# HG changeset patch
# User greg
# Date 1491568498 14400
# Node ID cc4dba9f6ecd3b994d43033cd8644c23976586d2
# Parent  2553e8e46fab7d1e62caa6c001fa53b5bc068736
Uploaded

diff -r 2553e8e46fab -r cc4dba9f6ecd .shed.yml
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd assembly_post_processor.xml
--- 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},
diff -r 2553e8e46fab -r cc4dba9f6ecd macros.xml
--- /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>
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/assembly.fasta
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cds
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cleaned.cds
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cleaned.nr.cds
--- /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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cleaned.nr.pep
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cleaned.pep
--- /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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cleaned.pep1
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.cleaned.pep2
--- 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
diff -r 2553e8e46fab -r cc4dba9f6ecd test-data/transcripts.pep
--- 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