Mercurial > repos > greg > assembly_post_processor

--- a/.shed.yml	Tue Mar 21 10:42:51 2017 -0400
+++ b/.shed.yml	Fri Apr 07 08:34:58 2017 -0400
@@ -1,5 +1,5 @@
-name: assembly_post_processor
-owner: iuc
+name: plant_tribes_assembly_post_processor
+owner: greg
 description: |
   Contains a tool that postprocesses de novo assembly transcripts into putative coding sequences and their
   corresponding amino acid translations, locally assembling targeted gene families.
@@ -9,8 +9,7 @@
   utilize objective classifications of complete protein sequences from sequenced plant genomes to perform
   comparative evolutionary studies. It postprocesses de novo assembly transcripts into putative coding
   sequences and their corresponding amino acid translations, locally assembling targeted gene families.
-remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/plant_tribes/assembly_post_processor
+remote_repository_url: https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/plant_tribes/assembly_post_processor
 type: unrestricted
 categories:
-- Assembly
 - Phylogenetics
--- a/assembly_post_processor.xml	Tue Mar 21 10:42:51 2017 -0400
+++ b/assembly_post_processor.xml	Fri Apr 07 08:34:58 2017 -0400
@@ -1,16 +1,10 @@
 <tool id="plant_tribes_assembly_post_processor" name="AssemblyPostProcessor" version="0.4.0">
     <description>post-processes de novo transcriptome assembly</description>
-    <requirements>
-        <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
-    </requirements>
-    <stdio>
-        <!-- Anything other than zero is an error -->
-        <exit_code range="1:" />
-        <exit_code range=":-1" />
-        <!-- In case the return code has not been set propery check stderr too -->
-        <regex match="Error:" />
-        <regex match="Exception:" />
-    </stdio>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements_assembly_post_processor" />
+    <expand macro="stdio" />
     <command>
         <![CDATA[
             AssemblyPostProcesser
@@ -153,14 +147,7 @@

     </help>
     <citations>
-        <citation type="bibtex">
-            @misc{None,
-            journal = {None},
-            author = {1. Wafula EK},
-            title = {Manuscript in preparation},
-            year = {None},
-            url = {https://github.com/dePamphilis/PlantTribes},}
-        </citation>
+        <expand macro="citation1" />
         <citation type="bibtex">
             @article{Honaas2016,
             journal = {PloS one},
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Fri Apr 07 08:34:58 2017 -0400
@@ -0,0 +1,85 @@
+<?xml version='1.0' encoding='UTF-8'?>
+<macros>
+    <xml name="requirements_assembly_post_processor">
+        <requirements>
+            <requirement type="package" version="0.4">plant_tribes_assembly_post_processor</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_classifier">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_classifier</requirement>
+        </requirements>
+    </xml>
+    <xml name="requirements_gene_family_integrator">
+        <requirements>
+            <requirement type="package" version="0.8">plant_tribes_gene_family_integrator</requirement>
+        </requirements>
+    </xml>
+    <xml name="stdio">
+        <stdio>
+            <exit_code range="1:"/>
+            <exit_code range=":-1"/>
+            <regex match="Error:"/>
+            <regex match="Exception:"/>
+        </stdio>
+    </xml>
+    <xml name="param_scaffold">
+        <param name="scaffold" type="select" label="Orthogroups or gene families proteins scaffold">
+            <options from_data_table="plant_tribes_scaffolds" />
+            <validator type="no_options" message="No PlantTribes scaffolds are available.  Use the PlantTribes Scaffolds Download Data Manager tool in Galaxy to install and populate the PlantTribes scaffolds data table." />
+        </param>
+    </xml>
+    <xml name="param_method">
+        <param name="method" type="select" label="Protein clustering method">
+            <option value="gfam" selected="true">GFam</option>
+            <option value="orthofinder">OrthoFinder</option>
+            <option value="orthomcl">OrthoMCL</option>
+        </param>
+    </xml>
+    <xml name="param_orthogroup_fna">
+        <param name="orthogroup_fna" type="select" display="radio" label="Process corresponding gene family classification orthogroups CDS fasta files?">
+            <option value="yes" selected="true">Yes</option>
+            <option value="no">No</option>
+        </param>
+    </xml>
+    <xml name="citation1">
+        <citation type="bibtex">
+            @misc{None,
+            journal = {None},
+            author = {1. Wafula EK},
+            title = {Manuscript in preparation},
+            year = {None},
+            url = {https://github.com/dePamphilis/PlantTribes},}
+        </citation>
+    </xml>
+    <xml name="citations2to4">
+        <citation type="bibtex">
+            @article{Sasidharan2012,
+            journal = {Nucleic Acids Research},
+            author = {2. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A},
+            title = {GFam: a platform for automatic annotation of gene families},
+            year = {2012},
+            pages = {gks631},}
+        </citation>
+        <citation type="bibtex">
+            @article{Li2003,
+            journal = {Genome Research}
+            author = {3. Li L, Stoeckert CJ, Roos DS},
+            title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes},
+            year = {2003},
+            volume = {13},
+            number = {9},
+            pages = {2178-2189},}
+        </citation>
+        <citation type="bibtex">
+            @article{Emms2015,
+            journal = {Genome Biology}
+            author = {4. Emms DM, Kelly S},
+            title = {OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy},
+            year = {2015},
+            volume = {16},
+            number = {1},
+            pages = {157},}
+        </citation>
+    </xml>
+</macros>
--- a/test-data/assembly.fasta	Tue Mar 21 10:42:51 2017 -0400
+++ b/test-data/assembly.fasta	Fri Apr 07 08:34:58 2017 -0400
@@ -5,69 +5,3 @@
 CCGGTATTCACCAGATCCAGAACACTGAGCCCTTGACTCTCAACGGCATCTTGCTCATTT
 AATTTAACACCTTCAACCCACTCCATTGTTAGCACCTTTCCACTCGTGTAATCCCAGAAA
 ATATCTGGGACAAGGATATCTTCCTTGTCTCCATATAATTTTTTAA
->contig_2
-CCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCC
-GGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCAT
-ACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCC
-CGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATG
-GGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCC
-GATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTAC
-AACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTG
-TACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACA
-ACTGTTAAATTATGTGCGCTTTGATGATTAAAAACACGGGGTAATTGAACTCAAGGGATG
-GTTGAGAATTGTAATATTTCTGTAAGTGTCGGGGGATGGTTGAAATGCTTTTTATTATGA
-AGTGTTAAAATGTAAGATAAA
->contig_3
-CGGGGGCAAGGTTTACATGAAAGTACATCTACAGGACCTAGATAAGCATCATCACCTGAC
-AAAAAGCCATACATAGTAACACTTGCTAGTTGATCTGTGAAAATGGTGCACGAGTCGTAA
-CAGACGGCATTAGTTCCTTTCCTGTAACAGCAGATTCGTATGAATGGTTTTCTCGAAATT
-CTTCTTCAAGTGCATCTATAGGCATGGCACGAAGTGACTCTATTGTGCCTTTGCTGGGAA
-TATCCGGCTCGCTCCTAACTGGCGTGGACCCTGTAGGCTCGTAATCCATGTATTTTTGCC
-TGAAAGTATCATTCGTGTGCTGTTCGATACAGGATACCTGCTGGGAATGATCTCTCTTAA
-GGTTCTCAATTGTTTCTGAATGAGCTCTAGCAGTTGTCAGAATTTCAGAAACAGATGCCT
-TCTCCTGCTCTGACAAGCCAGCAACAACAACTCCTTCATCCACA
->contig_4
-CTGACGATGTTCATATTCATGCCACTCTAAATGTATGCCATCCATGTTGAGGAGAAATGC
-TTGTGTAAAGAAGAAACTGGAGTCAAGCGGTCCCGGTTTTACAGTTGAACGTTGCTCTAA
-ATTAGTCAAAGTACCCGACTACCCGCTCATCAAACTGGCGAGCTCGTTTTCCTCGCCGCC
-CTACTCGGTGTCTTGGCGGGGCACATGGGGGTGGCGTGTGGCGTGCGGGGATGCGACAAC
-ATCATAAATTCATAATCGAAGG
->contig_5
-GTGAGAGTGTCGCCTTTTCCATGCTACCCCTTTCCAGATCTGACTTGTTCGAACCTTCCA
-TCATCCGGTTCGACGTCAGCAGTCGGTCCTTCTTCTCCAAGCACGAGAGCAGACGGTGCG
-AGAGCGAGCAAAGACTCGCCTGCCGCGCCTCTCGTGACCTGGCTCGCATCTCCAGGATTC
-ATGGCTCCTTAGCTCGCCCTTCTTCGATACTTCGCTAGACGCCCGAGGACGTCATCGAAG
-GCGAGGGTCGGCACAACGGAGTGCTCCTTGCATGATGTCGGGGCCTGGCATCACGCGGCA
-TCGGCCAAATCGTCCCTCTCGACGTGCGTCACGGAGAGGGCCGAGCGCCGGGACGACCGC
-GTGGAAGAGCCCGCGGGATGCGGGATCCCGCTTGACGTGTGTTTGTGGCGGACCACCG
->contig_6
-TATAACAATTCAAAATATTCCTATGAAAACCAAGACCAGAGGCAACACCGGTATAACCAA
-AGCCAGAGGCAATATCCCTTTATTCTTCGGGAACAGAAAAATACACGATATGCTACAGAC
-AAAAAAATAAATCCAAACCATTCTTCTGTGCATAAACATTGTAAAAGTTTATTAGACCGC
-TGTAAAACTCGTAAATGAAATCCCTGGCAATTGAATCTGTTAAACCTGCTCC
->contig_7
-GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT
-AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG
-TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC
-AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGCG
-AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACG
->contig_8
-TGGCATGAAGTCGGCTCGACTCGTGCCCGCTCGTCTATAGACGAATTGAGCTAGATTCAC
-TCATTCCATGAACTCGACTCGTTCATGAGTCGGCTCGTAGTTGTCCGGACTCGCTCCATG
-GCCAGCTCTACAACAGACTGCCTGTATGTAGATGATTGTATTGATTTGTTCTTCTCTTGT
-TTAAATCCAACCAAATATCAACATGATATTTGCAATTTC
->contig_9
-ACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTT
-TGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCC
-TGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAG
-AATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAAC
-AGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAA
-ACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGC
-ACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGA
->contig_10
-GGGGCATTGCCGCCGATTAATTCGAGCGCGAGGTTTCGCGTATCAGGCGGAATTGGGATT
-TGGCGCCACAAAGAGCGCCACCTATGATTTCTGTGGCGGACGACTTCACGAACTCGGACG
-GGACTATCTAACCAATCTTCCAAGTTCATTGCGACATCAGTATAAGGGCGTGATGAAGGT
-TCGCTATCGTCGCTTGAGTTATTGATGGGGCCCAAATTGAGATCGAGGTTCATTGTAGTG
-GTGTTCTCTTCTGCCATTTGAGAATTTCACAAGTTCTAACAAACGAAAACGCAAATCTTC
-GGGACTAATATGCAGAATTTCCCTAAATAGAAGGGGTTTAAAA
--- a/test-data/transcripts.cds	Tue Mar 21 10:42:51 2017 -0400
+++ b/test-data/transcripts.cds	Fri Apr 07 08:34:58 2017 -0400
@@ -1,24 +1,2 @@
->contig_1|m.1 contig_1|g.1 type:internal len:115 contig_1:344-3(-)
+>Gene.1::contig_1::g.1::m.1 type:internal len:115 contig_1:344-3(-)
 AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAAT
->contig_2|m.2 contig_2|g.2 type:5prime_partial len:170 contig_2:2-511(+)
-CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA
->contig_3|m.3 contig_3|g.3 type:5prime_partial len:126 contig_3:463-86(-)
-GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAACTAG
->contig_9|m.4 contig_9|g.4 type:internal len:132 contig_9:2-394(+)
-CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT
->contig_11|m.5 contig_11|g.5 type:5prime_partial len:108 contig_11:2-325(+)
-ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGGCGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCCAAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCATGATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTATTGA
->contig_11|m.6 contig_11|g.6 type:5prime_partial len:100 contig_11:443-144(-)
-GCTGCTAAAGTCACGGTTGCTCCCGGATCTCGCGTCGCTGCTGCTGGAAGCGGCGTTGCCTCAGAATCTCCGGCGACTGCTGAAGCCGGCGTTGCCCCAGGATCTCCCGCGGTCGACTTCAATAGCCACAGCGGGAGTTTCTGGAGCAACACCGACTGCAGCAGCAACAACGGGAGATTCGGAGCAACTCCGACGGGATATCATGGAGCAACCCCGACTTCAACAGTGGCGACGGGAGATTTTGGAACAACGCCGACTTCAGGAGCCGCGGTGGGAGAGCTTGGAGTAAATCCGACTTAA
->contig_18|m.7 contig_18|g.7 type:internal len:143 contig_18:426-1(-)
-ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAAAATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGTACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTGGAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTTGCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGCTTTGGTTGGCATTGGATGAGGTTACC
->contig_20|m.8 contig_20|g.8 type:internal len:104 contig_20:1-309(+)
-GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCATTTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA
->contig_20|m.9 contig_20|g.9 type:internal len:103 contig_20:2-307(+)
-GCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCATTTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGAT
->contig_20|m.10 contig_20|g.10 type:internal len:103 contig_20:307-2(-)
-ATCCAAGTAGTTGATCCAACGAGACCAGCCCAACATGTAGCGGGTAGGAATGACGAAACCAGTGTAAATGACCAGCGCAAGGATAAGGATAGCTGCGGGAGCCATGGCCTGCGACAGTGTACGCGAAACGGATCCAATAGTGCGGAAGAGCATCGACATGACAAGCGTCAGCGTGAACGATATCAGCAGGAAGAAGAAGAATGCTCCTGGTTCGCGGCGAAGGTTCGTCATGAAGTACAAGATCAAGTTGAAACAGATCGCGTTGCCAATCTTGTAGGGCATATCCGTGAGCATCGATGCGTAAGC
->contig_21|m.11 contig_21|g.11 type:5prime_partial len:168 contig_21:519-16(-)
-GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTATGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATGACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAGAATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAACCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTATGCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGCACCCAAAGACTTGCATTCGAGTGA
->contig_24|m.12 contig_24|g.12 type:internal len:111 contig_24:331-2(-)
-AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTATGTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAAACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAAATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAATTTACTTAAC
--- a/test-data/transcripts.cleaned.cds	Tue Mar 21 10:42:51 2017 -0400
+++ b/test-data/transcripts.cleaned.cds	Fri Apr 07 08:34:58 2017 -0400
@@ -4,21 +4,3 @@
 CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT
 ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG
 TCATGTTGTACACATGGTTAAT
->contig_100
-TGCAAGCTTCAGGAAATATCCTCAACTCTCATAACAATCCTTGTCATTCTCTCCCCAGACAAACTCATATTCTTCGCATC
-AACAAACCGCGATTCCTTGAACAATGTCACGATCTCCTCCACCTCATCTACCCCACACTCTTCCACAGTCACAACACAAA
-CCCCACCACTCCTCACCGTCCTTTCAATCTGTCCTGCGTACCGCCTGGGGAACAGAGCCCGATCTAAGTACAGCCCGAGC
-CCGAGATCAAACATTCCATCAAAAAATGGCAAGTTATGGGGATCCGCCCGGCTCACCAGTGGAGGCGCTTCAACCAGTTC
-CACCCCCGTGACGTCCTCCACGCCCAGTTCCTGCAGCGCTTGGACGGCATGGCCTGGCCCGGCGGACGAAACTAGGACCC
-GAGAGTCGTTCGTAATGCAGTTTTGGGCC
->contig_107
-TTTGGCCTTTACCTTGAACGAATTTCTGCTCGCCAAAGTCGTCTCTTTGTCGATCGCAGATCGCGGGTTGCAGCTCCAGC
-GCAGGCCGAAGTTCGGGGACGACGGAAGCTTCGATTTCCTACTGCACCAGGTCGCAGTCGGGCCCAGTCGCAGATCGCCC
-TGCATCGCCGCCACATGACCGATCTGGAAACCACTGCATGTTTGACTTATGATTTTGGTGCTCGATTTGCGGGTGTTTGT
-GCGAGCGTGAGTTATATGTTAAGAAAATCTTGTAGAAGTGGATCGAGAATTAGAGAGAGGGAGGGGCAAGAAGATGCAGA
-G
->contig_11
-ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGG
-CGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCC
-AAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCAT
-GATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCC
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcripts.cleaned.nr.cds	Fri Apr 07 08:34:58 2017 -0400
@@ -0,0 +1,6 @@
+>contig_1
+AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT
+GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA
+CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT
+ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG
+TCATGTTGTACACATGGTTAAT
--- a/test-data/transcripts.cleaned.nr.pep	Tue Mar 21 10:42:51 2017 -0400
+++ b/test-data/transcripts.cleaned.nr.pep	Fri Apr 07 08:34:58 2017 -0400
@@ -1,25 +1,3 @@
 >contig_1
 KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA
 TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN
->contig_100
-CKLQEISSTLITILVILSPDKLIFFASTNRDSLNNVTISSTSSTPHSSTVTTQTPPLLTVLSICPAYRLGNRARSKYSPS
-PRSNIPSKNGKLWGSARLTSGGASTSSTPVTSSTPSSCSAWTAWPGPADETRTRESFVMQFWA
->contig_107
-FGLYLERISARQSRLFVDRRSRVAAPAQAEVRGRRKLRFPTAPGRSRAQSQIALHRRHMTDLETTACLTYDFGARFAGVC
-ASVSYMLRKSCRSGSRIREREGQEDAE
->contig_11
-AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGD
-FGTTPTSGAAVGELGVNPTX
->contig_111
-MGNCCSDVSGGQSAVGGTTSSSAGNDAVDAFIRSRGYNGLFSQIELSLSAANLRDRDVLSKSDPMAVLYMKGSDGLLQEL
-GRTEVVLNSLSPKWIIKYTVTYQFEMVQNLVFRVYDVDTQFHNMDVKALKLEDQQFLGEASCTLSQIVTKPNRILTLDLG
-HEEGSFPAHTRKFGQLMVYAEESVASKTTAELIL
->contig_115
-DTDVPAGDIGVGGREIGYLFGAYRAERNRWEGVLTGKGSSWGGSLIRPEATGYGLVYYVEHMINYASGGKESFAGKRVAL
-SGSGNVAQYAALKLIELGATVISLSDSKGSLIAEDDKGFTPEIINQ
->contig_116
-HKTNEDSGAIEAVLVNTNQFYKWFTDLEAAMKSETEEKYQHYVRTLTERIQTCDTILYQVDETLELFNELQLQHQAVATK
-TKTLHDACDRLLLEKQRLFEFADSLRAKLNYFDELENVATSFHS
->contig_117
-EMLAGTSTRPRTFKKEEADRTALAGMPQSPPHRKAYSYSGQLTNTVGHLKRQQNHPRNHSLDEINLLTEGTVNSSGEDDF
-YRYCNTTSGGVTNNLVDYHNMSQRMEGMEIGGGCCSEERR
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/transcripts.cleaned.pep	Fri Apr 07 08:34:58 2017 -0400
@@ -0,0 +1,3 @@
+>contig_1
+KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA
+TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN
--- a/test-data/transcripts.cleaned.pep1	Tue Mar 21 10:42:51 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
->contig_1
-KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA
-TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN
->contig_100
-CKLQEISSTLITILVILSPDKLIFFASTNRDSLNNVTISSTSSTPHSSTVTTQTPPLLTVLSICPAYRLGNRARSKYSPS
-PRSNIPSKNGKLWGSARLTSGGASTSSTPVTSSTPSSCSAWTAWPGPADETRTRESFVMQFWA
->contig_107
-FGLYLERISARQSRLFVDRRSRVAAPAQAEVRGRRKLRFPTAPGRSRAQSQIALHRRHMTDLETTACLTYDFGARFAGVC
-ASVSYMLRKSCRSGSRIREREGQEDAE
->contig_11
-AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGD
-FGTTPTSGAAVGELGVNPTX
->contig_111
-MGNCCSDVSGGQSAVGGTTSSSAGNDAVDAFIRSRGYNGLFSQIELSLSAANLRDRDVLSKSDPMAVLYMKGSDGLLQEL
-GRTEVVLNSLSPKWIIKYTVTYQFEMVQNLVFRVYDVDTQFHNMDVKALKLEDQQFLGEASCTLSQIVTKPNRILTLDLG
-HEEGSFPAHTRKFGQLMVYAEESVASKTTAELIL
->contig_115
-DTDVPAGDIGVGGREIGYLFGAYRAERNRWEGVLTGKGSSWGGSLIRPEATGYGLVYYVEHMINYASGGKESFAGKRVAL
-SGSGNVAQYAALKLIELGATVISLSDSKGSLIAEDDKGFTPEIINQ
->contig_116
-HKTNEDSGAIEAVLVNTNQFYKWFTDLEAAMKSETEEKYQHYVRTLTERIQTCDTILYQVDETLELFNELQLQHQAVATK
-TKTLHDACDRLLLEKQRLFEFADSLRAKLNYFDELENVATSFHS
->contig_117
-STLLRAAAAPDLHPLHPLAHIMIIHEVIGNAAAGRVTVTIKIIFAGGIDGAFGEEVDLVEAVVARVVLLPLEVSDGVGKL
-SAVGIGFPMRRRLGHPRQGCSVCFFLLKGARTSGGTSQHL
--- a/test-data/transcripts.cleaned.pep2	Tue Mar 21 10:42:51 2017 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
->contig_1
-KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA
-TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN
->contig_100
-CKLQEISSTLITILVILSPDKLIFFASTNRDSLNNVTISSTSSTPHSSTVTTQTPPLLTVLSICPAYRLGNRARSKYSPS
-PRSNIPSKNGKLWGSARLTSGGASTSSTPVTSSTPSSCSAWTAWPGPADETRTRESFVMQFWA
->contig_107
-FGLYLERISARQSRLFVDRRSRVAAPAQAEVRGRRKLRFPTAPGRSRAQSQIALHRRHMTDLETTACLTYDFGARFAGVC
-ASVSYMLRKSCRSGSRIREREGQEDAE
->contig_11
-AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGD
-FGTTPTSGAAVGELGVNPTX
->contig_111
-MGNCCSDVSGGQSAVGGTTSSSAGNDAVDAFIRSRGYNGLFSQIELSLSAANLRDRDVLSKSDPMAVLYMKGSDGLLQEL
-GRTEVVLNSLSPKWIIKYTVTYQFEMVQNLVFRVYDVDTQFHNMDVKALKLEDQQFLGEASCTLSQIVTKPNRILTLDLG
-HEEGSFPAHTRKFGQLMVYAEESVASKTTAELIL
->contig_115
-DTDVPAGDIGVGGREIGYLFGAYRAERNRWEGVLTGKGSSWGGSLIRPEATGYGLVYYVEHMINYASGGKESFAGKRVAL
-SGSGNVAQYAALKLIELGATVISLSDSKGSLIAEDDKGFTPEIINQ
->contig_116
-HKTNEDSGAIEAVLVNTNQFYKWFTDLEAAMKSETEEKYQHYVRTLTERIQTCDTILYQVDETLELFNELQLQHQAVATK
-TKTLHDACDRLLLEKQRLFEFADSLRAKLNYFDELENVATSFHS
->contig_117
-EMLAGTSTRPRTFKKEEADRTALAGMPQSPPHRKAYSYSGQLTNTVGHLKRQQNHPRNHSLDEINLLTEGTVNSSGEDDF
-YRYCNTTSGGVTNNLVDYHNMSQRMEGMEIGGGCCSEERR
--- a/test-data/transcripts.pep	Tue Mar 21 10:42:51 2017 -0400
+++ b/test-data/transcripts.pep	Fri Apr 07 08:34:58 2017 -0400
@@ -1,24 +1,2 @@
->contig_1|m.1 contig_1|g.1 type:internal len:115 gc:universal contig_1:344-3(-)
+>Gene.1::contig_1::g.1::m.1 type:internal len:115 gc:universal contig_1:344-3(-)
 KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN
->contig_2|m.2 contig_2|g.2 type:5prime_partial len:170 gc:universal contig_2:2-511(+)
-LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD*
->contig_3|m.3 contig_3|g.3 type:5prime_partial len:126 gc:universal contig_3:463-86(-)
-VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN*
->contig_9|m.4 contig_9|g.4 type:internal len:132 gc:universal contig_9:2-394(+)
-LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV
->contig_11|m.5 contig_11|g.5 type:5prime_partial len:108 gc:universal contig_11:2-325(+)
-IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLHDIPSELLRISRCCCCSRCCSRNSRCGY*
->contig_11|m.6 contig_11|g.6 type:5prime_partial len:100 gc:universal contig_11:443-144(-)
-AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGDFGTTPTSGAAVGELGVNPT*
->contig_18|m.7 contig_18|g.7 type:internal len:143 gc:universal contig_18:426-1(-)
-TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMVEKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT
->contig_20|m.8 contig_20|g.8 type:internal len:104 gc:universal contig_20:1-309(+)
-GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGHLHWFRHSYPLHVGLVSLDQLLGS
->contig_20|m.9 contig_20|g.9 type:internal len:103 gc:universal contig_20:2-307(+)
-AYASMLTDMPYKIGNAICFNLILYFMTNLRREPGAFFFFLLISFTLTLVMSMLFRTIGSVSRTLSQAMAPAAILILALVIYTGFVIPTRYMLGWSRWINYLD
->contig_20|m.10 contig_20|g.10 type:internal len:103 gc:universal contig_20:307-2(-)
-IQVVDPTRPAQHVAGRNDETSVNDQRKDKDSCGSHGLRQCTRNGSNSAEEHRHDKRQRERYQQEEEECSWFAAKVRHEVQDQVETDRVANLVGHIREHRCVS
->contig_21|m.11 contig_21|g.11 type:5prime_partial len:168 gc:universal contig_21:519-16(-)
-VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLKNAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVGTQRLAFE*
->contig_24|m.12 contig_24|g.12 type:internal len:111 gc:universal contig_24:331-2(-)
-KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKEIEELTQKLASEGQKLQSQISSIMEENNLLN