Mercurial > repos > dcorreia > phylogeny_tools
changeset 8:035fdf55035d draft
Uploaded
| author | dcorreia |
|---|---|
| date | Fri, 22 Apr 2016 08:22:55 -0400 |
| parents | 044a03b4a79d |
| children | 298be0f4b9a7 |
| files | Oneclick_FastME_workflow.ga fasta2phylip/fasta_to_phylip.py fasta2phylip/fasta_to_phylip.xml fasta2phylip/test.fasta fasta2phylip/test.phy fasta2phylip/tool_dependencies.xml repository_dependencies.xml seqtypedetect/seqtypedetect.py seqtypedetect/seqtypedetect.xml workflows/Oneclick_FastME_workflow.ga |
| diffstat | 10 files changed, 973 insertions(+), 351 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta2phylip/fasta_to_phylip.py Fri Apr 22 08:22:55 2016 -0400 @@ -0,0 +1,159 @@ +# -*- coding: utf-8 -*- +#!/usr/bin/env python +"""fasta_to_phylip.py: Convert Fasta to Phylip Relaxed format, use biopython if it's possible.""" + +__version__ = '1' + +from optparse import OptionParser + +BIOPYTHON_INSTALLED = True + +try: + from Bio import AlignIO +except ImportError: + BIOPYTHON_INSTALLED = False + + +def fasta_to_phylipE(fasta_input, phylip_output, sequential=False): + """Convert fasta file to phylip relaxed format with biopython library + """ + input_handle = open(fasta_input, "rU") + output_handle = open(phylip_output, "w") + + alignments = AlignIO.parse(input_handle, "fasta") + + if sequential: + AlignIO.write(alignments, output_handle, "phylip-sequential") + else: + AlignIO.write(alignments, output_handle, "phylip-relaxed") + + output_handle.close() + input_handle.close() + + +class Sequence(object): + """ + Sequence + """ + + def __init__(self, name, seq): + self.name = name + self.seq = seq + + +def fasta_parse(path): + """ + Reads the file and yields Sequence objects + """ + + name = '' + seq = '' + with open(path) as fasta: + for line in fasta: + if line.startswith('>'): + if seq: + yield Sequence(name, seq) + name = line.rstrip('\n').lstrip('>') + seq = "" + else: + seq += line.rstrip('\n') + + yield Sequence(name, seq) + + +class Alignment(object): + """ Take a list of Sequence objects build Alignment object + """ + + def __init__(self, sequences): + self.seqs_length = 0 + self.max_name_length = 64 #relaxed + self.name_length = 0 + self.sequences = [] + for obj in sequences: + self.add_sequence(obj) + + + + def __len__(self): + return len(self.sequences) + + def add_sequence(self, Sequence): + + self.sequences.append(Sequence) + self.name_length = min(max(self.name_length, len(Sequence.name)+1), self.max_name_length ) + + if self.seqs_length == 0: + self.seqs_length = len(Sequence.seq) + + elif self.seqs_length != len(Sequence.seq): + print self.seqs_length , len(Sequence.seq) + raise ValueError('Sequences must all be the same length') + + + def write_phylip_relaxed_sequencial(self, path): + """ write Phylip-relaxed format into path file""" + + with open(path, "w") as f: + f.write("%s %s\n" % (len(self), self.seqs_length)) + + for seq in self.sequences: + + seq_name = seq.name[:self.name_length].replace(' ', '_') + seq_name = seq_name.ljust(self.name_length) + + f.write(seq_name) + f.write("%s" % seq.seq) + f.write("\n") + + def write_phylip_relaxed_interleave(self, path): + + wrap_length = 80 + nb_chunk = 0 + + with open(path, "w") as f: + f.write("%s %s\n" % (len(self), self.seqs_length)) + + while (nb_chunk*wrap_length) < self.seqs_length : + for seq in self.sequences: + + if nb_chunk == 0: + chunk_seq = seq.seq[0: (wrap_length - self.name_length)] + + seq_name = seq.name[:self.name_length].replace(' ', '_') + seq_name = seq_name.ljust(self.name_length) + + f.write(seq_name) + f.write("%s" % chunk_seq) + f.write("\n") + + else: + chunk_seq = seq.seq[((wrap_length * nb_chunk) - self.name_length) : ((wrap_length * (nb_chunk + 1)) - self.name_length)] + f.write("%s" % chunk_seq) + f.write("\n") + + f.write("\n") + nb_chunk += 1 + + +if __name__ == "__main__": + + # define option + parser = OptionParser() + parser.add_option("-i", "--input") + parser.add_option("-o", "--output") + parser.add_option("--sequencial", action='store_true') + # parse + options, args = parser.parse_args() + + if BIOPYTHON_INSTALLED: + fasta_to_phylipE(options.input, options.output, options.sequencial) + + else: + algn = Alignment(fasta_parse(options.input)) + + if options.sequencial: + algn.write_phylip_relaxed_sequencial(options.output) + else: + algn.write_phylip_relaxed_interleave(options.output) +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta2phylip/fasta_to_phylip.xml Fri Apr 22 08:22:55 2016 -0400 @@ -0,0 +1,25 @@ +<tool id="fasta_to_phylip" name="Fasta to Phylip" > + <description>file conversion</description> + <requirements> + <requirement type="package" version="1.66">biopython</requirement> + </requirements> + <command interpreter="python"> + fasta_to_phylip.py -i $input -o $output + </command> + <inputs> + <param name="input" format="fasta" type="data" label="Source file" help="fasta or phylip format"/> + <param name="format" type="select" label="format" help="Sequencial: sequences are one one line"> + <option value="">Interleave</option> + <option value="--sequencial">Sequencial</option> + </param> + </inputs> + <outputs> + <data name="output" format="phylip" label="${input.name}"></data> + </outputs> + <help> +=========== +Overview: +=========== +Convert fasta file to phylip Extended format, using Biopython library if possible + </help> +</tool> \ No newline at end of file
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+YLDPLILKHDVSKILQDTMKRPFLCLNKEFHERMDWRSIIICLVLSPTMFVETRALLHNW +FLITGLASVLQLLIEVVSMILDVVSRPTGWGISVEMGSKLPFSIAYFPYNHH-VYRILSG +TLSSESFLHLVSIINVPIS-RAGNHSMPTIKQVPMKISTIGHK---------SVWAAAMN +FPDWFFFASVLLFSEKS-FQDNFYSKCGIGVPRTEKRHDVEPLCFSSAAARYIAWILSPA +DKSHQDLLVDWLTKLSESWTLKQFGS---------DTYNKEIADYRKKLKKTKFPVYKGD +YNLPKEYNYVTIVLWLKEFQNSYTKNQYKTASSLAFCEHNLSYSLRFQHSVLFRRIPLGI +LIGCPYYLDESGCEMLLHYSATGTIPLLRETHSGALKHLKLDSEGQKDSIMWTEEY-TKE +EAAAGASLVFRLTDVVLSMAASLFETDESGLEFICQVKVKAGRYLIKCIKKLLQFND--- +-------GIMLMDLFNRLVQWRNQGQEVFQGCTDLDDVINGLGLKLSSL----------- +- +>BRADI +---MAPPLDGLTKLLAEVASRLSRPPGVIGAGPSS-SSSSSGDSLSASISSLAAALNPRP +AA----AATGTRVLDAALSLMCFDPLEAIPIPFGSRVDRARVECLVRTITSALSASVSCR +VVRTD-DCGGEMLCVGSSVSPGDCRELVSLCASLVEKLGDRDDAMRGNAVTIKQTYGTPE +IHDTQDVLGVCLF---PLPYYRENGEKKYEMATVAVDLTRHPSYQVIPSDGSIPLRVLLW +HLDPSILKHDLSAMLHEAITRPFLC----------------------------------- +L-------------------RKELHDRIAWRVIIICLVCFPPAFLEMTSLFH-------- +-------------------------------------------------SWFLATSTITN +FPIWFSFAAALLFHREG-FQGYL-SEILSEEKVSESISDISL---ARRAAFYLSWVLCPS +NEDECQMLANNMVELSNSWARNIKSRPSY-------AYHTSTVNHRRRLRIPTVGDTEKL +HMSTNPVSSL-----IQEFDNRCVNFCNQTAVSQVQD-ELSGFP-PSCISFLHLQIPLGV +LLVSSSCVKDHDHDVLLHYASSGLILEADKVQTKTKDHVGNHGFS-----AS-RRGFTER +WALSGACVIFSWFDVIDDMSAVIFECEDTCQHFVSELRTKTSPYLINCVNL---VL---- +-NEAGQDKDSVIDLHDRLLDWNNKLK-SFDGCEAFKDVILQLKKKVLLPS---------- +- +>CARPA +----MTTLPEIADLFSRLASNLQTLKPKSIVDEGK-----EEVSLNLSISKLNQSLNLC- +------KDSSVRVLDTLLSLMCFKAPQ---------VFGSTIDYLVKTIVTVLHSSVSCE +VLMFE---NEETLQIGSSILPRDCLKLIEMCNAVIQKLEGHEVLA--SSLLHAVV----R +-VAVSTSFCQFSFQFPPTLEEK----EVDERSVAFSKLHCHLPRECSLQNHEIPLRLLFW +YLDPASLQHDISKILQDAVTMPFLCLSNEFHKRMDWRNLVICLALSPVMFIETRALLHNW +FLMTGFAFILEFLVALISVILDLLSRPTWWGIPMDLGFKLPLSDAYFPCQSH-LLRTLAG +PLFSEKFVHLVHVIGSPIS-GARKQSASSFKRTGIKLATINQN---------SLWALAVN +FPDWFYFASILLFSGKS-FQDHFQPKCMIGAPKNRGPHDSVLL--SQAAARYIAWVMSPL +NKSNQDLLVGCLIKISEAWTRQQFGP---------GVHDKKALGCDKL-KKHKF-HGSKD +YNLTKVGNSKMIDLWLREFQSTYLDFAKEAFYGSASRETNASCGHSLHEDLLVRGIPLGV +LVGCPNSITDDGCELLLHYAATGRIGLMESKFSG-SKHAEQISEFKEGSNTQAGMCNTKR +EAIAGACLAFRLTDIVQSMSASFFENQEIGQEYIYQVKLKASKYLIKCIKRLIQLGVD-- +----EDGPMLLMGLHDRLLQWRHQGKEVIEVNKDLDDITSDLSHKLSLL----------- +- +>RICCO +----MATLEEITDLFSKLAFHLQTLSHASSP------KD-SNSFIDLSISKLNQSLNII- +------DNTQTRVLDTALSLMCFRAPQ---------VFDSTIEYLVKTIVSVLSSSIRCN +VLRLE---KEEVLQIGSAISKKSFLEFIQVVNDVVSKLEENGMPC--HLLLCAFA----R +-VAVSASCYRYLVPTMHVLDTK----SINGKSSALSKLLCSLPKD-SLNNHEIPPRLLSW +YLDPLALKHNISNILQVTMERPFLLSSKEFYDRMEWRSILMCLVLSPTMFIHTKALLHNW +FMLTGLGSILELLIELVALILDVISRPTWWGMSMELGSKLPYANAYFPYKNH-LLRILVG +PLSSISFLQLVYRTTESVS-HIMEQFGRTCKASVLKIASTESK---------SIWALAIC +FPDWFYFASVLLFSTNC-FQKSHQSKRIFGVPKSGKTNNKEQSPPAAAAARYIAWILSPN +NQSQQDWLFGGLTKISEFWTLRQIDL---------GTSGRDIASCRKKLKNSKCYNIEED +FSLGTEDNCQTIGLWLKEFQSIM-KHGNESVNNLYSCEAN-SYVFAFENHMFFRRIPLGI +LIGFPSYVNEDGFELLLHYAATGRMLPL-TTKNDRKDHLEKKSMGLEDLGL--G-SNSKK +EAVAGACLVFSLSDTVERISASLFENEKSGLDAISQVKLRAGRYLIKCLKSLIQLNIA-- +----EDGHATQMDLHDRLERWRHQGQEMLNIDKDLDDAIKALSNELLPS----------- +- +>POPTR +MRTTSPTSPEIMELFSKLAFELQTLTHNSPINQEQQQQEFNDSSIDPSISKLT--LSLT- +------HNPGVRVLDTALSLMCFKAPQ---------VLDSVVEYSVKTIVSVLSSSICCE +VFRFH---NEEVLQIGSFISRGHCMELIECVFDVISKLKEHGMPI--DLLLSAVV----R +-VAASASCYKYLSPSMRVLDVK----SIDGSITAISKLLCHLPMDFSLSNHEIPTRLLIW +YLDPLALKHDISKILQETIKRPFLCLSMEFYERMDWRSILVCLVLSPIMFIDTRALLHDW +FLQTGLSSVVELLMELVSLILDVISRPTWWGLSLELGLKLPFSNAYFPYKSD-FLRTLTG +PFSYESFLQLVHMTRKSAY-LHRELCDPTIKPSAVRVASIDHK---------SIWALAIS +FPDWFYFASVLLFSDDKNSQQNIQVKCPLGVPEFGQ------LPASAAAATFIAWILSPV +NKSNQDALFENLTKLSKCWNLKEISS---------DNSQNGMAGYKKKLKKPRFCDSKED +STLGNKYDCQVIILWLKQFQNIM-KHN-ETIDELAFCEAK-SYALLPQHDKLFRRIPLGI +LTGSSGYINENGCELLLHYAATGRILDSLGTENTSLKHINYNSSGPEDL-F--G-GINKE +EAVLGACLVFSLTDVVDRMSVSLFETEKTGEDFLCLVKLRAGRYLLKCIKRLTHFNVD-- +----EDGVPMLLDLQGRLERWRHQGKEVPEFHKDLDDALKGLSTESS------------- +- +>MUSAC +---MATSPAEIARLFAELASRIQSPQDDTDGGDGV-G---PGGELASAISSLAASLSFG- +------DAPRVGVLNAALSLMCFRASE---------VHRARVECLVGTIVAMLSSSVSCR +VLRLPDKRDEGFLRIGTSFSSEDCVQLIRVCVDVLASLKGHCGDL--HALLYAVV----K +-AVISSSTYQGLLPSLPIGYLRN-EDTDCGVQTEISKLAYSLSDQTSCTGHEFPLRLQFW +YLDPLILKHDISEILKEVIRRPFLCLRKELHDRMSWRNIITCLVTSPTFFKETKATLHTW +FLFTGLTSVLDLKIGIVLSVLDILSRPMWWGVPVELGLRFPSSYAYFSIRHHDLLTILTG +QLSCKNLLHLVQYIKTEVA-ILSNIC-QSASHPSVTNY--NHEGLA----------NVID +FPAWFYFANALIFYRNS-SQDYL-SEALCGRLRTEPVNDLEL---HRAALYYISWVLCPI +GEAHRDMLAENIDELSRSFVTQHKAKSIYEERSFSDMHPKNVLSRSKKLKIPKANSFEKH +RMAPQEVSSLNIGVWLENFNAIHIEVCNENTASNVQSAVTSEQDANMKPNLLLARVPLGI +LLVSPSYLDELGCEILLHYAATGETMLAKEI-RKLKDHYGYSDLG-----VL-FHSDPSK +WALKGACLVFNLLDVIEDMSIMLFDSEDNRIGFVNQMKGKAGRFLIRCLRMLLNHQEIE- +-IDGVAVGDMMLDVHHRLLKWNKLGLGMFEGYKEFDDFVECFLTFLILSFEDETLTTVLE +S +>THECC +----MATPQSITDLFARLAFHLQL----PISEREN-----EEEALNLAISKLNQSLNLNE +-N----HDSRVRVMDTALSLMCFKAPQ---------VFDSVIEYLVKTIVSVLSSSVNCK +VFLLQ---NQEFLLIGSASLGQNSVELVEMCNNVYAQLEGKGVFS--HLLLRAVV----R +-GTVLASRYQYSYPFVPILDVK----SIEGRSAAVSKLHCHLPTELSLENEELPLRLLFW +YLDPLILKQAISKILEDTTGRPFICLSEEFHQRIDWRSIIICLVLSPVMFIETRALLHSW +FLKTGLASVLQLLVGLVSAVLDVISRPTWWGISMELGSKLPFSCAYFPNKNH-LLRILAG +TFSAENFLHLVHATSELVS-LGKEQLHPAVKPKSMDVTSIDHK---------SLWALAVD +FPDWFYFASCLLFPENS-LRKEFHLKCTFAASKVGETHDKELL--SISAARYISWILSPV +SKSNQDLLVDFLTKISESWALKQYDS---------VMHNKEAAACKKKCKKPKLYDKREH +YSLANEYDCQKMGIWLNEIENIYLQYANKTVNSSASADSNASH-GSTQQNVLLRRIPLGI +LIGCPNCITEDACALLLHYAATGNILRPRETVTSGLRHVKQKSER-QDLTIWMGKC-SKR +DVLAGACLVFTLTDAVDSISASLFDTEDSELEYIYQVKVKAGKYLMKCIKRLSQLNID-- +----KDEVLTLRDLRSRLGRWRHQGQETLQVQNDIDDVINDLSQKLSSL----------- +- +>MANES +----MATLGEITDLFCKLAFHLQTLTHTAQMHYQDEETE-HSDSVDLSISSITQSLNLN- +------DNAGVRVLDTALSLMCFTAPQ---------VFDSMIEYFVKTIVSVLSTSISCK +VLPFG---KEEILRVGSCISQRDCVEFIEVVNDVVSKLDQHGVPS--HLLLRSAA----R +-VAVSTSCCRYMVPSMHVLDVK----SIDRRSTAISNLLSHLPGDLSLDNNKLPLRLLSW +YLDPLTLKHDISNILQETMKRPFLTLSKEFYERMEWRSILLCLVLSPMMFIHTRALLHDW +FMLTDLGSVLEFLIELVAVILDVISRPTWWGIPLELASELPFSNAYFPCKDH-LLRILSG +PLVSSSFQQLVQVTSESDS-LVCKQFGPISKSSTLKFASVDRK---------SIWALVIC +FPDWFYFASGLLFSNNC-YQNNCQLNCLLEAPNS------IMEQPAVSAASFIAWILSPN +SKPHQDLLFEGLTRMSECWSRKQIDS---------DVH---------------------- +---ENEYGCQVIGLWLNEFHRVM-KYGVESTDKSSNCEAE-SYYFVLQNSMLFRRITLGV +LIGCPSYVKEDGFELLLHYAATGRVLHL-TSNNARMKHVDE---------------FNRK +EAVAGACLIFSLTDIVERISASSFENEKSGLDIICQVKLGASKYLIKCMKKLIEPNIF-- +----EDNK-MLVDLHDRLERWRHQGQEMLELDKDLDDTIKGLSNELLLL----------- +- +>MALDO +----MTXLPEITDLFARLAIHLKIPNDTSFPPRTS-KEDLDDAALDLSISELNQSLNPN- +------GDSRVRVLDTVLSLMCFKAPQ---------VFDSEIEYLVNTIAAVLLSSVRCK +VFRYP---KGEILLIGSSISQXDCGHLIEACADVLEKLEGHGKLS--DSILCAIV----R +-VASSASFYR--HQLMPVLGVK----SVDAKNTMISKLLCHLPREKFLENNKIPLRLLLW +YLDPLILKRDISNILQETMERPFLCLSRKFHESNDWRSIITLLVLSPFMFVEARALLHRW +FLVTGLASVLELLIQLVSTTLDVVSRPMFWGISAEVGAKLPFLNAYFPYNQP-LLRTLVG +PLSYDGLLQLVHNTKDXVP-FAQKQLYPTFKPPTVKMASTPSPFYNPTDPQMLHRSLAIN +FPDWFYLASALLFSEKS-THDSCHPECXLAASKVGKTHEELP---YVAAARYIAWILSPL +XKSHHASLXDCLIKXSXSLALKQFGS---------GSHDKEIHGYKKKLKKPKLCEE--- +-------ESASIAVWLNGFSNIYTRYCNETSET------KPSCGLNLQKNVLFRRIPLGI +LLSCPHRINEDECELLLHYAATGRIFQLRETKTTGLKHVKWSSKWHTNSTAWGDEC-NEK +EASAGACLVFSLTDIIESMSASLFETEDAGADFICRVKMQVSKYLIKCIKRLIQLKID-- +----NG-NWEVMDLRRRLENWRHQGQEVPELNKDLDDEWGKDYAKQQFFGTEPRCIRLAS +F +>ZEAMA +---MAPPLEDLTRVLAELASGLAQPPAGG-------GTFSSTDSLPASISSLAAALNPSG +DGA-A-ASSGTGVLDAALSLMCFDPLE---------VNSARVNCLVRTLVSVLSASVSCC +VVRPDGDAAEEMLCVGSSVSPLDCRELLRSCAALVEKLGDCGDRRHSYDLLYAVV----K +-TILLSPHYQCLS---PLPYYKEEEERVSHMGTIAAELINHSSDHILPSDHSIPPRLLSW +HLDPLILRHDLSAMLQEVIRRPLLC----------------------------------- +L-------------------RKELYNRMEWRIIIICLVCCPTIFMEM------------- +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +- +>PHODA +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------------------------------ +---------------------------MWWGISMEMGMKYPSSYAYFPCRHHELLAIISG +HISCNSFLDLVHYIKTRLA-PLAKHSDPTASHPSHGIF--GHEALVDLVDNDSAWTMLMD +FPAWFYFATALIFHGND-SQDYI-SSVICGEVKTETVKEMQR---KAK------------ +------------------------------------------------------------ +------------------------------------------------------------ +------------------------------------GCIGHDEFT-----PW-SADDATK +WALNGACLVFNLLDLIEDMSVMLFDCEDTRVDFLHQMKGKASGYLLKCVKLLFECECHEF +YNGAIGVRDNVLDLYRRLVTWRQQGPEGFEGYKAFDDVVDDFAKRFRIVE---------- +-
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta2phylip/test.phy Fri Apr 22 08:22:55 2016 -0400 @@ -0,0 +1,151 @@ +14 781 +ARATH ----MPSPSAVADLLAALAYRLQNGDELF---EEEEEAEESTSSMGLAISELNRSLTLDIGC----EDSGVRVV +ORYSA MASPPSPLEAIARLLADLARRRSHPPPGG-------GR--SGDSLAASVSSLAAALNPHGGGASSSSSSGTRVL +SORBI ---MAPPLEDLTRVLAELAARLSQPPAGG-------GSSSSGDSLSASISSLAAALNPSPDGGNS-ASSGTRVL +VITVI -------------------------------------------------------------------------- +BRADI ---MAPPLDGLTKLLAEVASRLSRPPGVIGAGPSS-SSSSSGDSLSASISSLAAALNPRPAA----AATGTRVL +CARPA ----MTTLPEIADLFSRLASNLQTLKPKSIVDEGK-----EEVSLNLSISKLNQSLNLC-------KDSSVRVL +RICCO ----MATLEEITDLFSKLAFHLQTLSHASSP------KD-SNSFIDLSISKLNQSLNII-------DNTQTRVL +POPTR MRTTSPTSPEIMELFSKLAFELQTLTHNSPINQEQQQQEFNDSSIDPSISKLT--LSLT-------HNPGVRVL +MUSAC ---MATSPAEIARLFAELASRIQSPQDDTDGGDGV-G---PGGELASAISSLAASLSFG-------DAPRVGVL +THECC ----MATPQSITDLFARLAFHLQL----PISEREN-----EEEALNLAISKLNQSLNLNE-N----HDSRVRVM +MANES ----MATLGEITDLFCKLAFHLQTLTHTAQMHYQDEETE-HSDSVDLSISSITQSLNLN-------DNAGVRVL +MALDO ----MTXLPEITDLFARLAIHLKIPNDTSFPPRTS-KEDLDDAALDLSISELNQSLNPN-------GDSRVRVL +ZEAMA ---MAPPLEDLTRVLAELASGLAQPPAGG-------GTFSSTDSLPASISSLAAALNPSGDGA-A-ASSGTGVL +PHODA -------------------------------------------------------------------------- + +DAALSIMCFKAPQ---------VFDSAIEFMVRTIVCALSSSSNCKVIRYR---NEETLQFGSSNLPGCSEELIEISKDI +DAVLSLMCFDPME---------VDRARVDCLVRTTVSALSASVSCRVDHID---GAEMLTVGSSVAPGDCRELVHSCAAL +DAALSLMCFDPLE---------VNSARVDCLVRTLVSVLSASVSCRVVRPDGDAGEEMLCVGSSLSPVDCQELLQSCATL +-------------------------------------------------------------------------------- +DAALSLMCFDPLEAIPIPFGSRVDRARVECLVRTITSALSASVSCRVVRTD-DCGGEMLCVGSSVSPGDCRELVSLCASL +DTLLSLMCFKAPQ---------VFGSTIDYLVKTIVTVLHSSVSCEVLMFE---NEETLQIGSSILPRDCLKLIEMCNAV +DTALSLMCFRAPQ---------VFDSTIEYLVKTIVSVLSSSIRCNVLRLE---KEEVLQIGSAISKKSFLEFIQVVNDV +DTALSLMCFKAPQ---------VLDSVVEYSVKTIVSVLSSSICCEVFRFH---NEEVLQIGSFISRGHCMELIECVFDV +NAALSLMCFRASE---------VHRARVECLVGTIVAMLSSSVSCRVLRLPDKRDEGFLRIGTSFSSEDCVQLIRVCVDV +DTALSLMCFKAPQ---------VFDSVIEYLVKTIVSVLSSSVNCKVFLLQ---NQEFLLIGSASLGQNSVELVEMCNNV +DTALSLMCFTAPQ---------VFDSMIEYFVKTIVSVLSTSISCKVLPFG---KEEILRVGSCISQRDCVEFIEVVNDV +DTVLSLMCFKAPQ---------VFDSEIEYLVNTIAAVLLSSVRCKVFRYP---KGEILLIGSSISQXDCGHLIEACADV +DAALSLMCFDPLE---------VNSARVNCLVRTLVSVLSASVSCCVVRPDGDAAEEMLCVGSSVSPLDCRELLRSCAAL +-------------------------------------------------------------------------------- + +IEKLWGNGRLA--TLLFEAVV----R-SAASTCKISS-----FNAHGK----LMDGRNRAVSKLLAYLPGESSIENHKIP +LEKLGDPDVADHSYDLLYAVV----K-AALLSPRYLCLF---PLPYYREDEDSTCDMGTISSVLTRHPTYQVLPNDYTIP +VEKLRDCDDGRHSYDLLYAVA----K-TVVLSPHYQCLF---PLPYYKEEGERVSHMGTIAAELIKHPSNLVLPSDHSIP +----------------------------------------------------------------------------MIFF +VEKLGDRDDAMRGNAVTIKQTYGTPEIHDTQDVLGVCLF---PLPYYRENGEKKYEMATVAVDLTRHPSYQVIPSDGSIP +IQKLEGHEVLA--SSLLHAVV----R-VAVSTSFCQFSFQFPPTLEEK----EVDERSVAFSKLHCHLPRECSLQNHEIP +VSKLEENGMPC--HLLLCAFA----R-VAVSASCYRYLVPTMHVLDTK----SINGKSSALSKLLCSLPKD-SLNNHEIP +ISKLKEHGMPI--DLLLSAVV----R-VAASASCYKYLSPSMRVLDVK----SIDGSITAISKLLCHLPMDFSLSNHEIP +LASLKGHCGDL--HALLYAVV----K-AVISSSTYQGLLPSLPIGYLRN-EDTDCGVQTEISKLAYSLSDQTSCTGHEFP +YAQLEGKGVFS--HLLLRAVV----R-GTVLASRYQYSYPFVPILDVK----SIEGRSAAVSKLHCHLPTELSLENEELP +VSKLDQHGVPS--HLLLRSAA----R-VAVSTSCCRYMVPSMHVLDVK----SIDRRSTAISNLLSHLPGDLSLDNNKLP +LEKLEGHGKLS--DSILCAIV----R-VASSASFYR--HQLMPVLGVK----SVDAKNTMISKLLCHLPREKFLENNKIP +VEKLGDCGDRRHSYDLLYAVV----K-TILLSPHYQCLS---PLPYYKEEEERVSHMGTIAAELINHSSDHILPSDHSIP +-------------------------------------------------------------------------------- + +LRILFWYRDPLSLKVDVSRILKEVVERPFLCVKRELFERGEWRDIVICLAISPTMFINTRSLLHKWLLLTGLASVFEVLA +L--------------------------------------------------------------------RGLGAVLELQT +PRLLLWHLDPSIIRHDLSAILQEMRSLLHFW-----------------------------------FLATGLGSVLELHN +FRLLLWYLDPLILKHDVSKILQDTMKRPFLCLNKEFHERMDWRSIIICLVLSPTMFVETRALLHNWFLITGLASVLQLLI +LRVLLWHLDPSILKHDLSAMLHEAITRPFLC-----------------------------------L------------- +LRLLFWYLDPASLQHDISKILQDAVTMPFLCLSNEFHKRMDWRNLVICLALSPVMFIETRALLHNWFLMTGFAFILEFLV +PRLLSWYLDPLALKHNISNILQVTMERPFLLSSKEFYDRMEWRSILMCLVLSPTMFIHTKALLHNWFMLTGLGSILELLI +TRLLIWYLDPLALKHDISKILQETIKRPFLCLSMEFYERMDWRSILVCLVLSPIMFIDTRALLHDWFLQTGLSSVVELLM +LRLQFWYLDPLILKHDISEILKEVIRRPFLCLRKELHDRMSWRNIITCLVTSPTFFKETKATLHTWFLFTGLTSVLDLKI +LRLLFWYLDPLILKQAISKILEDTTGRPFICLSEEFHQRIDWRSIIICLVLSPVMFIETRALLHSWFLKTGLASVLQLLV +LRLLSWYLDPLTLKHDISNILQETMKRPFLTLSKEFYERMEWRSILLCLVLSPMMFIHTRALLHDWFMLTDLGSVLEFLI +LRLLLWYLDPLILKRDISNILQETMERPFLCLSRKFHESNDWRSIITLLVLSPFMFVEARALLHRWFLVTGLASVLELLI +PRLLSWHLDPLILRHDLSAMLQEVIRRPLLC-----------------------------------L------------- +-------------------------------------------------------------------------------- + +GLASAIMDTISRPSLWGIPMELASMLPFSDTYFPFQCQ-FLRILAGPLSSKSLLMLAHTVSKASAVPGQQQRDTNCKPTP +AVVSSVLDVLFEPMAWGISMELGQKLPFSYDYFPHQHVDLLAILTGPLSCRKFVDLTSYIDSQS---------------- +ALVSSALDILLKPMSWGICIELGQRFPFSHAYFPNQQSDLLAILTGPLSCKGFLDLVSYISALVH-LDNSR----TRCSS +EVVSMILDVVSRPTGWGISVEMGSKLPFSIAYFPYNHH-VYRILSGTLSSESFLHLVSIINVPIS-RAGNHSMPTIKQVP +------RKELHDRIAWRVIIICLVCFPPAFLEMTSLFH------------------------------------------ +ALISVILDLLSRPTWWGIPMDLGFKLPLSDAYFPCQSH-LLRTLAGPLFSEKFVHLVHVIGSPIS-GARKQSASSFKRTG +ELVALILDVISRPTWWGMSMELGSKLPYANAYFPYKNH-LLRILVGPLSSISFLQLVYRTTESVS-HIMEQFGRTCKASV +ELVSLILDVISRPTWWGLSLELGLKLPFSNAYFPYKSD-FLRTLTGPFSYESFLQLVHMTRKSAY-LHRELCDPTIKPSA +GIVLSVLDILSRPMWWGVPVELGLRFPSSYAYFSIRHHDLLTILTGQLSCKNLLHLVQYIKTEVA-ILSNIC-QSASHPS +GLVSAVLDVISRPTWWGISMELGSKLPFSCAYFPNKNH-LLRILAGTFSAENFLHLVHATSELVS-LGKEQLHPAVKPKS +ELVAVILDVISRPTWWGIPLELASELPFSNAYFPCKDH-LLRILSGPLVSSSFQQLVQVTSESDS-LVCKQFGPISKSST +QLVSTTLDVVSRPMFWGISAEVGAKLPFLNAYFPYNQP-LLRTLVGPLSYDGLLQLVHNTKDXVP-FAQKQLYPTFKPPT +------RKELYNRMEWRIIIICLVCCPTIFMEM----------------------------------------------- +-------------MWWGISMEMGMKYPSSYAYFPCRHHELLAIISGHISCNSFLDLVHYIKTRLA-PLAKHSDPTASHPS + +IKVQALDDK---------TEWALAINFPDWFYFASAMLFSEGK-SFENIHHICASKVADCRQVCDVEDL--SIAAATYIS +--------HASKGSVKYNSSWSMIVNFPLWFNFATALLFHREG-SHGYL-SEALSMEIISESIRDVNL---AHRAAMYLS +QKNL--QLQPSKGLVNYNSAWCMIINFPVWFSFATALLFYREG-SQDYL-SETLSKEITVESISDVSL---VQRAAFYLS +MKISTIGHK---------SVWAAAMNFPDWFFFASVLLFSEKS-FQDNFYSKCGIGVPRTEKRHDVEPLCFSSAAARYIA +---------------SWFLATSTITNFPIWFSFAAALLFHREG-FQGYL-SEILSEEKVSESISDISL---ARRAAFYLS +IKLATINQN---------SLWALAVNFPDWFYFASILLFSGKS-FQDHFQPKCMIGAPKNRGPHDSVLL--SQAAARYIA +LKIASTESK---------SIWALAICFPDWFYFASVLLFSTNC-FQKSHQSKRIFGVPKSGKTNNKEQSPPAAAAARYIA +VRVASIDHK---------SIWALAISFPDWFYFASVLLFSDDKNSQQNIQVKCPLGVPEFGQ------LPASAAAATFIA +VTNY--NHEGLA----------NVIDFPAWFYFANALIFYRNS-SQDYL-SEALCGRLRTEPVNDLEL---HRAALYYIS +MDVTSIDHK---------SLWALAVDFPDWFYFASCLLFPENS-LRKEFHLKCTFAASKVGETHDKELL--SISAARYIS +LKFASVDRK---------SIWALVICFPDWFYFASGLLFSNNC-YQNNCQLNCLLEAPNS------IMEQPAVSAASFIA +VKMASTPSPFYNPTDPQMLHRSLAINFPDWFYLASALLFSEKS-THDSCHPECXLAASKVGKTHEELP---YVAAARYIA +-------------------------------------------------------------------------------- +HGIF--GHEALVDLVDNDSAWTMLMDFPAWFYFATALIFHGND-SQDYI-SSVICGEVKTETVKEMQR---KAK------ + +WILNPGSGTIQESVSKSLIRVSEICISKSCGS---------EAYRTETITGKRK--KPDR------LVSGKINASSIVED +WVLCPSNEDQRQILAGNILELSHSWARNNKKGPSH-------VHHTSTVNHRRKLRIPTVGDTEKLHLSTNPVSSL---- +WVLCPSNDDQCEVLSNNILEISRSWARNNKRCL----------GYQSTVNHRRKLRIPTAASSEKFHVPINTVSSL---- +WILSPADKSHQDLLVDWLTKLSESWTLKQFGS---------DTYNKEIADYRKKLKKTKFPVYKGDYNLPKEYNYVTIVL +WVLCPSNEDECQMLANNMVELSNSWARNIKSRPSY-------AYHTSTVNHRRRLRIPTVGDTEKLHMSTNPVSSL---- +WVMSPLNKSNQDLLVGCLIKISEAWTRQQFGP---------GVHDKKALGCDKL-KKHKF-HGSKDYNLTKVGNSKMIDL +WILSPNNQSQQDWLFGGLTKISEFWTLRQIDL---------GTSGRDIASCRKKLKNSKCYNIEEDFSLGTEDNCQTIGL +WILSPVNKSNQDALFENLTKLSKCWNLKEISS---------DNSQNGMAGYKKKLKKPRFCDSKEDSTLGNKYDCQVIIL +WVLCPIGEAHRDMLAENIDELSRSFVTQHKAKSIYEERSFSDMHPKNVLSRSKKLKIPKANSFEKHRMAPQEVSSLNIGV +WILSPVSKSNQDLLVDFLTKISESWALKQYDS---------VMHNKEAAACKKKCKKPKLYDKREHYSLANEYDCQKMGI 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fasta2phylip/tool_dependencies.xml Fri Apr 22 08:22:55 2016 -0400 @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="biopython" version="1.66"> + <repository changeset_revision="ef89610ae47c" name="package_biopython_1_66" owner="biopython" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> \ No newline at end of file
--- a/repository_dependencies.xml Fri Apr 22 08:21:47 2016 -0400 +++ b/repository_dependencies.xml Fri Apr 22 08:22:55 2016 -0400 @@ -1,9 +1,8 @@ <?xml version="1.0"?> <repositories description="Tools to launch FastME workflow"> <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="mafft" owner="rnateam" changeset_revision="c9affca9656a" prior_installation_required="False"/> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="noisy" owner="dcorreia" changeset_revision="3fa6508ee174" prior_installation_required="False"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="noisy" owner="dcorreia" changeset_revision="dc60058d559e" prior_installation_required="False"/> <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="fastme" owner="gandres" changeset_revision="df9e53f419c5" prior_installation_required="False"/> <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="newick_display" owner="dcorreia" changeset_revision="ceba45fbfcb8" prior_installation_required="False"/> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="fasta_to_phylip" owner="mish" changeset_revision="1c14c7a6539f" prior_installation_required="False"/> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="dna_or_protein" owner="dcorreia" changeset_revision="b3e38ba307bc" prior_installation_required="False"/> + <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="phyml" owner="derepeer" changeset_revision="c23bdc214b14" prior_installation_required="False"/> </repositories> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtypedetect/seqtypedetect.py Fri Apr 22 08:22:55 2016 -0400 @@ -0,0 +1,53 @@ +#!/usr/bin/python +# -*- coding: utf-8 -*- +import sys +import argparse + +def analyse_file( inputfile ): + """ + Take a fasta file and detect if it contain "dna" or "protein" + """ + DNA_Alphabet = "atgcn" + missing_letters="_- ?\n\b\t\r" + nb_gap = 0 + protein = False + nucleotid = False + typeofseq = "dna" + + with open(inputfile, "rU") as input_handle: + + for line in input_handle: + if not line.startswith('>') and not line.startswith('#'): + for n, letter in enumerate(line.lower()): + if letter in missing_letters: + nb_gap +=1 + else: + if not (letter in DNA_Alphabet): + protein = True + break + + #reduce time threshold + #The probability of observing a protein sequence containing + #only DNA Alphabet in the first twenty residues is almost null + if n > (20 - nb_gap) : + nucleotid = True + break + + if protein and nucleotid: + sys.stderr.write( "Warning ! Two types of sequences detected\n") + + elif protein: + typeofseq = "protein" + + elif not protein: #and too small + typeofseq = "dna" + + return typeofseq + +if __name__ == "__main__": + + parser = argparse.ArgumentParser() + parser.add_argument('file', nargs='?', type=str, action="store", default="", help="input fasta file") + args = parser.parse_args() + + print "%s"%(analyse_file(args.file)) \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/seqtypedetect/seqtypedetect.xml Fri Apr 22 08:22:55 2016 -0400 @@ -0,0 +1,19 @@ +<tool id="seqtypedetect" name="Sequence type detection" version="1.0"> + <description>Detect sequence datatype on fasta file</description> + <command interpreter="python">seqtypedetect.py $input > $output</command> + <inputs> + <param name="input" format="fasta" type="data" label="Source file" help="Fasta sequence file"/> + </inputs> + <outputs> + <data format="txt" name="output" label="Information"/> + </outputs> + <help> +=========== +Overview: +=========== + +Detect sequence type. + +This tool is needed for the OneClick phylogeny workflow analysis. + </help> +</tool> \ No newline at end of file
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