo "##FASTA" >> genes.gff +cat ORI/IRGSPb5.fa >> genes.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/data/rice5/mRnaAddParent.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,28 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# Add 'Parent' option in mRNA lines +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +while( $l = <STDIN> ) { + chomp $l; + @t = split /\t/,$l; + + $type = $t[2]; + + # Is it an mRNA? + if( $type eq 'mRNA' ) { + # Parse ID in options + $opts = $t[8]; + if( $opts =~ /ID=(.*?)-\d+;/ ) { + $pid = $1; + $pid =~ tr/t/g/; + # Add 'Parent' option + $l .= ";Parent=$pid"; + } + } + + print "$l\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/distro.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,47 @@ +#!/bin/sh + +#------------------------------------------------------------------------------ +# Create a zip file for distribution +# Note: Only binary data is included (no raw gene info / genomes) +# +# Pablo Cingolani 2010 +#------------------------------------------------------------------------------ + +VERSION="2_1" +VERSION_REV=$VERSION"a" +DIR=$HOME/snpEff_$VERSION_REV +rm -rvf $DIR +mkdir $DIR + +# Copy core files +cp snpEff.config snpEff.jar $DIR +cp -rvfH galaxy scripts $DIR + +cd $DIR +rm -rvf `find . -name "CVS" -type d` +cd - + +# Create 'core' zip file +cd $HOME +ZIP="snpEff_v"$VERSION_REV"_core.zip" +rm -f $ZIP 2> /dev/null +zip -r $ZIP snpEff_$VERSION_REV +cd - + +# Create ZIP file for each database +for d in `ls data/*/snpEffectPredictor.bin` +do + DIR=`dirname $d` + GEN=`basename $DIR` + + echo $GEN + ZIP="snpEff_v"$VERSION"_"$GEN".zip" + zip -r $ZIP data/$GEN/*.bin +done + +# Look for missing genomes +echo Missing genomes: +ls -d data/*/snpEffectPredictor.bin | grep -v genomes | cut -f 2 -d / | sort > genomes_bins.txt +ls -d data/* | grep -v genomes | cut -f 2 -d / | sort > genomes_dirs.txt +diff genomes_dirs.txt genomes_bins.txt | grep "^<" +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/download.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,120 @@ +#!/bin/sh -e + +RELEASE=66 + +# mkdir download +cd download + +#--- +# Download +#--- + +# # Download GTF files (annotations) +# wget -r -A "*gtf.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/" +# +# # Download FASTA files (reference genomes) +# wget -r -A "*toplevel.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" +# +# # Download CDS sequences +# wget -r -A "*cdna.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" +# +# # Download PROTEIN sequences +# wget -r -A "*.pep.all.fa.gz" "ftp://ftp.ensembl.org/pub/release-$RELEASE/fasta/" + +#--- +# Create directory structure +#--- + +# # Move all downloaded file to this directory +# mv `find ftp.ensembl.org -type f` . + +# # Gene annotations files +# for gtf in *.gtf.gz +# do +# short=`../scripts/file2GenomeName.pl $gtf | cut -f 5` +# echo ANNOTATIONS: $short +# +# mkdir -p data/$short +# cp $gtf data/$short/genes.gtf.gz +# done +# +# # Reference genomes files +# mkdir -p data/genomes +# for fasta in *.dna.toplevel.fa.gz +# do +# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5` +# echo REFERENCE: $genome +# +# cp $fasta data/genomes/$genome.fa.gz +# done +# +# # CDS genomes files +# for fasta in *.cdna.all.fa.gz +# do +# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 5` +# echo CDS: $genome +# +# cp $fasta data/$genome/cds.fa.gz +# done +# +# # Protein seuqence files +# for pep in *.pep.all.fa.gz +# do +# short=`../scripts/file2GenomeName.pl $pep | cut -f 5` +# echo PROTEIN: $short +# +# mkdir -p data/$short +# cp $pep data/$short/protein.fa.gz +# done + +#--- +# Config file entries +#--- + +# for fasta in *.cdna.all.fa.gz +# do +# genome=`../scripts/file2GenomeName.pl $fasta | cut -f 4` +# short=`../scripts/file2GenomeName.pl $fasta | cut -f 5` +# +# # Individual genome entry +# echo -e "$short.genome : $genome" +# echo -e "$short.reference : ftp://ftp.ensembl.org/pub/release-$RELEASE/gtf/" +# echo +# done + +# Back to parent dir +cd - > /dev/null + +#--- +# Create build queue entries +#--- + +# rm -vf queue_build.txt +# +# # Build from TXT files +# for genes in data/*/genes.txt* +# do +# dir=`dirname $genes` +# genomeName=`basename $dir` +# echo "./scripts/snpEffXL.sh build -v $genomeName" +# done | sort >> queue_build.txt +# +# # Build from GFF2 files +# echo "./scripts/snpEffXL.sh build -v -gff2 amel2" >> queue_build.txt +# +# # Build from GFF3 files +# for genes in `ls data/*/genes.gff* | grep -v amel2` +# do +# dir=`dirname $genes` +# genomeName=`basename $dir` +# echo "./scripts/snpEffXL.sh build -v -gff3 $genomeName" +# done | sort >> queue_build.txt +# +# # Build from GTF22 files +# for genes in data/*/genes.gtf* +# do +# dir=`dirname $genes` +# genomeName=`basename $dir` +# echo "./scripts/snpEffXL.sh build -v -gtf22 $genomeName" +# done | sort >> queue_build.txt +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/fasta2tab.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,32 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------ +# Split a fasta file (create one file per sequence) +# +# +#------------------------------------------------------------------------------ + +use strict; + +#------------------------------------------------------------------------------ +# Main +#------------------------------------------------------------------------------ + +my($seq, $name) = ('', ''); +my($lineNum, $l, $newName); +#--- +# Read fasta file +#--- +for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { + chomp $l; + if( $l =~/^>\s*(.*)\s*$/ ) { + $newName = $1; + if( $seq ne "" ) { print "$name\t$seq\n"; } + # New sequence + $name = $newName; + $seq = ""; + } else { $seq .= $l; } +} + +if( $seq ne "" ) { print "$name\t$seq\n"; } +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/fastaSample.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,41 @@ +#!/usr/bin/perl + +#--- +# Initialize parameters +#--- +$sampleStart = $ARGV[0]; +$sampleEnd = $ARGV[1]; +if(( $ARGV[0] eq '' ) || ($ARGV[1] eq '')) { die "Usage: fastaSample sampleStart sampleEnd\n"; } + +$sampleStart--; +$sampleEnd--; +$sampleLen = $sampleEnd - $sampleStart + 1; + +#--- +# Read fasta file +#--- +for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { + if( $l =~/^>/ ) { + # Sample if not empty + if( $seq ne "" ) { + $s = substr( $seq, $sampleStart, $sampleLen); + print "$s\n"; + } + # New sequence + $seq = ""; + } else { + chomp($l); + $seq .= $l; + } +} + +# Sample if not empty +if( $seq ne "" ) { + $s = substr( $seq, $sampleStart, $sampleLen); + print "$s\n"; +} + +$len = length($seq); +print STDERR "Lines: $lineNum\n"; +print STDERR "Sequence size: $len\n"; +print STDERR "Sample size: $sampleLen\n";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/fastaSplit.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,42 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------ +# Split a fasta file (create one file per sequence) +# +# +#------------------------------------------------------------------------------ + +use strict; + +#------------------------------------------------------------------------------ +# Write fasta file +#------------------------------------------------------------------------------ +sub writeSeq($$) { + my($name, $seq) = @_; + $name = "chr" . $name . ".fa"; + print "Writing to $name\n"; + open OUT, "> $name"; + print OUT $seq; + close OUT; +} + +#------------------------------------------------------------------------------ +# Main +#------------------------------------------------------------------------------ + +my($seq, $name) = ('', ''); +my($lineNum, $l, $newName); +#--- +# Read fasta file +#--- +for($lineNum=0 ; $l = <STDIN> ; $lineNum++ ) { + if( $l =~/^>\s*(.*?)\s+.*/ ) { + $newName = $1; + if( $seq ne "" ) { writeSeq($name, $seq); } + # New sequence + $name = $newName; + $seq = $l; + } else { $seq .= $l; } +} + +if( $seq ne "" ) { writeSeq($name, $seq); }
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/file2GenomeName.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,24 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Transform file name to genome short name +# +#------------------------------------------------------------------------------- + +$file = $ARGV[0]; +print "$file"; + +$base = `basename $file`; +chomp $base; +print "\t$base"; + +if( $base =~ /(.*?)\.(.*)\..?dna\.(.*)\.fa\.gz/ ) { ($gen, $short) = ($1, $2); } +elsif( $base =~ /(.*?)\.(.*)\.gtf\.gz/ ) { ($gen, $short) = ($1, $2); } +elsif( $base =~ /(.*?)\.(.*)\.pep\.all\.fa\.gz/ ) { ($gen, $short) = ($1, $2); } +$full = "$gen.$short"; +print "\t$full\t$gen\t$short"; + + +print "\n"; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/filterOutBoringPredictions.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,11 @@ +#!/bin/sh + +# Remove some (boring) predictions +grep -v DOWNSTREAM \ + | grep -v UPSTREAM \ + | grep -v INTRON \ + | grep -v UTR_5_PRIME \ + | grep -v UTR_3_PRIME \ + | grep -v INTERGENIC \ + | grep -v " SYNONYMOUS_CODING" \ + | grep -v WITHIN_NON_CODING_GENE
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/filterOutBoringPredictionsVcf.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,6 @@ +#!/bin/sh + +# Keep interesting predictions +java -jar $HOME/tools/VcfEtc.jar filter \ + "( EFF =~ 'NON_SYN' ) | ( EFF =~ 'CODON') | ( EFF =~ 'SPLICE') | ( EFF =~ 'STOP') | ( EFF =~ 'START') | ( EFF =~ 'FRAME') | ( EFF =~ 'LOST') | ( EFF =~ 'DELETED' )" \ +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/genesTxtColumnNames.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,33 @@ +#!/bin/sh + +#------------------------------------------------------------------------------- +# Convert the gene names in order to be used in an R script +# +# Usage: cat snpEff_genes.txt | ./scripts/genesTxtColumnNames.sh > genes.txt +# +# Once in R, you can: +# - Load this table: +# data <- read.csv("genes.txt", sep= "\t", header=TRUE); +# +# - Access the data: +# data$countINTRON +# +# - Add missing or empty columns: +# if( is.null(data$countINTRON ) { data$countINTRON <- 0 * (1:length(data$geneId) ); } +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +cat \ + | grep -v "^# The following"\ + | sed "s/Bases affected (/bases/g" \ + | sed "s/Length (/len/g" \ + | sed "s/Count (/count/g" \ + | sed "s/Total score (/score/g" \ + | sed "s/)//g" \ + | sed "s/#GeneId/geneId/" \ + | sed "s/GeneName/geneName/" \ + | sed "s/BioType/bioType/" \ + | sed "s/_PRIME//g" \ + | sed "s/SPLICE_SITE_//g" \ + | sed "s/SYNONYMOUS_CODING/SYN/g" \
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/hist.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,88 @@ +#!/usr/bin/perl +#------------------------------------------------------------------------------- +# +# Plot a histogram (using R) +# Data is feed as a 1 column of numbers +# +# Note: Any line that does not match a numeric regular expression, is filtered out). +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- + +# Parse command line option (file base name) +$base = 'hist'; +if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } + +$pngFile = "$base.png"; +$txtFile = "$base.txt"; + +# Read STDIN and create an R vector +open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; +print TXT "x\n"; +for( $ln = 0 ; $l = <STDIN> ; ) { + chomp $l; + + # Does the string contain exactly one number? (can be float) + if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; } +} +close TXT; + +#--- +# Create an R program, save histogram plot as PNG image +#--- + +open R, "| R --vanilla --slave " or die "Cannot open R program\n"; +print R <<EOF; + +histDens <- function( x, title, q=1.0, breaks = 30 ) { + # Show only this part of the data + xmin <- quantile( x, 1-q ) + xmax <- quantile( x, q ) + data <- x[ (x >= xmin) & (x <= xmax) ]; + + dens <- density(data) + + h <- hist(data, main=title, xlab = "data", ylab = "Frequency", freq = T, breaks=breaks); + + # Adjust density height to 'frecuency' + dens\$y <- max(h\$counts) * dens\$y/max(dens\$y) + lines(dens, col='red') + + # Mean & median calculated over the whola data + abline( v=mean(x), col='blue', lty=2, lwd=2); + abline( v=median(x), col='green', lty=2, lwd=2); + + legend("topright",c("Mean","Median"),lty=c(1,1),col=c("blue","green")) + +} + +png('$pngFile', width = 1024, height = 1024); +par( mfrow=c(2,1) ); + +data <- read.csv("$txtFile", sep='\\t', header = TRUE); +x <- data\$x + +histDens( x, "Histogram: All data", 1.0 ); +histDens( x, "Histogram: Quantile [2% - 98%]", 0.98 ); + +print( summary( x ) ) + +dev.off(); +quit( save='no' ) +EOF + +close R; + +#--- +# Show figure +#--- + +$os = `uname`; +$show = "eog"; +if( $os =~ "Darwin" ) { $show = "open"; } +`$show $pngFile`; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/joinSnpEff.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,125 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------ +# +# Mark snps as X1, X2 or 'Both' +# +#------------------------------------------------------------------------------ + +use strict; + +my($debug) = 0; + +#------------------------------------------------------------------------------ +# Read a file and index lines by SNP +#------------------------------------------------------------------------------ +sub readSnps($) { + my($file) = (@_); + my($l, %snps); + + open SNP, $file || die "Cannot open file '$file'\n"; + while( $l = <SNP> ) { + my($chr, $pos, $ref, $var) = split /\t/, $l; + my($snp) = "$chr:$pos\_$ref/$var"; + $snps{$snp} .= $l; + } + close SNP; + return %snps; +} + +#------------------------------------------------------------------------------ +# Print SNP info and quals +#------------------------------------------------------------------------------ +sub printLine($$$$) { + my($snp, $lines, $quals, $q) = (@_); + my($line, @lines); + (@lines) = split '\n', $lines; + foreach $line ( @lines ) { + my($l) = replaceSnpQ($line, $q); + print "$l\t$quals\n"; + } +} + +#------------------------------------------------------------------------------ +# Parse snp quality parameter +#------------------------------------------------------------------------------ +sub parseSnpQ($) { + my($l) = @_; + my(@t); + (@t) = split /\t/,$l; + return $t[6]; +} + +#------------------------------------------------------------------------------ +# Replace a quality +#------------------------------------------------------------------------------ +sub replaceSnpQ($$) { + my($line, $q) = @_; + my(@t); + (@t) = split /\t/, $line; + $t[1] = $q; + return join("\t", @t); +} + +#------------------------------------------------------------------------------ +# Main +#------------------------------------------------------------------------------ +# Read arguments +my(@file); +(@file) = @ARGV; +if( $#file <= 0 ) { die "Usage: ./joinSnpEff.pl tag1 file1 tag2 file2 ... tagN fileN\n"; } + +# Parse arguments +print STDERR "Reading files:\n"; +my($i, $j, $file, $tag, $snp, @snpsAll, %snps, @tags); +for( $i=0 , $j=0 ; $i < $#ARGV ; $i+=2, $j++ ) { + # Read tag + $tags[$j] = $tag = $ARGV[$i]; + + # Read file + $file = $ARGV[$i+1]; + if( $file eq '' ) { die "Missing file for tag '$tag'\n"; } + print STDERR "\tTags[$j]: $tag\t'$file'\n"; + %snps = readSnps($file); + + # Add all snps + foreach $snp ( keys %snps ) { $snpsAll[$j]->{$snp} = $snps{$snp}; } +} + +#--- +# Print SNPS +#--- +my($snp, %done, %snpsi); +my($j, $jj); +$i = 0; +print STDERR "Joining SNP from all files\n"; +for( $i=0 ; $i <= $#tags ; $i++ ) { # For all tags + print "TAG:\ttags[$i] = '$tags[$i]'\n" if $debug; + my($uniq, $shared) = (0, 0); + %snpsi = %{$snpsAll[$i]}; + foreach $snp (sort keys %snpsi) { # For all snps... + if( ! $done{$snp} ) { # Not done yet? + + # Get qualities from all SNPs + my($quals, $qSum, $qCount) = ("", 0, 0); + my($all) = "ALL "; + for( $j=0, $jj=1 ; $j <= $#snpsAll ; $j++ , $jj++ ) { + if( exists $snpsAll[$j]{$snp} ) { + my($q) = parseSnpQ($snpsAll[$j]->{$snp}); + $quals .= "$tags[$j]:$q "; + $qSum += $q; + $qCount++; + } else { $all = ""; } + } + + if( $qCount <= 1 ) { $uniq++; } # Count unique SNPs for this file + else { $shared++; } + + $done{$snp} = 1; + my($qAvg) = ( $qCount > 0 ? int($qSum/$qCount) : 0); + printLine($snp, $snpsi{$snp}, "$all $quals", $qAvg); + } else { $shared++; } + } + print STDERR "\tTags[$i]: $tags[$i]\tUnique / Shared snps: $uniq / $shared\n"; +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/nOutOfM.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,10 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Keep variants present in N out of M samples (multi-sample VCF file) +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/promoterSequences.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,8 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ + +java -Xmx3G \ + -classpath "$DIR/lib/charts4j-1.2.jar:$DIR/lib/flanagan.jar:$DIR/lib/freemarker.jar:$DIR/lib/junit.jar:$DIR/lib/trove-2.1.0.jar:$DIR" \ + ca.mcgill.mcb.pcingola.PromoterSequences \ + $*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/proteinFasta2NM.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,45 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Convert fasta headers from protein ID (NP_XXXX) into transcript ID NM_XXXX +# +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +# Parse command line arguments +$refLink = $ARGV[0]; +die "Usage: cat file.fasta | ./proteinFasta2NM.pl refLink.txt > protein_NM.fasta" if $refLink eq ''; + +# Read refLink file +open RL, $refLink or die "Cannot opne file '$refLink'\n"; +while( <RL> ) { + chomp; + @t = split /\t/; + ($nm, $np) = ($t[2], $t[3]); + + if( $np ne '' ) { + if( $trId{$np} ne '' ) { print STDERR "Error: Non empty entry '$np' = $trId{$np}\n"; } + else { $trId{$np} = $nm; } + } +} + +# Read fasta file +while( <STDIN> ) { + chomp; + + if( /^>(.*)/ ) { # Header? => change form protein NP_XXX to transcript NM_XXXX + # Get NM_ field + @t = split /\|/; + $np = $t[3]; + + # Remove anything after the dot + if( $np =~ /(.*)\./ ) { $np = $1; } + + # Found a transcript ID? + if( $trId{$np} ne '' ) { print ">$trId{$np}\n"; } + else { print "$l\n"; } + } else { print "$_\n"; } # Show line +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/qqplot.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,80 @@ +#!/usr/bin/perl +#------------------------------------------------------------------------------- +# +# Plot a QQ plot (using R) +# Data is feed as a 1 column of numbers +# +# Note: Any line that does not match a numeric regular expression, is filtered out). +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- + +# Parse command line option (file base name) +$base = 'QQ-plot'; +if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } + +$pngFile = "$base.png"; +$txtFile = "$base.txt"; + +# Read STDIN and create an R vector +open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; +print TXT "x\n"; +for( $ln = 0 ; $l = <STDIN> ; ) { + chomp $l; + + # Does the string contain exactly one number? (can be float) + if( $l =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) { print TXT "$l\n"; } +} +close TXT; + +#--- +# Create an R program, save QQ-plot as PNG image +#--- + +open R, "| R --vanilla --slave " or die "Cannot open R program\n"; +print R <<EOF; + +qqplot <- function( x, title ) { + keep <- (x > 0) & (x <= 1) & ( ! is.na(x) ); + x <- x[keep] + s <- sort(x); + ly <- -log10(s); + + n <- length(s); + lx <- -log10( (1:n) / (n+1) ) + + # Show auto range + #par( mfrow=c(2,1) ); + #plot( lx, ly, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" ); + #abline( 0 , 1 , col='red'); + + # Show full range in both plots + range <- c(0 , max(lx, ly) ); + plot( lx, ly, xlim=range, ylim=range, main=title, xlab="-Log[ rank / (N+1) ]", ylab="-Log[ p ]" ); + abline( 0 , 1 , col='red'); +} + +png('$pngFile', width = 1024, height = 1024); + +data <- read.csv("$txtFile", sep='\t', header = TRUE); +qqplot( data\$x, "$base" ); + +dev.off(); +quit( save='no' ) +EOF + +close R; + +#--- +# Show figure +#--- + +$os = `uname`; +$show = "eog"; +if( $os =~ "Darwin" ) { $show = "open"; } +`$show $pngFile`; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,127 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# Simple queue management program +# Attempts to keep 'numProc' processes running at the same time +# +# Proceses are defined in a file (one line per process) +# +# Every executed process creates two files: 'pid.stdout' and 'pid.stderr' where +# pid is the process ID. The files contain STDOUT and STDERR for that process. +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +use strict; +use POSIX; + + +my($uptimeCmd) = "/usr/bin/uptime"; # Uptime command +my($maxUptime); +$| = 1; # Don't use buffers for STDIN/STDOUT + +#------------------------------------------------------------------------------- +# Should a new process be run? +# Check some conditions before trying to run the next process +#------------------------------------------------------------------------------- +sub shouldRun() { + if( $maxUptime < 0 ) { return 1; } # Always true if $maxUptime is negative + my($utRes) = `$uptimeCmd`; + my($ut) = 0; + if( $utRes =~ /load average:\s+(\d+\.\d+),/ ) { $ut = $1; } + return $ut < $maxUptime; +} + +#------------------------------------------------------------------------------- +# Print something 'printLog' style +#------------------------------------------------------------------------------- +sub printLog($) { + my($str) = @_; + my($now) = strftime "%Y-%m-%d %H:%M:%S", localtime; + print "$now\t$str\n"; +} + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- +# Usage: queue numProc File +my($maxNumProc, $sleepTime, $file); +($maxNumProc, $maxUptime, $sleepTime, $file) = @ARGV; +if( $file eq '' ) { + print "Usage: queue.pl maxNumProc maxUptime sleepTime file\n"; + print "Where:\n"; + print "\tnumProc Number of simultaneous processes\n"; + print "\tmaxUptime Maximum allowed uptime (otherwise, pause before launching the next process). Negative means don't care.\n"; + print "\tsleepTime Number of seconds to sleep after running a process (zero means no sleep)\n"; + print "\tfile File containing all commands to be executed (one per line)\n"; + exit(10); +} + +#--- +# Read file and launch processes +#--- +my($cmd); +my($startTime) = time(); +my($numProc) = 0; +open BATCH, $file; +while( $cmd = <BATCH> ) { + chomp $cmd; + + # Can we launch more processes? + if( $numProc < $maxNumProc ) { + + my( $run ) = 0; + + do { + # Should the next process run now? (don't run if CPU is too high) + if( shouldRun() ) { + my $retFork = fork(); + $run = 1; + + if( $retFork == 0 ) { # Child process + # Redirect STDOUT and STDERR to files + open STDOUT, '>', "$$.stdout" or die "Can't redirect STDOUT (PID=$$): $!"; + open STDERR, '>', "$$.stderr" or die "Can't redirect STDERR (PID=$$): $!"; + exec($cmd); + } elsif ($retFork == '' ) { # Error launching process + print STDERR "Error launching process:\t'$cmd'\n"; + } else { + printLog("Executing (PID=$retFork):\t'$cmd'"); + $numProc++; + } + } else { printLog("No running"); } + + # Sleep before next process + if( $sleepTime > 0 ) { + printLog "Sleep $sleepTime seconds"; + sleep($sleepTime); + } + } while( ! $run ); + } + + # Number of processes exceded? => Wait until one finishes + if( $numProc >= $maxNumProc ) { + # Wait for processes to die + my $deadPid = wait(); + printLog "Process PID=$deadPid finished."; + $numProc--; + if( $numProc > 0 ) { print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; } + } +} + +#--- +# Done, wait for the remining processes to die +#--- +my($deadPid); +while( ($deadPid = wait()) >= 0 ) { # Wait for processes to die + $numProc--; + my($now) = localtime(); + printLog "Process PID=$deadPid finished."; + if( $numProc > 0 ) { print "There " . ($numProc > 1 ? "are" : "is" ) . " still $numProc processes running.\n"; } +} + +my($elapsed) = time() - $startTime; +print "All processes finished.\nElapsed time $elapsed seconds.\n"; + +close BATCH; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue_build.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,3 @@ +#!/bin/sh + +./scripts/queue.pl 22 24 15 ./scripts/queue_build.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue_build.txt Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,387 @@ +./scripts/snpEffXL.sh build -v anoCar1.0.60 +./scripts/snpEffXL.sh build -v btau4.0.59 +./scripts/snpEffXL.sh build -v btau4.0.60 +./scripts/snpEffXL.sh build -v bushBaby1.60 +./scripts/snpEffXL.sh build -v calJac3.2.1.60 +./scripts/snpEffXL.sh build -v canFam2.59 +./scripts/snpEffXL.sh build -v canFam2.60 +./scripts/snpEffXL.sh build -v cat1.60 +./scripts/snpEffXL.sh build -v cavPor3.60 +./scripts/snpEffXL.sh build -v ce.WS210.60 +./scripts/snpEffXL.sh build -v chimp2.1.59 +./scripts/snpEffXL.sh build -v chimp2.1.60 +./scripts/snpEffXL.sh build -v choHof1.60 +./scripts/snpEffXL.sh build -v cInt2.60 +./scripts/snpEffXL.sh build -v cSav2.0.60 +./scripts/snpEffXL.sh build -v danRer8.59 +./scripts/snpEffXL.sh build -v danRer9.60 +./scripts/snpEffXL.sh build -v dasNov2.60 +./scripts/snpEffXL.sh build -v dipOrd1.60 +./scripts/snpEffXL.sh build -v dm5.25.59 +./scripts/snpEffXL.sh build -v dm5.25.60 +./scripts/snpEffXL.sh build -v equCab2.60 +./scripts/snpEffXL.sh build -v eriEur1.60 +./scripts/snpEffXL.sh build -v fugu4.60 +./scripts/snpEffXL.sh build -v gacu1.60 +./scripts/snpEffXL.sh build -v ggallus2.59 +./scripts/snpEffXL.sh build -v ggallus2.60 +./scripts/snpEffXL.sh build -v gorGor3.60 +./scripts/snpEffXL.sh build -v hg19 +./scripts/snpEffXL.sh build -v hg37.59 +./scripts/snpEffXL.sh build -v hg37.60 +./scripts/snpEffXL.sh build -v hiv +./scripts/snpEffXL.sh build -v loxAfr3.60 +./scripts/snpEffXL.sh build -v medaka1.60 +./scripts/snpEffXL.sh build -v meug1.0.60 +./scripts/snpEffXL.sh build -v micMur1.60 +./scripts/snpEffXL.sh build -v mm37 +./scripts/snpEffXL.sh build -v mm37.59 +./scripts/snpEffXL.sh build -v mm37.60 +./scripts/snpEffXL.sh build -v mmul1.60 +./scripts/snpEffXL.sh build -v monDom5.60 +./scripts/snpEffXL.sh build -v myoLuc1.60 +./scripts/snpEffXL.sh build -v oana5.60 +./scripts/snpEffXL.sh build -v ochPri2.60 +./scripts/snpEffXL.sh build -v oryCun2.60 +./scripts/snpEffXL.sh build -v ppyg2.60 +./scripts/snpEffXL.sh build -v proCap1.60 +./scripts/snpEffXL.sh build -v pteVam1.60 +./scripts/snpEffXL.sh build -v rat3.4.59 +./scripts/snpEffXL.sh build -v rat3.4.60 +./scripts/snpEffXL.sh build -v sacCer2 +./scripts/snpEffXL.sh build -v sacCer2.59 +./scripts/snpEffXL.sh build -v sacCer2.60 +./scripts/snpEffXL.sh build -v SIVmac239 +./scripts/snpEffXL.sh build -v sorAra1.60 +./scripts/snpEffXL.sh build -v speTri1.60 +./scripts/snpEffXL.sh build -v sScrofa9.60 +./scripts/snpEffXL.sh build -v taeGut3.2.4.60 +./scripts/snpEffXL.sh build -v tarSyr1.60 +./scripts/snpEffXL.sh build -v tenrec1.60 +./scripts/snpEffXL.sh build -v testCase +./scripts/snpEffXL.sh build -v tetraodon8.60 +./scripts/snpEffXL.sh build -v tupBel1.60 +./scripts/snpEffXL.sh build -v turTru1.60 +./scripts/snpEffXL.sh build -v vicPac1.60 +./scripts/snpEffXL.sh build -v xtrop4.1.60 +./scripts/snpEffXL.sh build -v -gff2 amel2 +./scripts/snpEffXL.sh build -v -gff3 agam +./scripts/snpEffXL.sh build -v -gff3 alyrata107 +./scripts/snpEffXL.sh build -v -gff3 aquiCoer +./scripts/snpEffXL.sh build -v -gff3 athaliana130 +./scripts/snpEffXL.sh build -v -gff3 athalianaTair10 +./scripts/snpEffXL.sh build -v -gff3 athalianaTair9 +./scripts/snpEffXL.sh build -v -gff3 cAlbicansv21 +./scripts/snpEffXL.sh build -v -gff3 c_briggsae_WS230 +./scripts/snpEffXL.sh build -v -gff3 ce.WS201 +./scripts/snpEffXL.sh build -v -gff3 dm5.12 +./scripts/snpEffXL.sh build -v -gff3 dm5.22 +./scripts/snpEffXL.sh build -v -gff3 dm5.30 +./scripts/snpEffXL.sh build -v -gff3 dm5.31 +./scripts/snpEffXL.sh build -v -gff3 dm5.32 +./scripts/snpEffXL.sh build -v -gff3 dm5.34 +./scripts/snpEffXL.sh build -v -gff3 dm5.40 +./scripts/snpEffXL.sh build -v -gff3 dm5.42 +./scripts/snpEffXL.sh build -v -gff3 gmax1.09 +./scripts/snpEffXL.sh build -v -gff3 gmax1.09v8 +./scripts/snpEffXL.sh build -v -gff3 kw1407.2012 +./scripts/snpEffXL.sh build -v -gff3 kw1407.2012 +./scripts/snpEffXL.sh build -v -gff3 maizeZmB73 +./scripts/snpEffXL.sh build -v -gff3 mmm.2012 +./scripts/snpEffXL.sh build -v -gff3 myco_fh +./scripts/snpEffXL.sh build -v -gff3 myco_m129 +./scripts/snpEffXL.sh build -v -gff3 paeru.PA01 +./scripts/snpEffXL.sh build -v -gff3 paeru.PA14 +./scripts/snpEffXL.sh build -v -gff3 pfluo.SBW25.NC_009444 +./scripts/snpEffXL.sh build -v -gff3 pfluo.SBW25.NC_012660 +./scripts/snpEffXL.sh build -v -gff3 plasmo72 +./scripts/snpEffXL.sh build -v -gff3 ppersica139 +./scripts/snpEffXL.sh build -v -gff3 rice5 +./scripts/snpEffXL.sh build -v -gff3 rice6.1 +./scripts/snpEffXL.sh build -v -gff3 SL2.40 +./scripts/snpEffXL.sh build -v -gff3 spombe +./scripts/snpEffXL.sh build -v -gff3 vacwr +./scripts/snpEffXL.sh build -v -gff3 vibrio +./scripts/snpEffXL.sh build -v -gff3 xtrop7.1 +./scripts/snpEffXL.sh build -v -gtf22 agam2.6 +./scripts/snpEffXL.sh build -v -gtf22 ailmel1.61 +./scripts/snpEffXL.sh build -v -gtf22 ailMel1.63 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue_build_regulation.txt Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,73 @@ +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adipose_Nuclei GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adult_Kidney GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Adult_Liver GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Anterior_Caudate GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Cingulate_Gyrus GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Hippocampus_Middle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Inferior_Temporal_Lobe GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Mid_Frontal_Lobe GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Brain_Substantia_Nigra GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Luminal_Epithelial_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Myoepithelial_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_Stem_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Breast_vHMEC GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD15_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD19_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD34_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD34_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD3_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Memory_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Naive_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD4_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD56_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD8_Naive_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType CD8_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Colonic_Mucosa GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Duodenum_Mucosa GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType ES-I3 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType ES-WA7 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Adrenal_Gland GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Brain GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Heart GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Intestine_Large GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Intestine_Small GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney_Left GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Kidney_Right GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung_Left GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Lung_Right GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Fetal_Thymus GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType H1 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType H3K9me3 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType H9 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES48 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES6 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType HUES64 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType IMR90 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType input GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-11a GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-15b GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-18c GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS-20b GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_19 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_4 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType iPS_DF_6 GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Mobilized_CD34_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Mobilized_CD56_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Muscle_Satellite_Cultured_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Neurosphere_Cultured_Cells_Cortex_Derived GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Pancreatic_Islets GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Penis_Foreskin_Keratinocyte_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Peripheral_Blood_Mononuclear_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Rectal_Mucosa GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Rectal_Smooth_Muscle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Skeletal_Muscle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Stomach_Smooth_Muscle GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Th17_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType Treg_Primary_Cells GRCh37.64 +./scripts/snpEffXL.sh build -v -onlyReg -cellType uniques GRCh37.64
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue_dump.txt Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,137 @@ +./scripts/snpEff.sh dump agam > agam.dump +./scripts/snpEff.sh dump ailmel1.61 > ailmel1.61.dump +./scripts/snpEff.sh dump alyrata107 > alyrata107.dump +./scripts/snpEff.sh dump alyrata107 > alyrata107.dump +./scripts/snpEff.sh dump amel2 > amel2.dump +./scripts/snpEff.sh dump anoCar1.0.60 > anoCar1.0.60.dump +./scripts/snpEff.sh dump anoCar2.0.61 > anoCar2.0.61.dump +./scripts/snpEff.sh dump aquiCoer > aquiCoer.dump +./scripts/snpEff.sh dump athaliana130 > athaliana130.dump +./scripts/snpEff.sh dump btau4.0.59 > btau4.0.59.dump +./scripts/snpEff.sh dump btau4.0.60 > btau4.0.60.dump +./scripts/snpEff.sh dump btau4.0.61 > btau4.0.61.dump +./scripts/snpEff.sh dump bushBaby1.60 > bushBaby1.60.dump +./scripts/snpEff.sh dump bushBaby1.61 > bushBaby1.61.dump +./scripts/snpEff.sh dump calJac3.2.1.60 > calJac3.2.1.60.dump +./scripts/snpEff.sh dump calJac3.2.1.61 > calJac3.2.1.61.dump +./scripts/snpEff.sh dump canFam2.59 > canFam2.59.dump +./scripts/snpEff.sh dump canFam2.60 > canFam2.60.dump +./scripts/snpEff.sh dump canFam2.61 > canFam2.61.dump +./scripts/snpEff.sh dump cat1.60 > cat1.60.dump +./scripts/snpEff.sh dump cat1.61 > cat1.61.dump +./scripts/snpEff.sh dump cavPor3.60 > cavPor3.60.dump +./scripts/snpEff.sh dump cavPor3.61 > cavPor3.61.dump +./scripts/snpEff.sh dump ce.WS210.60 > ce.WS210.60.dump +./scripts/snpEff.sh dump ce.WS220.61 > ce.WS220.61.dump +./scripts/snpEff.sh dump chimp2.1.59 > chimp2.1.59.dump +./scripts/snpEff.sh dump chimp2.1.60 > chimp2.1.60.dump +./scripts/snpEff.sh dump chimp2.1.61 > chimp2.1.61.dump +./scripts/snpEff.sh dump choHof1.60 > choHof1.60.dump +./scripts/snpEff.sh dump choHof1.61 > choHof1.61.dump +./scripts/snpEff.sh dump cInt2.60 > cInt2.60.dump +./scripts/snpEff.sh dump cInt2.61 > cInt2.61.dump +./scripts/snpEff.sh dump cSav2.0.60 > cSav2.0.60.dump +./scripts/snpEff.sh dump cSav2.0.61 > cSav2.0.61.dump +./scripts/snpEff.sh dump danRer6 > danRer6.dump +./scripts/snpEff.sh dump danRer8.59 > danRer8.59.dump +./scripts/snpEff.sh dump danRer9.60 > danRer9.60.dump +./scripts/snpEff.sh dump danRer9.61 > danRer9.61.dump +./scripts/snpEff.sh dump dasNov2.60 > dasNov2.60.dump +./scripts/snpEff.sh dump dasNov2.61 > dasNov2.61.dump +./scripts/snpEff.sh dump dipOrd1.60 > dipOrd1.60.dump +./scripts/snpEff.sh dump dipOrd1.61 > dipOrd1.61.dump +./scripts/snpEff.sh dump dm5.12 > dm5.12.dump +./scripts/snpEff.sh dump dm5.22 > dm5.22.dump +./scripts/snpEff.sh dump dm5.25.59 > dm5.25.59.dump +./scripts/snpEff.sh dump dm5.25.60 > dm5.25.60.dump +./scripts/snpEff.sh dump dm5.25.61 > dm5.25.61.dump +./scripts/snpEff.sh dump dm5.30 > dm5.30.dump +./scripts/snpEff.sh dump dm5.31 > dm5.31.dump +./scripts/snpEff.sh dump dm5.32 > dm5.32.dump +./scripts/snpEff.sh dump dm5.34 > dm5.34.dump +./scripts/snpEff.sh dump equCab2.60 > equCab2.60.dump +./scripts/snpEff.sh dump equCab2.61 > equCab2.61.dump +./scripts/snpEff.sh dump eriEur1.60 > eriEur1.60.dump +./scripts/snpEff.sh dump eriEur1.61 > eriEur1.61.dump +./scripts/snpEff.sh dump fugu4.60 > fugu4.60.dump +./scripts/snpEff.sh dump fugu4.61 > fugu4.61.dump +./scripts/snpEff.sh dump gacu1.60 > gacu1.60.dump +./scripts/snpEff.sh dump gacu1.61 > gacu1.61.dump +./scripts/snpEff.sh dump ggallus2.59 > ggallus2.59.dump +./scripts/snpEff.sh dump ggallus2.60 > ggallus2.60.dump +./scripts/snpEff.sh dump ggallus2.61 > ggallus2.61.dump +./scripts/snpEff.sh dump gorGor3.60 > gorGor3.60.dump +./scripts/snpEff.sh dump gorGor3.61 > gorGor3.61.dump +./scripts/snpEff.sh dump hg36.54 > hg36.54.dump +./scripts/snpEff.sh dump hg37.59 > hg37.59.dump +./scripts/snpEff.sh dump hg37.60 > hg37.60.dump +./scripts/snpEff.sh dump hg37.61 > hg37.61.dump +./scripts/snpEff.sh dump hg37 > hg37.dump +./scripts/snpEff.sh dump hiv > hiv.dump +./scripts/snpEff.sh dump loxAfr3.60 > loxAfr3.60.dump +./scripts/snpEff.sh dump loxAfr3.61 > loxAfr3.61.dump +./scripts/snpEff.sh dump medaka1.60 > medaka1.60.dump +./scripts/snpEff.sh dump medaka1.61 > medaka1.61.dump +./scripts/snpEff.sh dump meug1.0.60 > meug1.0.60.dump +./scripts/snpEff.sh dump meug1.0.61 > meug1.0.61.dump +./scripts/snpEff.sh dump micMur1.60 > micMur1.60.dump +./scripts/snpEff.sh dump micMur1.61 > micMur1.61.dump +./scripts/snpEff.sh dump mm37.59 > mm37.59.dump +./scripts/snpEff.sh dump mm37.60 > mm37.60.dump +./scripts/snpEff.sh dump mm37.61 > mm37.61.dump +./scripts/snpEff.sh dump mm37 > mm37.dump +./scripts/snpEff.sh dump mmul1.60 > mmul1.60.dump +./scripts/snpEff.sh dump mmul1.61 > mmul1.61.dump +./scripts/snpEff.sh dump monDom5.60 > monDom5.60.dump +./scripts/snpEff.sh dump monDom5.61 > monDom5.61.dump +./scripts/snpEff.sh dump myoLuc1.60 > myoLuc1.60.dump +./scripts/snpEff.sh dump myoLuc1.61 > myoLuc1.61.dump +./scripts/snpEff.sh dump oana5.60 > oana5.60.dump +./scripts/snpEff.sh dump oana5.61 > oana5.61.dump +./scripts/snpEff.sh dump ochPri2.60 > ochPri2.60.dump +./scripts/snpEff.sh dump ochPri2.61 > ochPri2.61.dump +./scripts/snpEff.sh dump oryCun2.60 > oryCun2.60.dump +./scripts/snpEff.sh dump oryCun2.61 > oryCun2.61.dump +./scripts/snpEff.sh dump paeru.PA01 > paeru.PA01.dump +./scripts/snpEff.sh dump paeru.PA14 > paeru.PA14.dump +./scripts/snpEff.sh dump pfluo.SBW25.NC_009444 > pfluo.SBW25.NC_009444.dump +./scripts/snpEff.sh dump pfluo.SBW25.NC_012660 > pfluo.SBW25.NC_012660.dump +./scripts/snpEff.sh dump ppyg2.60 > ppyg2.60.dump +./scripts/snpEff.sh dump ppyg2.61 > ppyg2.61.dump +./scripts/snpEff.sh dump proCap1.60 > proCap1.60.dump +./scripts/snpEff.sh dump proCap1.61 > proCap1.61.dump +./scripts/snpEff.sh dump pteVam1.60 > pteVam1.60.dump +./scripts/snpEff.sh dump pteVam1.61 > pteVam1.61.dump +./scripts/snpEff.sh dump rat3.4.59 > rat3.4.59.dump +./scripts/snpEff.sh dump rat3.4.60 > rat3.4.60.dump +./scripts/snpEff.sh dump rat3.4.61 > rat3.4.61.dump +./scripts/snpEff.sh dump sacCer2.59 > sacCer2.59.dump +./scripts/snpEff.sh dump sacCer2.60 > sacCer2.60.dump +./scripts/snpEff.sh dump sacCer2.61 > sacCer2.61.dump +./scripts/snpEff.sh dump sacCer2 > sacCer2.dump +./scripts/snpEff.sh dump SIVmac239 > SIVmac239.dump +./scripts/snpEff.sh dump sorAra1.60 > sorAra1.60.dump +./scripts/snpEff.sh dump sorAra1.61 > sorAra1.61.dump +./scripts/snpEff.sh dump speTri1.60 > speTri1.60.dump +./scripts/snpEff.sh dump speTri1.61 > speTri1.61.dump +./scripts/snpEff.sh dump sScrofa9.60 > sScrofa9.60.dump +./scripts/snpEff.sh dump sScrofa9.61 > sScrofa9.61.dump +./scripts/snpEff.sh dump taeGut3.2.4.60 > taeGut3.2.4.60.dump +./scripts/snpEff.sh dump taeGut3.2.4.61 > taeGut3.2.4.61.dump +./scripts/snpEff.sh dump tarSyr1.60 > tarSyr1.60.dump +./scripts/snpEff.sh dump tarSyr1.61 > tarSyr1.61.dump +./scripts/snpEff.sh dump tenrec1.60 > tenrec1.60.dump +./scripts/snpEff.sh dump tenrec1.61 > tenrec1.61.dump +./scripts/snpEff.sh dump testCase > testCase.dump +./scripts/snpEff.sh dump tetraodon8.60 > tetraodon8.60.dump +./scripts/snpEff.sh dump tetraodon8.61 > tetraodon8.61.dump +./scripts/snpEff.sh dump tupBel1.60 > tupBel1.60.dump +./scripts/snpEff.sh dump tupBel1.61 > tupBel1.61.dump +./scripts/snpEff.sh dump turkey.UMD2.61 > turkey.UMD2.61.dump +./scripts/snpEff.sh dump turTru1.60 > turTru1.60.dump +./scripts/snpEff.sh dump turTru1.61 > turTru1.61.dump +./scripts/snpEff.sh dump vacwr > vacwr.dump +./scripts/snpEff.sh dump vicPac1.60 > vicPac1.60.dump +./scripts/snpEff.sh dump vicPac1.61 > vicPac1.61.dump +./scripts/snpEff.sh dump xtrop4.1.60 > xtrop4.1.60.dump +./scripts/snpEff.sh dump xtrop4.1.61 > xtrop4.1.61.dump
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue_test.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,3 @@ +#!/bin/sh + +./scripts/queue.pl 22 24 15 ./scripts/queue_test.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/queue_test.txt Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,231 @@ +./scripts/snpEffXL.sh cds -v ailmel1.61 data/ailmel1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v ailMel1.63 data/ailMel1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v ailMel1.64 data/ailMel1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v anoCar1.0.60 data/anoCar1.0.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v anoCar2.0.61 data/anoCar2.0.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v AnoCar2.0.63 data/AnoCar2.0.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v AnoCar2.0.64 data/AnoCar2.0.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v BDGP5.25.63 data/BDGP5.25.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v BDGP5.25.64 data/BDGP5.25.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v BROADD2.63 data/BROADD2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v BROADD2.64 data/BROADD2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v BROADO5.63 data/BROADO5.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v BROADO5.64 data/BROADO5.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v BROADS1.63 data/BROADS1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v BROADS1.64 data/BROADS1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v btau4.0.59 data/btau4.0.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v btau4.0.60 data/btau4.0.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v btau4.0.61 data/btau4.0.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v Btau_4.0.63 data/Btau_4.0.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v bushBaby1.60 data/bushBaby1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v bushBaby1.61 data/bushBaby1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v BUSHBABY1.63 data/BUSHBABY1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v BUSHBABY1.64 data/BUSHBABY1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v calJac3.2.1.60 data/calJac3.2.1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v calJac3.2.1.61 data/calJac3.2.1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v canFam2.59 data/canFam2.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v canFam2.60 data/canFam2.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v canFam2.61 data/canFam2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v cat1.60 data/cat1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v cat1.61 data/cat1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v CAT.63 data/CAT.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v CAT.64 data/CAT.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v cavPor3.60 data/cavPor3.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v cavPor3.61 data/cavPor3.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v cavPor3.63 data/cavPor3.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v cavPor3.64 data/cavPor3.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v ce.WS210.60 data/ce.WS210.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v ce.WS220.61 data/ce.WS220.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v chimp2.1.59 data/chimp2.1.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v chimp2.1.60 data/chimp2.1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v chimp2.1.61 data/chimp2.1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v CHIMP2.1.63 data/CHIMP2.1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v CHIMP2.1.64 data/CHIMP2.1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v choHof1.60 data/choHof1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v choHof1.61 data/choHof1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v choHof1.63 data/choHof1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v choHof1.64 data/choHof1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v cInt2.60 data/cInt2.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v cInt2.61 data/cInt2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v C_jacchus3.2.1.63 data/C_jacchus3.2.1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v C_jacchus3.2.1.64 data/C_jacchus3.2.1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v COMMON_SHREW1.63 data/COMMON_SHREW1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v COMMON_SHREW1.64 data/COMMON_SHREW1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v cSav2.0.60 data/cSav2.0.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v cSav2.0.61 data/cSav2.0.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v CSAV2.0.63 data/CSAV2.0.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v CSAV2.0.64 data/CSAV2.0.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v danRer8.59 data/danRer8.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v danRer9.60 data/danRer9.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v danRer9.61 data/danRer9.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v dasNov2.60 data/dasNov2.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v dasNov2.61 data/dasNov2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v dasNov2.63 data/dasNov2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v dasNov2.64 data/dasNov2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v DEVIL7.0.64 data/DEVIL7.0.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v dipOrd1.60 data/dipOrd1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v dipOrd1.61 data/dipOrd1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v dipOrd1.63 data/dipOrd1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v dipOrd1.64 data/dipOrd1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v dm5.12 data/dm5.12/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.22 data/dm5.22/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.25.59 data/dm5.25.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.25.60 data/dm5.25.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.25.61 data/dm5.25.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v dm5.30 data/dm5.30/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.31 data/dm5.31/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.32 data/dm5.32/cds.txt.gz +./scripts/snpEffXL.sh cds -v dm5.34 data/dm5.34/cds.fa.gz +./scripts/snpEffXL.sh cds -v EF3.63 data/EF3.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v EF3.64 data/EF3.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v equCab2.60 data/equCab2.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v equCab2.61 data/equCab2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v EquCab2.63 data/EquCab2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v EquCab2.64 data/EquCab2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v eriEur1.60 data/eriEur1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v eriEur1.61 data/eriEur1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v fugu4.60 data/fugu4.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v fugu4.61 data/fugu4.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v FUGU4.63 data/FUGU4.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v FUGU4.64 data/FUGU4.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v gacu1.60 data/gacu1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v gacu1.61 data/gacu1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v ggallus2.59 data/ggallus2.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v ggallus2.60 data/ggallus2.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v ggallus2.61 data/ggallus2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v gorGor3.1.64 data/gorGor3.1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v gorGor3.60 data/gorGor3.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v gorGor3.61 data/gorGor3.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v gorGor3.63 data/gorGor3.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v GRCh37.63 data/GRCh37.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v GRCh37.64 data/GRCh37.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v HEDGEHOG.63 data/HEDGEHOG.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v HEDGEHOG.64 data/HEDGEHOG.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v hg36.54 data/hg36.54/cds.fa.gz +./scripts/snpEffXL.sh cds -v hg37.59 data/hg37.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v hg37.60 data/hg37.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v hg37.61 data/hg37.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v hg37 data/hg37/cds.txt.gz +./scripts/snpEffXL.sh cds -v JGI2.63 data/JGI2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v JGI2.64 data/JGI2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v JGI_4.2.63 data/JGI_4.2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v JGI_4.2.64 data/JGI_4.2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v loxAfr3.60 data/loxAfr3.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v loxAfr3.61 data/loxAfr3.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v loxAfr3.63 data/loxAfr3.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v loxAfr3.64 data/loxAfr3.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v medaka1.60 data/medaka1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v medaka1.61 data/medaka1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v MEDAKA1.63 data/MEDAKA1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v MEDAKA1.64 data/MEDAKA1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v meug1.0.60 data/meug1.0.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v meug1.0.61 data/meug1.0.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v Meug_1.0.63 data/Meug_1.0.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v Meug_1.0.64 data/Meug_1.0.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v micMur1.60 data/micMur1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v micMur1.61 data/micMur1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v micMur1.63 data/micMur1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v micMur1.64 data/micMur1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v mm37.59 data/mm37.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v mm37.60 data/mm37.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v mm37.61 data/mm37.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v mm37 data/mm37/cds.txt.gz +./scripts/snpEffXL.sh cds -v mmul1.60 data/mmul1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v mmul1.61 data/mmul1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v MMUL_1.63 data/MMUL_1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v MMUL_1.64 data/MMUL_1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v monDom5.60 data/monDom5.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v monDom5.61 data/monDom5.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v myoLuc1.60 data/myoLuc1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v myoLuc1.61 data/myoLuc1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v Myoluc2.0.63 data/Myoluc2.0.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v Myoluc2.0.64 data/Myoluc2.0.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v NCBIM37.63 data/NCBIM37.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v NCBIM37.64 data/NCBIM37.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v Nleu1.0.63 data/Nleu1.0.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v Nleu1.0.64 data/Nleu1.0.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v oana5.60 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PPYG2.63 data/PPYG2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v PPYG2.64 data/PPYG2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v proCap1.60 data/proCap1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v proCap1.61 data/proCap1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v proCap1.63 data/proCap1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v proCap1.64 data/proCap1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v pteVam1.60 data/pteVam1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v pteVam1.61 data/pteVam1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v pteVam1.63 data/pteVam1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v pteVam1.64 data/pteVam1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v rat3.4.59 data/rat3.4.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v rat3.4.60 data/rat3.4.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v rat3.4.61 data/rat3.4.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v RGSC3.4.63 data/RGSC3.4.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v RGSC3.4.64 data/RGSC3.4.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v sacCer2.59 data/sacCer2.59/cds.txt.gz +./scripts/snpEffXL.sh cds -v sacCer2.60 data/sacCer2.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v sacCer2.61 data/sacCer2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v sacCer2 data/sacCer2/cds.txt.gz +./scripts/snpEffXL.sh cds -v sorAra1.60 data/sorAra1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v sorAra1.61 data/sorAra1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v speTri1.60 data/speTri1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v speTri1.61 data/speTri1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v SQUIRREL.63 data/SQUIRREL.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v SQUIRREL.64 data/SQUIRREL.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v sScrofa9.60 data/sScrofa9.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v sScrofa9.61 data/sScrofa9.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v Sscrofa9.63 data/Sscrofa9.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v Sscrofa9.64 data/Sscrofa9.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v taeGut3.2.4.60 data/taeGut3.2.4.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v taeGut3.2.4.61 data/taeGut3.2.4.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v taeGut3.2.4.63 data/taeGut3.2.4.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v taeGut3.2.4.64 data/taeGut3.2.4.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v tarSyr1.60 data/tarSyr1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v tarSyr1.61 data/tarSyr1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v tarSyr1.63 data/tarSyr1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v tarSyr1.64 data/tarSyr1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v tenrec1.60 data/tenrec1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v tenrec1.61 data/tenrec1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v TENREC.63 data/TENREC.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v TENREC.64 data/TENREC.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v testCase data/testCase/cds.txt.gz +./scripts/snpEffXL.sh cds -v tetraodon8.60 data/tetraodon8.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v tetraodon8.61 data/tetraodon8.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v TETRAODON8.63 data/TETRAODON8.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v TETRAODON8.64 data/TETRAODON8.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v TREESHREW.63 data/TREESHREW.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v TREESHREW.64 data/TREESHREW.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v tupBel1.60 data/tupBel1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v tupBel1.61 data/tupBel1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v turkey.UMD2.61 data/turkey.UMD2.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v turTru1.60 data/turTru1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v turTru1.61 data/turTru1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v turTru1.63 data/turTru1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v turTru1.64 data/turTru1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v UMD2.63 data/UMD2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v UMD2.64 data/UMD2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v UMD3.1.64 data/UMD3.1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v vicPac1.60 data/vicPac1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v vicPac1.61 data/vicPac1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v vicPac1.63 data/vicPac1.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v vicPac1.64 data/vicPac1.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v WASHUC2.63 data/WASHUC2.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v WASHUC2.64 data/WASHUC2.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v WS220.63 data/WS220.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v WS220.64 data/WS220.64/cds.fa.gz +./scripts/snpEffXL.sh cds -v xtrop4.1.60 data/xtrop4.1.60/cds.txt.gz +./scripts/snpEffXL.sh cds -v xtrop4.1.61 data/xtrop4.1.61/cds.fa.gz +./scripts/snpEffXL.sh cds -v Zv9.63 data/Zv9.63/cds.fa.gz +./scripts/snpEffXL.sh cds -v Zv9.64 data/Zv9.64/cds.fa.gz
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/randBedIntervals.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,36 @@ +#!/usr/bin/perl + +# Number of intervals per chromosome +$intsPerChr = 10; + +# Max interval len +$maxLen = 1000; + +# Chromosome length +$len{'chr2L'} = 23299195; +$len{'chr2LHet'} = 373492; +$len{'chr2R'} = 21411048; +$len{'chr2RHet'} = 3329880; +$len{'chr3L'} = 24850358; +$len{'chr3LHet'} = 2587444; +$len{'chr3R'} = 28253873; +$len{'chr3RHet'} = 2548985; +$len{'chr4'} = 1368761; +$len{'chrdmel_mitochondrion_genome'} = 19790; +$len{'chrUextra'} = 29367225; +$len{'chrU'} = 10174655; +$len{'chrX'} = 22703118; +$len{'chrXHet'} = 206671; +$len{'chrYHet'} = 351384; + +foreach $chr ( sort keys %len ) { + $max = $len{$chr} - $maxLen - 1000; + + for( $i=0 ; $i < $intsPerChr ; $i++ ) { + $start = int( rand() * $max ); + $end = int( rand() * $maxLen ) + $start; + + print "$chr\t$start\t$end\n"; + } +} +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/sift2vcf.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,19 @@ +#!/usr/bin/perl + + +print "##INFO=<ID=SIFT_SCORE,Number=1,Type=Float,Description=\"SIFT score, 0 = Damaging, 1=Tolerated\">\n"; +print "##INFO=<ID=SIFT_CONS,Number=1,Type=Float,Description=\"SIFT median conservation value, as log2. 0=High confidence, 4.32=Low confidence\">\n"; +print "##INFO=<ID=SIFT_SEQS,Number=1,Type=Integer,Description=\"SIFT number of sequences at position\">\n"; +print "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\n"; + +while( $l = <STDIN> ) { + chomp $l; + ($chr, $coord1, $nt1, $nt2, $score, $median, $seqs_rep) = split /\t/, $l; + + # Trim spaces + if( $seqs_rep =~ /\s(.*)/ ) { $seqs_rep = $1; } + + $coord1++; # Get it in one-based coordinates + + print "$chr\t$coord1\t.\t$nt1\t$nt2\t.\t.\tSIFT_SCORE=$score;SIFT_CONS=$median;SIFT_SEQS=$seqs_rep\n"; +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/sift2vcf.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,47 @@ +#!/bin/sh -e + +SQLITE=$HOME/tools/sqlite3 +SQLITE=sqlite3 +OUT_FILE="sift.txt" +OUT_SORT_FILE="sift.sort.txt" +OUT_VCF="sift.vcf" + +# Download files +for f in Human_CHR1.sqlite.gz Human_CHR10.sqlite.gz Human_CHR11.sqlite.gz Human_CHR12.sqlite.gz Human_CHR13.sqlite.gz Human_CHR14.sqlite.gz Human_CHR15.sqlite.gz Human_CHR16.sqlite.gz Human_CHR17.sqlite.gz Human_CHR18.sqlite.gz Human_CHR19.sqlite.gz Human_CHR2.sqlite.gz Human_CHR20.sqlite.gz Human_CHR21.sqlite.gz Human_CHR22.sqlite.gz Human_CHR3.sqlite.gz Human_CHR4.sqlite.gz Human_CHR5.sqlite.gz Human_CHR6.sqlite.gz Human_CHR7.sqlite.gz Human_CHR8.sqlite.gz Human_CHR9.sqlite.gz Human_CHRX.sqlite.gz Human_CHRY.sqlite.gz Human_Supp.sqlite.gz Human_enst.sqlite.gz +do + url=ftp://ftp.jcvi.org/pub/data/sift/Human_db_37_ensembl_63/$f + echo Getting file $url + #wget $url +done + +# Unzip files +for f in Human_CHR*.sqlite.gz +do + echo Decompressing file $f + #gunzip $f +done + +# Dumping data +rm -f $OUT_FILE +for f in Human_CHR*.sqlite +do + echo Dumping Database $f to $OUT_FILE + + TABLES=`$SQLITE $f ".tables" | tr "\n" "\t"` + for t in $TABLES + do + echo " Dumping Table $t" + + $SQLITE $f "select CHR, COORD1, NT1, NT2, SCORE, MEDIAN, SEQS_REP from $t where SCORE != '' AND NT1 != NT2;" \ + | tr "|" "\t" \ + | sed "s/^chr//" \ + >> $OUT_FILE + done +done + +echo Sorting file +sort -k 1 -n -k 2 -n -o $OUT_SORT_FILE $OUT_FILE + +echo Creating VCF +cat $OUT_SORT_FILE | sift2vcf.pl > $OUT_VCF +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/smoothScatter.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,82 @@ +#!/usr/bin/perl +#------------------------------------------------------------------------------- +# +# Plot a smooth scatter plot +# Data is feed as two column of numbers +# +# Note: Any line that does not match a numeric regular expression, is filtered out). +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#------------------------------------------------------------------------------- +# Main +#------------------------------------------------------------------------------- + +# Parse command line option (file base name) +$base = 'smoothScatter'; +if( $ARGV[0] ne '' ) { $base = $ARGV[0]; } + +$pngFile = "$base.png"; +$txtFile = "$base.txt"; + +# Read STDIN and create an R table +open TXT, "> $txtFile" or die "Cannot open output file '$txtFile'\n"; +print TXT "x\ty\n"; +for( $ln = 0 ; $l = <STDIN> ; ) { + chomp $l; + ($x, $y) = split /\t/, $l; + + # Does the string contain exactly one number? (can be float) + if(( $x =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ ) && ( $y =~ /^[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?$/ )) { print TXT "$x\t$y\n"; } +} +close TXT; + +#--- +# Create an R program, save histogram plot as PNG image +#--- + +open R, "| R --vanilla --slave " or die "Cannot open R program\n"; +print R <<EOF; + +smoothLowess <- function( x, y, title, q=1.0 ) { + # Show only this part of the data + xmin <- quantile( x, 1-q ) + xmax <- quantile( x, q ) + + ymin <- quantile( y, 1-q ) + ymax <- quantile( y, q ) + + keep <- (x >= xmin) & (x <= xmax) & (y >= ymin) & (y <= ymax); + qx <- x[ keep ] + qy <- y[ keep ] + + smoothScatter(qx, qy, main=title, ylab='Y (column 2)', xlab='X (column 1)'); + lines( lowess(qx,qy), col='orange' ); +} + +png('$pngFile', width = 1024, height = 1024); +par( mfrow=c(2,1) ); + +data <- read.csv("$txtFile", sep='\\t', header = TRUE); +x <- data\$x +y <- data\$y + +smoothLowess(x, y, "Smooth scatter plot and Lowess", 1.0); +smoothLowess(x, y, "Smooth scatter plot and Lowess: Quantile [2% - 98%]", 0.98); + +dev.off(); +quit( save='no' ) +EOF + +close R; + +#--- +# Show figure +#--- + +$os = `uname`; +$show = "eog"; +if( $os =~ "Darwin" ) { $show = "open"; } +`$show $pngFile`; +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/snpEff.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,9 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +LIB=$HOME/snpEff/lib + +java -Xmx1G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ + ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ + $*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/snpEffM.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,9 @@ +#!/bin/sh + +DIR=$HOME/snpEff +LIB=$HOME/snpEff/lib + +java -Xmx3G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ + ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ + $*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/snpEffXL.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,9 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +LIB=$HOME/snpEff/lib + +java -Xmx20G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR" \ + ca.mcgill.mcb.pcingola.snpEffect.commandLine.SnpEff \ + $*
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/snpSift.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,15 @@ +#!/bin/sh + +DIR=$HOME/snpEff/ +DIR_SNPSIFT=$HOME/snpEff/snpSiftBin/ +LIB=$HOME/snpEff/lib +LIB_SNPSIFT=$HOME/snpEff/snpSiftLib/ + +# Old library reference: +# -classpath "$LIB/charts4j-1.2.jar:$LIB/flanagan.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$DIR:$DIR_SNPSIFT" \ + +java -Xmx1G \ + -classpath "$LIB/charts4j-1.2.jar:$LIB/freemarker.jar:$LIB/junit.jar:$LIB/trove-3.0.2.jar:$LIB/akka-actor-2.0-M4.jar:$LIB/scala-library.jar:$LIB_SNPSIFT/antlr-3.4-complete.jar:$DIR:$DIR_SNPSIFT" \ + ca.mcgill.mcb.pcingola.vcfEtc.SnpSift \ + $* +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/test.Broad_NS_SYN.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,25 @@ +#!/bin/sh + +REF=GRCh37.66 + +IN_VCF=$HOME/snpEff/1kg/test.Broad_NS_SYN.vcf.gz +OUT_VCF=all.vcf + +# Run SnpEff +./scripts/snpEffXL.sh eff -v -noStats -o vcf $REF $IN_VCF > $OUT_VCF + +# Calculate number of lines +SILENT=`cat $OUT_VCF | grep "SILENT" | wc -l` +MISSENSE=`cat $OUT_VCF | grep "MISSENSE" | wc -l` +NONSENSE=`cat $OUT_VCF | grep "NONSENSE" | wc -l` +SILENT_AND_MISSENSE=`cat $OUT_VCF | grep "SILENT" | grep "MISSENSE" | wc -l` + +PSILENT=`echo "100 * $SILENT/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` +PMISSENSE=`echo "100 * $MISSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` +PNONSENSE=`echo "100 * $NONSENSE/($SILENT + $MISSENSE + $NONSENSE ) " | bc -l` + +echo -e "Silent :\t$SILENT ($PSILENT %)" +echo -e "Missense :\t$MISSENSE ($PMISSENSE %)" +echo -e "Nonsense :\t$NONSENSE ($PNONSENSE %)" +echo -e "Silent and missense :\t$SILENT_AND_MISSENSE" +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/uniqCount.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,13 @@ +#!/usr/bin/perl + +while( $l = <STDIN> ) { + chomp $l; + $count{$l}++; +} + +$tot = 0; +foreach $key ( sort keys %count ) { + print "$count{$key}\t$key\n"; + $tot += $count{$key}; +} +print "$tot\tTotal\n";
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/vcfEffOnePerLine.pl Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/perl + +#------------------------------------------------------------------------------- +# +# Read a VCF file (via STDIN), split EFF fields from INFO column into many lines +# leaving one line per effect. +# +# Note: In lines having multiple effects, all other information will be +# repeated. Only the 'EFF' field will change. +# +# Pablo Cingolani 2012 +#------------------------------------------------------------------------------- + +$INFO_FIELD_NUM = 7; + +while( $l = <STDIN> ) { + # Show header lines + if( $l =~ /^#/ ) { print $l; } + else { + chomp $l; + + @t = @infos = @effs = (); # Clear arrays + + # Non-header lines: Parse fields + @t = split /\t/, $l; + + # Get INFO column + $info = $t[ $INFO_FIELD_NUM ]; + + # Parse INFO column + @infos = split /;/, $info; + + # Find EFF field + $infStr = ""; + foreach $inf ( @infos ) { + # Is this the EFF field? => Find it and split it + if( $inf =~/^EFF=(.*)/ ) { @effs = split /,/, $1; } + else { $infStr .= ( $infStr eq '' ? '' : ';' ) . $inf; } + } + + # Print VCF line + if( $#effs <= 0 ) { print "$l\n"; } # No EFF found, just show line + else { + $pre = ""; + for( $i=0 ; $i < $INFO_FIELD_NUM ; $i++ ) { $pre .= ( $i > 0 ? "\t" : "" ) . "$t[$i]"; } + + $post = ""; + for( $i=$INFO_FIELD_NUM+1 ; $i <= $#t ; $i++ ) { $post .= "\t$t[$i]"; } + + foreach $eff ( @effs ) { print $pre . "\t" . $infStr . ( $infStr eq '' ? '' : ';' ) . "EFF=$eff" . $post . "\n" ; } + } + } +}
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/scripts/vcfSpeedTest.sh Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,8 @@ +#!/bin/sh + +for testNum in 1 2 3 4 +do + ./scripts/snpEffM.sh test $testNum test.1M.vcf > test.1M.out.vcf + echo +done +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snpEff_2_1a/snpEff.config Fri Apr 20 14:47:09 2012 -0400 @@ -0,0 +1,1160 @@ + +#------------------------------------------------------------------------------- +# +# SnpEff configuration file +# +# Pablo Cingolani +#------------------------------------------------------------------------------- + +#--- +# Databases are stored here +# E.g.: Information for 'hg19' is stored in data_dir/hg19/ +# +# Note: Since version 2.1 you can use tilde ('~') as first character to refer to your home directory +#--- +data_dir = ~/snpEff/data/ + +#--- +# Database repository: A URL to the server where you can download databases (command: 'snpEff download dbName') +#--- +database_repository = http://downloads.sourceforge.net/project/snpeff/databases + +#------------------------------------------------------------------------------- +# Genomes +# +# One entry per genome version. +# +# For genome version 'ZZZ' the entries look like +# ZZZ.genome : Real name for ZZZ (e.g. 'Human') +# ZZZ.reference : [Optional] Comma separated list of URL to site/s where information for building ZZZ database was extracted. +# ZZZ.chrName.codonTable : [Optional] Define codon table used for chromosome 'chrName' (Default: 'codon.Standard') +# +#------------------------------------------------------------------------------- + +# Ailuropoda_melanoleuca +ailmel1.61.genome : Ailuropoda_melanoleuca + +# Anopheles_gambiae +agam.genome : Anopheles_gambiae +agam.reference : http://agambiae.vectorbase.org/GetData/ + +agam2.6.genome : Anopheles_gambiae +agam2.6.reference : http://agambiae.vectorbase.org/GetData/ + +# Arabidopsis lyrata +alyrata107.genome : Arabidopsis_lyrata +alyrata107.reference : http://www.phytozome.net/search.php?method=Org_Alyrata + +alyrata1.genome : Arabidopsis_lyrata +alyrata1.reference : http://genome.jgi-psf.org/Araly1/Araly1.download.ftp.html + +# Apis mellifera +amel2.genome : Bee +amel2.reference : http://beebase.org + +# Anolis carolinensis genes (AnoCar1.0) (ENSEMBL) +anoCar1.0.60.genome : Anolis_carolinensis +anoCar2.0.61.genome : Anolis_carolinensis + +# Aquilegia coerulea +aquiCoer.genome : Aquilegia_coerulea + +# Arabidopsis Thaliana +athaliana130.genome : Arabidopsis_Thaliana +athaliana130.reference : http://www.phytozome.net/dataUsagePolicy.php?org=Org_Athaliana + +athalianaTair9.genome : Arabidopsis_Thaliana +athalianaTair9.reference : ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR9_genome_release + +athalianaTair10.genome : Arabidopsis_Thaliana +athalianaTair10.reference : ftp://ftp.arabidopsis.org/home/tair/Genes/TAIR10_genome_release + +# Bos taurus genes (Btau_4.0) (ENSEMBL) +btau4.0.59.genome : Bos_taurus +btau4.0.60.genome : Bos_taurus +btau4.0.61.genome : Bos_taurus + +# Otolemur garnettii genes (otoGar1) (ENSEMBL) +bushBaby1.60.genome : Otolemur_garnettii +bushBaby1.61.genome : Otolemur_garnettii + +# Candida_albicans_SC5314 +cAlbicansv21.genome: Candida_albicans_SC5314 +cAlbicansv21.reference: http://www.candidagenome.org/download/gff/C_albicans_SC5314/ + +# C. Briggsae +c_briggsae_WS230.genome : Caenorhabditis_briggsae +c_briggsae_WS230.reference : ftp://ftp.wormbase.org/pub/wormbase/releases/WS230/species/c_briggsae/ + +# Cryptococcus neoformans +c_neoformans.genome: Cryptococcus_neoformans +c_neoformans.reference: http://www.broadinstitute.org/annotation/genome/cryptococcus_neoformans/MultiDownloads.html + +# Callithrix jacchus genes (calJac3) (ENSEMBL) +calJac3.2.1.60.genome : Callithrix_jacchus +calJac3.2.1.61.genome : Callithrix_jacchus + +# Canis familiaris genes (CanFam_2.0) (ENSEMBL) +canFam2.59.genome : Canis_familiaris +canFam2.60.genome : Canis_familiaris +canFam2.61.genome : Canis_familiaris + +# Felis catus genes (CAT) (ENSEMBL) +cat1.60.genome : Felis_catus +cat1.61.genome : Felis_catus + +# Cavia porcellus genes (cavPor3) (ENSEMBL) +cavPor3.60.genome : Cavia_porcellus +cavPor3.61.genome : Cavia_porcellus + +# Caenorhabditis elegans genes (WS210) (ENSEMBL) +ce.WS201.genome : Caenorhabditis_elegans +ce.WS210.60.genome : Caenorhabditis_elegans +ce.WS220.61.genome : Caenorhabditis_elegans + +# Pan troglodytes genes (CHIMP2.1) (ENSEMBL) +chimp2.1.59.genome : Pan_troglodytes +chimp2.1.60.genome : Pan_troglodytes +chimp2.1.61.genome : Pan_troglodytes + +# Choloepus hoffmanni genes (choHof1) (ENSEMBL) +choHof1.60.genome : Choloepus_hoffmanni +choHof1.61.genome : Choloepus_hoffmanni + +# Ciona intestinalis genes (JGI2) (ENSEMBL) +cInt2.60.genome : Ciona_intestinalis +cInt2.61.genome : Ciona_intestinalis + +# CP000730 +CP000730.genome : Staphylococcus_aureus +CP000730.reference : http://www.ncbi.nlm.nih.gov/nuccore/CP000730.1 + +# Capsella_rubella_v1.0 (Toronto University, Grandiflora) +crubella.genome : Capsella_rubella_v1.0 + +# Ciona savignyi genes (CSAV2.0) (ENSEMBL) +cSav2.0.60.genome : Ciona_savignyi +cSav2.0.61.genome : Ciona_savignyi + +# Danio rerio genes (Zv9) (ENSEMBL) +danRer8.59.genome : Danio_rerio +danRer9.60.genome : Danio_rerio +danRer9.61.genome : Danio_rerio + +# Dasypus novemcinctus genes (dasNov2) (ENSEMBL) +dasNov2.60.genome : Dasypus_novemcinctus +dasNov2.61.genome : Dasypus_novemcinctus + +# Dipodomys ordii genes (dipOrd1) (ENSEMBL) +dipOrd1.60.genome : Dipodomys_ordii +dipOrd1.61.genome : Dipodomys_ordii + +# Drosophila melanogaster (ENSEMBL) +dm5.25.59.genome : Drosophila_melanogaster +dm5.25.60.genome : Drosophila_melanogaster +dm5.25.61.genome : Drosophila_melanogaster +dm5.25.63.genome : Drosophila_melanogaster + +# Drosophila melanogaster (FlyBase) +dm5.12.genome : Drosophila_melanogaster +dm5.22.genome : Drosophila_melanogaster +dm5.30.genome : Drosophila_melanogaster +dm5.31.genome : Drosophila_melanogaster +dm5.32.genome : Drosophila_melanogaster +dm5.34.genome : Drosophila_melanogaster +dm5.40.genome : Drosophila_melanogaster +dm5.42.genome : Drosophila_melanogaster + +# Equus caballus genes (EquCab2) (ENSEMBL) +equCab2.60.genome : Equus_caballus +equCab2.61.genome : Equus_caballus + +# Erinaceus europaeus genes (eriEur1) (ENSEMBL) +eriEur1.60.genome : Erinaceus_europaeus +eriEur1.61.genome : Erinaceus_europaeus + +# Takifugu rubripes genes (FUGU4.0) (ENSEMBL) +fugu4.60.genome : Takifugu_rubripes +fugu4.61.genome : Takifugu_rubripes + +# Gasterosteus aculeatus genes (BROADS1) (ENSEMBL) +gacu1.60.genome : Gasterosteus_aculeatus +gacu1.61.genome : Gasterosteus_aculeatus + +# Gallus gallus genes (WASHUC2) (ENSEMBL) +ggallus2.59.genome : Gallus_gallus +ggallus2.60.genome : Gallus_gallus +ggallus2.61.genome : Gallus_gallus + +# Glycine max +gmax1.09.genome: Glycine_Max +gmax1.09.reference: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v7.0/Gmax/ + +gmax1.09v8.genome: Glycine_Max +gmax1.09v8.reference: ftp://ftp.jgi-psf.org/pub/JGI_data/phytozome/v8.0/Gmax/ + +# Gorilla gorilla genes (gorGor3) (ENSEMBL) +gorGor3.60.genome : Gorilla_gorilla +gorGor3.61.genome : Gorilla_gorilla + +# Human herpesvirus 1, complete genome. NCBI Reference Sequence: NC_001806.1 +herpesvirus1.genome: Herpesvirus + +# Homo sapiens genes (GRCh37.p2) (ENSEMBL) +hg36.54.genome : Homo_sapiens +hg37.59.genome : Homo_sapiens +hg37.60.genome : Homo_sapiens +hg37.61.genome : Homo_sapiens +hg37.63.genome : Homo_sapiens + +# Homo sapiens (hg19) (UCSC) +hg19.genome : Homo_sapiens +hg19.reference : http://hgdownload.cse.ucsc.edu \ # Gene information from 'table' download + , http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/chromFa.tar.gz \ # Genome sequence + , ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.protein.faa.gz \ # Protein + , ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/mRNA_Prot/human.rna.fna.gz \ # CDS + , http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/refLink.txt.gz # Reflink + + +# HIV_nc_001802_1 +hiv.genome : HIV + +# Grosmannia clavigera +kw1407.2012.genome: Grosmannia_clavigera + +# Leishmania genome +lmjf4.genome : LmajorFriedlin + +# Loxodonta africana genes (loxAfr3) (ENSEMBL) +loxAfr3.60.genome : Loxodonta_africana +loxAfr3.61.genome : Loxodonta_africana + +# Mycobacterium tuberculosis +m_tuberculosis.genome : Mycobacterium_tuberculosis +m_tuberculosis.reference : ftp://ftp.sanger.ac.uk/pub/pathogens/Mycobacterium/tuberculosis/ + +# Neurospora Crassa +ncrassa.genome : Neurospora_Crassa +ncrassa.reference : http://www.broadinstitute.org/annotation/genome/neurospora/MultiDownloads.html + +# Ecoli K12 MG1655 +NC_000913.genome : Escherichia_coli + +# Clostridium difficile +NC_009089.1.genome : Clostridium_difficile + +# Maize +maizeZmB73.genome : Maize_ZmB73 +maizeZmB73.reference : http://ftp.maizesequence.org/ + +# Oryzias latipes genes (HdrR) (ENSEMBL) +medaka1.60.genome : Oryzias_latipes +medaka1.61.genome : Oryzias_latipes + +# Macropus eugenii genes (Meug_1.0) (ENSEMBL) +meug1.0.60.genome : Macropus_eugenii +meug1.0.61.genome : Macropus_eugenii + +# Microcebus murinus genes (micMur1) (ENSEMBL) +micMur1.60.genome : Microcebus_murinus +micMur1.61.genome : Microcebus_murinus + +# Mus musculus genes (NCBIM37) (ENSEMBL) +mm37.genome : Mus_musculus +mm37.59.genome : Mus_musculus +mm37.60.genome : Mus_musculus +mm37.61.genome : Mus_musculus + +# Macaca mulatta genes (MMUL_1.0) (ENSEMBL) +mmul1.60.genome : Macaca_mulatta +mmul1.61.genome : Macaca_mulatta + +# Mycobacterium marinum M strain genome, version 31012012 +mmm.2012.genome : Mycobacterium_marinum_M + +# Monodelphis domestica genes (monDom5) (ENSEMBL) +monDom5.60.genome : Monodelphis_domestica +monDom5.61.genome : Monodelphis_domestica + +# Mycoplasma pneumoninae FH +myco_fh.genome : Mycoplasma_pneumoninae_FH + +# Mycoplasma pneumoninae M129 +myco_m129.genome : Mycoplasma_pneumoninae_M129 + +# Myotis lucifugus genes (myoLuc1) (ENSEMBL) +myoLuc1.60.genome : Myotis_lucifugus +myoLuc1.61.genome : Myotis_lucifugus + +# Ornithorhynchus anatinus genes (OANA5) (ENSEMBL) +oana5.60.genome : Ornithorhynchus_anatinus +oana5.61.genome : Ornithorhynchus_anatinus + +# Ochotona princeps genes (OchPri2.0) (ENSEMBL) +ochPri2.60.genome : Ochotona_princeps +ochPri2.61.genome : Ochotona_princeps + +# Oryctolagus cuniculus genes (oryCun2.0) (ENSEMBL) +oryCun2.60.genome : Oryctolagus_cuniculus +oryCun2.61.genome : Oryctolagus_cuniculus + +# Pseudomonas aeruginosa, N_008463 +paeru.PA01.genome : Pseudomonas_aeruginosa + paeru.PA01.chromosomes : NC_002516.2 + paeru.PA01.NC_002516.2.codonTable: Bacterial_and_Plant_Plastid + +# Pseudomonas aeruginosa, N_008463 +paeru.PA14.genome : Pseudomonas_aeruginosa + paeru.PA14.chromosomes : NC_008463.1 + paeru.PA14.NC_008463.1.codonTable: Bacterial_and_Plant_Plastid + +# Peromyscus leucopus (white footed deer mice) +peromyscus.genome : Peromyscus leucopus + +# Plasmodium falciparum +plasmo72.genome: Plasmodium_falciparum +plasmo72.reference: http://plasmodb.org/common/downloads/release-7.2/Pfalciparum/ + +# Peach (Prunus persica). +ppersica139.genome : Peach +ppersica139.reference : ftp://ftp.plantgdb.org/download/Genomes/PeGDB/ + +# Pseudomonas fluorescens +pfluo.SBW25.NC_009444.genome : Pseudomonas_fluorescens + pfluo.SBW25.NC_009444.chromosomes : NC_009444.1 + pfluo.SBW25.NC_009444.NC_009444.1.codonTable: Bacterial_and_Plant_Plastid + +# Pseudomonas fluorescens +pfluo.SBW25.NC_012660.genome : Pseudomonas_fluorescens + pfluo.SBW25.NC_012660.chromosomes : NC_012660.1 + pfluo.SBW25.NC_012660.NC_012660.1.codonTable: Bacterial_and_Plant_Plastid + +# Pongo pygmaeus abelii genes (PPYG2) (ENSEMBL) +ppyg2.60.genome : Pongo_pygmaeus +ppyg2.61.genome : Pongo_pygmaeus + +# Procavia capensis genes (proCap1) (ENSEMBL) +proCap1.60.genome : Procavia_capensis +proCap1.61.genome : Procavia_capensis + +# Pteropus vampyrus genes (pteVam1) (ENSEMBL) +pteVam1.60.genome : Pteropus_vampyrus +pteVam1.61.genome : Pteropus_vampyrus + +# Rattus norvegicus genes (RGSC3.4) (ENSEMBL) +rat3.4.59.genome : Rattus_norvegicus +rat3.4.60.genome : Rattus_norvegicus +rat3.4.61.genome : Rattus_norvegicus + +# Rice: http://rapdb.dna.affrc.go.jp/download/index.html +rice5.genome: Rice +rice5.reference: http://rapdb.dna.affrc.go.jp/download/index.html + +rice6.1.genome: Rice +rice6.1.reference: ftp://ftp.plantbiology.msu.edu,ftp://ftp.plantbiology.msu.edu/pub/data/Eukaryotic_Projects/o_sativa/annotation_dbs/ + +# Saccharomyces cerevisiae genes (SGD1.01) (ENSEMBL) +sacCer2.genome : Saccharomyces_cerevisiae +sacCer2.59.genome : Saccharomyces_cerevisiae +sacCer2.60.genome : Saccharomyces_cerevisiae +sacCer2.61.genome : Saccharomyces_cerevisiae + +# SCU49845 +SCU49845.genome : SCU49845 + +# HIV virus +SIVmac239.genome : HIV +SIVmac239.reference : http://www.ncbi.nlm.nih.gov/nuccore/334647 + +# Tomato +SL2.40.genome : Tomato +SL2.40.reference : ftp://ftp.solgenomics.net/,ftp://ftp.solgenomics.net/genomes/Solanum_lycopersicum/wgs/assembly/build_2.40/S_lycopersicum_chromosomes.2.40.fa.gz,http://solgenomics.net/itag/release/2.3/list_files(ITAG2.3_gene_models.gff3) + +# Sorex araneus genes (sorAra1) (ENSEMBL) +sorAra1.60.genome : Sorex_araneus +sorAra1.61.genome : Sorex_araneus + +# Spermophilus tridecemlineatus genes (speTri1) (ENSEMBL) +speTri1.60.genome : Spermophilus_tridecemlineatus +speTri1.61.genome : Spermophilus_tridecemlineatus + +# Schizosaccharomyces pombe (fission yeast). +spombe.genome : Schizosaccharomyces_pombe +spombe.reference : ftp://ftp.sanger.ac.uk/pub/yeast/pombe/GFF + +# Sus scrofa genes (Sscrofa9) (ENSEMBL) +sScrofa9.60.genome : Sus_scrofa +sScrofa9.61.genome : Sus_scrofa + +# Taeniopygia guttata genes (taeGut3.2.4) (ENSEMBL) +taeGut3.2.4.60.genome : Taeniopygia_guttata +taeGut3.2.4.61.genome : Taeniopygia_guttata + +# Tarsius syrichta genes (tarSyr1) (ENSEMBL) +tarSyr1.60.genome : Tarsius_syrichta +tarSyr1.61.genome : Tarsius_syrichta + +# Echinops telfairi genes (TENREC) (ENSEMBL) +tenrec1.60.genome : Echinops_telfairi +tenrec1.61.genome : Echinops_telfairi + +# Used for debugging +test.genome : TestCase +testHg3761Chr15.genome : TestCase +testHg3761Chr16.genome : TestCase +testHg3763Chr1.genome : TestCase +testHg3763Chr20.genome : TestCase +testHg3763ChrY.genome : TestCase +testHg3765Chr22.genome : TestCase +testCase.genome : TestCase + testCaseHg.chromosomes: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y +test_ENSG00000158062.genome : TestCase + +# Tetraodon nigroviridis genes (TETRAODON8.0) (ENSEMBL) +tetraodon8.60.genome : Tetraodon_nigroviridis +tetraodon8.61.genome : Tetraodon_nigroviridis + +# Tupaia belangeri genes (tupBel1) (ENSEMBL) +tupBel1.60.genome : Tupaia_belangeri +tupBel1.61.genome : Tupaia_belangeri + +# Meleagris_gallopavo (Turkey) +turkey.UMD2.61.genome : Meleagris_gallopavo + +# Tursiops truncatus genes (turTru1) (ENSEMBL) +turTru1.60.genome : Tursiops_truncatus +turTru1.61.genome : Tursiops_truncatus + +# Bos taurus : University of Maryland version 3.1 +UMD3_1.genome : Bos_taurus + +# Vaccinia WR (NCBIM37) (ENSEMBL) gi|29692106|gb|AY243312.1| +vacwr.genome : Vaccinia_Western_Reserve + +# Vibrio Cholerae +vibrio.genome : Vibrio Cholerae + vibrio.chromosomes : NC_002505.1, NC_002506.1 + vibrio.NC_002505.1.codonTable : Bacterial_and_Plant_Plastid + vibrio.NC_002506.1.codonTable : Bacterial_and_Plant_Plastid + +# Vicugna pacos genes (vicPac1) (ENSEMBL) +vicPac1.60.genome : Vicugna_pacos +vicPac1.61.genome : Vicugna_pacos + +# Xenopus tropicalis genes +xtrop4.1.60.genome : Xenopus_tropicalis +xtrop4.1.61.genome : Xenopus_tropicalis + +# Xenopus tropicalis +xtrop7.1.genome : Xenopus_tropicalis +xtrop7.1.reference : ftp://ftp.xenbase.org/pub/Genomics/JGI/Xentr7.1/ + +#--- +# Ensembl 63 versions +#--- + +ailMel1.63.genome : Ailuropoda_melanoleuca +ailMel1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +AnoCar2.0.63.genome : Anolis_carolinensis +AnoCar2.0.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +Btau_4.0.63.genome : Bos_taurus +Btau_4.0.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +WS220.63.genome : Caenorhabditis_elegans +WS220.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +C_jacchus3.2.1.63.genome : Callithrix_jacchus +C_jacchus3.2.1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +BROADD2.63.genome : Canis_familiaris +BROADD2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +cavPor3.63.genome : Cavia_porcellus +cavPor3.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +choHof1.63.genome : Choloepus_hoffmanni +choHof1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +JGI2.63.genome : Ciona_intestinalis +JGI2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +CSAV2.0.63.genome : Ciona_savignyi +CSAV2.0.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +Zv9.63.genome : Danio_rerio +Zv9.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +dasNov2.63.genome : Dasypus_novemcinctus +dasNov2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +dipOrd1.63.genome : Dipodomys_ordii +dipOrd1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +BDGP5.25.63.genome : Drosophila_melanogaster +BDGP5.25.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +TENREC.63.genome : Echinops_telfairi +TENREC.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +EquCab2.63.genome : Equus_caballus +EquCab2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +HEDGEHOG.63.genome : Erinaceus_europaeus +HEDGEHOG.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +CAT.63.genome : Felis_catus +CAT.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +WASHUC2.63.genome : Gallus_gallus +WASHUC2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +BROADS1.63.genome : Gasterosteus_aculeatus +BROADS1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +gorGor3.63.genome : Gorilla_gorilla +gorGor3.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +GRCh37.63.genome : Homo_sapiens +GRCh37.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +loxAfr3.63.genome : Loxodonta_africana +loxAfr3.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +MMUL_1.63.genome : Macaca_mulatta +MMUL_1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +Meug_1.0.63.genome : Macropus_eugenii +Meug_1.0.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +UMD2.63.genome : Meleagris_gallopavo +UMD2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +micMur1.63.genome : Microcebus_murinus +micMur1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +BROADO5.63.genome : Monodelphis_domestica +BROADO5.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +NCBIM37.63.genome : Mus_musculus +NCBIM37.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +Myoluc2.0.63.genome : Myotis_lucifugus +Myoluc2.0.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +Nleu1.0.63.genome : Nomascus_leucogenys +Nleu1.0.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +pika.63.genome : Ochotona_princeps +pika.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +OANA5.63.genome : Ornithorhynchus_anatinus +OANA5.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +oryCun2.63.genome : Oryctolagus_cuniculus +oryCun2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +MEDAKA1.63.genome : Oryzias_latipes +MEDAKA1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +BUSHBABY1.63.genome : Otolemur_garnettii +BUSHBABY1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +CHIMP2.1.63.genome : Pan_troglodytes +CHIMP2.1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +PPYG2.63.genome : Pongo_abelii +PPYG2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +proCap1.63.genome : Procavia_capensis +proCap1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +pteVam1.63.genome : Pteropus_vampyrus +pteVam1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +RGSC3.4.63.genome : Rattus_norvegicus +RGSC3.4.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +EF3.63.genome : Saccharomyces_cerevisiae +EF3.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +COMMON_SHREW1.63.genome : Sorex_araneus +COMMON_SHREW1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +SQUIRREL.63.genome : Spermophilus_tridecemlineatus +SQUIRREL.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +Sscrofa9.63.genome : Sus_scrofa +Sscrofa9.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +taeGut3.2.4.63.genome : Taeniopygia_guttata +taeGut3.2.4.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +FUGU4.63.genome : Takifugu_rubripes +FUGU4.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +tarSyr1.63.genome : Tarsius_syrichta +tarSyr1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +TETRAODON8.63.genome : Tetraodon_nigroviridis +TETRAODON8.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +TREESHREW.63.genome : Tupaia_belangeri +TREESHREW.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +turTru1.63.genome : Tursiops_truncatus +turTru1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +vicPac1.63.genome : Vicugna_pacos +vicPac1.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +JGI_4.2.63.genome : Xenopus_tropicalis +JGI_4.2.63.reference : ftp://ftp.ensembl.org/pub/release-63/ + +#--- +# Ensembl 64 versions +#--- + +ailMel1.64.genome : Ailuropoda_melanoleuca +ailMel1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +AnoCar2.0.64.genome : Anolis_carolinensis +AnoCar2.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +UMD3.1.64.genome : Bos_taurus +UMD3.1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +WS220.64.genome : Caenorhabditis_elegans +WS220.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +C_jacchus3.2.1.64.genome : Callithrix_jacchus +C_jacchus3.2.1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +BROADD2.64.genome : Canis_familiaris +BROADD2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +cavPor3.64.genome : Cavia_porcellus +cavPor3.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +choHof1.64.genome : Choloepus_hoffmanni +choHof1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +JGI2.64.genome : Ciona_intestinalis +JGI2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +CSAV2.0.64.genome : Ciona_savignyi +CSAV2.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +Zv9.64.genome : Danio_rerio +Zv9.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +dasNov2.64.genome : Dasypus_novemcinctus +dasNov2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +dipOrd1.64.genome : Dipodomys_ordii +dipOrd1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +BDGP5.25.64.genome : Drosophila_melanogaster +BDGP5.25.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +TENREC.64.genome : Echinops_telfairi +TENREC.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +EquCab2.64.genome : Equus_caballus +EquCab2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +HEDGEHOG.64.genome : Erinaceus_europaeus +HEDGEHOG.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +CAT.64.genome : Felis_catus +CAT.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +WASHUC2.64.genome : Gallus_gallus +WASHUC2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +BROADS1.64.genome : Gasterosteus_aculeatus +BROADS1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +gorGor3.1.64.genome : Gorilla_gorilla +gorGor3.1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +GRCh37.64.genome : Homo_sapiens +GRCh37.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +loxAfr3.64.genome : Loxodonta_africana +loxAfr3.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +MMUL_1.64.genome : Macaca_mulatta +MMUL_1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +Meug_1.0.64.genome : Macropus_eugenii +Meug_1.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +UMD2.64.genome : Meleagris_gallopavo +UMD2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +micMur1.64.genome : Microcebus_murinus +micMur1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +BROADO5.64.genome : Monodelphis_domestica +BROADO5.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +NCBIM37.64.genome : Mus_musculus +NCBIM37.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +Myoluc2.0.64.genome : Myotis_lucifugus +Myoluc2.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +Nleu1.0.64.genome : Nomascus_leucogenys +Nleu1.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +pika.64.genome : Ochotona_princeps +pika.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +OANA5.64.genome : Ornithorhynchus_anatinus +OANA5.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +oryCun2.64.genome : Oryctolagus_cuniculus +oryCun2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +MEDAKA1.64.genome : Oryzias_latipes +MEDAKA1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +BUSHBABY1.64.genome : Otolemur_garnettii +BUSHBABY1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +CHIMP2.1.64.genome : Pan_troglodytes +CHIMP2.1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +Petromyzon_marinus_7.0.64.genome : Petromyzon_marinus +Petromyzon_marinus_7.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +PPYG2.64.genome : Pongo_abelii +PPYG2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +proCap1.64.genome : Procavia_capensis +proCap1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +pteVam1.64.genome : Pteropus_vampyrus +pteVam1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +RGSC3.4.64.genome : Rattus_norvegicus +RGSC3.4.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +EF3.64.genome : Saccharomyces_cerevisiae +EF3.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +DEVIL7.0.64.genome : Sarcophilus_harrisii +DEVIL7.0.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +COMMON_SHREW1.64.genome : Sorex_araneus +COMMON_SHREW1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +SQUIRREL.64.genome : Spermophilus_tridecemlineatus +SQUIRREL.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +Sscrofa9.64.genome : Sus_scrofa +Sscrofa9.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +taeGut3.2.4.64.genome : Taeniopygia_guttata +taeGut3.2.4.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +FUGU4.64.genome : Takifugu_rubripes +FUGU4.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +tarSyr1.64.genome : Tarsius_syrichta +tarSyr1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +TETRAODON8.64.genome : Tetraodon_nigroviridis +TETRAODON8.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +TREESHREW.64.genome : Tupaia_belangeri +TREESHREW.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +turTru1.64.genome : Tursiops_truncatus +turTru1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +vicPac1.64.genome : Vicugna_pacos +vicPac1.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +JGI_4.2.64.genome : Xenopus_tropicalis +JGI_4.2.64.reference : ftp://ftp.ensembl.org/pub/release-64/ + +#--- +# Ensembl 65 versions +#--- + +ailMel1.65.genome : Ailuropoda_melanoleuca +ailMel1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +AnoCar2.0.65.genome : Anolis_carolinensis +AnoCar2.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +UMD3.1.65.genome : Bos_taurus +UMD3.1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +WS220.65.genome : Caenorhabditis_elegans +WS220.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +C_jacchus3.2.1.65.genome : Callithrix_jacchus +C_jacchus3.2.1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +BROADD2.65.genome : Canis_familiaris +BROADD2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +cavPor3.65.genome : Cavia_porcellus +cavPor3.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +choHof1.65.genome : Choloepus_hoffmanni +choHof1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +JGI2.65.genome : Ciona_intestinalis +JGI2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +CSAV2.0.65.genome : Ciona_savignyi +CSAV2.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +Zv9.65.genome : Danio_rerio +Zv9.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +dasNov2.65.genome : Dasypus_novemcinctus +dasNov2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +dipOrd1.65.genome : Dipodomys_ordii +dipOrd1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +BDGP5.25.65.genome : Drosophila_melanogaster +BDGP5.25.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +TENREC.65.genome : Echinops_telfairi +TENREC.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +EquCab2.65.genome : Equus_caballus +EquCab2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +HEDGEHOG.65.genome : Erinaceus_europaeus +HEDGEHOG.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +CAT.65.genome : Felis_catus +CAT.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +WASHUC2.65.genome : Gallus_gallus +WASHUC2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +BROADS1.65.genome : Gasterosteus_aculeatus +BROADS1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +gorGor3.1.65.genome : Gorilla_gorilla +gorGor3.1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +GRCh37.65.genome : Homo_sapiens +GRCh37.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +loxAfr3.65.genome : Loxodonta_africana +loxAfr3.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +MMUL_1.65.genome : Macaca_mulatta +MMUL_1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +Meug_1.0.65.genome : Macropus_eugenii +Meug_1.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +UMD2.65.genome : Meleagris_gallopavo +UMD2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +micMur1.65.genome : Microcebus_murinus +micMur1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +BROADO5.65.genome : Monodelphis_domestica +BROADO5.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +NCBIM37.65.genome : Mus_musculus +NCBIM37.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +Myoluc2.0.65.genome : Myotis_lucifugus +Myoluc2.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +Nleu1.0.65.genome : Nomascus_leucogenys +Nleu1.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +pika.65.genome : Ochotona_princeps +pika.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +OANA5.65.genome : Ornithorhynchus_anatinus +OANA5.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +oryCun2.65.genome : Oryctolagus_cuniculus +oryCun2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +MEDAKA1.65.genome : Oryzias_latipes +MEDAKA1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +BUSHBABY1.65.genome : Otolemur_garnettii +BUSHBABY1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +CHIMP2.1.65.genome : Pan_troglodytes +CHIMP2.1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +Petromyzon_marinus_7.0.65.genome : Petromyzon_marinus +Petromyzon_marinus_7.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +PPYG2.65.genome : Pongo_abelii +PPYG2.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +proCap1.65.genome : Procavia_capensis +proCap1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +pteVam1.65.genome : Pteropus_vampyrus +pteVam1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +RGSC3.4.65.genome : Rattus_norvegicus +RGSC3.4.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +EF4.65.genome : Saccharomyces_cerevisiae +EF4.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +DEVIL7.0.65.genome : Sarcophilus_harrisii +DEVIL7.0.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +COMMON_SHREW1.65.genome : Sorex_araneus +COMMON_SHREW1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +SQUIRREL.65.genome : Spermophilus_tridecemlineatus +SQUIRREL.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +Sscrofa9.65.genome : Sus_scrofa +Sscrofa9.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +taeGut3.2.4.65.genome : Taeniopygia_guttata +taeGut3.2.4.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +FUGU4.65.genome : Takifugu_rubripes +FUGU4.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +tarSyr1.65.genome : Tarsius_syrichta +tarSyr1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +TETRAODON8.65.genome : Tetraodon_nigroviridis +TETRAODON8.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +TREESHREW.65.genome : Tupaia_belangeri +TREESHREW.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +turTru1.65.genome : Tursiops_truncatus +turTru1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +vicPac1.65.genome : Vicugna_pacos +vicPac1.65.reference : ftp://ftp.ensembl.org/pub/release-65/ + +#--- +# Ensembl 66 versions +#--- + +ailMel1.66.genome : Ailuropoda_melanoleuca +ailMel1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +AnoCar2.0.66.genome : Anolis_carolinensis +AnoCar2.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +UMD3.1.66.genome : Bos_taurus +UMD3.1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +WS220.66.genome : Caenorhabditis_elegans +WS220.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +C_jacchus3.2.1.66.genome : Callithrix_jacchus +C_jacchus3.2.1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +BROADD2.66.genome : Canis_familiaris +BROADD2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +cavPor3.66.genome : Cavia_porcellus +cavPor3.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +choHof1.66.genome : Choloepus_hoffmanni +choHof1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +KH.66.genome : Ciona_intestinalis +KH.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +CSAV2.0.66.genome : Ciona_savignyi +CSAV2.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +Zv9.66.genome : Danio_rerio +Zv9.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +dasNov2.66.genome : Dasypus_novemcinctus +dasNov2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +dipOrd1.66.genome : Dipodomys_ordii +dipOrd1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +BDGP5.66.genome : Drosophila_melanogaster +BDGP5.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +TENREC.66.genome : Echinops_telfairi +TENREC.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +EquCab2.66.genome : Equus_caballus +EquCab2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +HEDGEHOG.66.genome : Erinaceus_europaeus +HEDGEHOG.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +CAT.66.genome : Felis_catus +CAT.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +gadMor1.66.genome : Gadus_morhua +gadMor1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +WASHUC2.66.genome : Gallus_gallus +WASHUC2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +BROADS1.66.genome : Gasterosteus_aculeatus +BROADS1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +gorGor3.1.66.genome : Gorilla_gorilla +gorGor3.1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +GRCh37.66.genome : Homo_sapiens +GRCh37.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +LatCha1.66.genome : Latimeria_chalumnae +LatCha1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +loxAfr3.66.genome : Loxodonta_africana +loxAfr3.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +MMUL_1.66.genome : Macaca_mulatta +MMUL_1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +Meug_1.0.66.genome : Macropus_eugenii +Meug_1.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +UMD2.66.genome : Meleagris_gallopavo +UMD2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +micMur1.66.genome : Microcebus_murinus +micMur1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +BROADO5.66.genome : Monodelphis_domestica +BROADO5.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +NCBIM37.66.genome : Mus_musculus +NCBIM37.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +Myoluc2.0.66.genome : Myotis_lucifugus +Myoluc2.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +Nleu1.0.66.genome : Nomascus_leucogenys +Nleu1.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +pika.66.genome : Ochotona_princeps +pika.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +OANA5.66.genome : Ornithorhynchus_anatinus +OANA5.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +oryCun2.66.genome : Oryctolagus_cuniculus +oryCun2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +MEDAKA1.66.genome : Oryzias_latipes +MEDAKA1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +OtoGar3.66.genome : Otolemur_garnettii +OtoGar3.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +CHIMP2.1.4.66.genome : Pan_troglodytes +CHIMP2.1.4.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +Pmarinus_7.0.66.genome : Petromyzon_marinus +Pmarinus_7.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +PPYG2.66.genome : Pongo_abelii +PPYG2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +proCap1.66.genome : Procavia_capensis +proCap1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +pteVam1.66.genome : Pteropus_vampyrus +pteVam1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +RGSC3.4.66.genome : Rattus_norvegicus +RGSC3.4.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +EF4.66.genome : Saccharomyces_cerevisiae +EF4.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +DEVIL7.0.66.genome : Sarcophilus_harrisii +DEVIL7.0.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +COMMON_SHREW1.66.genome : Sorex_araneus +COMMON_SHREW1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +SQUIRREL.66.genome : Spermophilus_tridecemlineatus +SQUIRREL.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +Sscrofa9.66.genome : Sus_scrofa +Sscrofa9.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +taeGut3.2.4.66.genome : Taeniopygia_guttata +taeGut3.2.4.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +FUGU4.66.genome : Takifugu_rubripes +FUGU4.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +tarSyr1.66.genome : Tarsius_syrichta +tarSyr1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +TETRAODON8.66.genome : Tetraodon_nigroviridis +TETRAODON8.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +TREESHREW.66.genome : Tupaia_belangeri +TREESHREW.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +turTru1.66.genome : Tursiops_truncatus +turTru1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +vicPac1.66.genome : Vicugna_pacos +vicPac1.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +JGI_4.2.66.genome : Xenopus_tropicalis +JGI_4.2.66.reference : ftp://ftp.ensembl.org/pub/release-66/gtf/ + +#------------------------------------------------------------------------------- +# Codon tables +# +# Format: It's a comma separated "codon/aminoAcid[+*]" list +# Where 'codon' is in uppper case, aminoAcid is a one letter coce, '+' denotes start codon and '*' denotes stop codon +# +# References: http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi +# ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt +#------------------------------------------------------------------------------- + +codon.Standard: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Vertebrate_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Yeast_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Mold_Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Protozoan_Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Coelenterate: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Mitochondrial: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Mycoplasma: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Spiroplasma: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Invertebrate_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Ciliate_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Dasycladacean_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Hexamita_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Echinoderm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Euplotid_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Bacterial_and_Plant_Plastid: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Alternative_Yeast_Nuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Ascidian_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Alternative_Flatworm_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Blepharisma_Macronuclear: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Chlorophycean_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Trematode_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Scenedesmus_obliquus_Mitochondrial: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +codon.Thraustochytrium_Mitochondrial: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G +