| Previous changeset 9:9c72c91d291f (2019-01-10) Next changeset 11:2c2ad8af0a4e (2024-06-12) |
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Commit message:
"planemo upload for repository https://github.com/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor commit 71ba0e157346927bf42b788f552b95a71556b28a" |
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modified:
assembly_post_processor.xml test-data/target_orthos.ids test-data/transcripts.cds test-data/transcripts.pep test-data/transcripts_tgf.cds test-data/transcripts_tgf.pep tool_data_table_conf.xml.test |
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added:
test-data/plant_tribes_scaffolds.loc tool-data/plant_tribes_scaffolds.loc.sample |
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removed:
.shed.yml plant_tribes_scaffolds.loc test-data/arabidopsis_thaliana.smat test-data/tool-data/plant_tribes/scaffolds/README.txt test-data/transcripts2.cds test-data/transcripts2.pep |
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| diff -r 9c72c91d291f -r 4d73965d99a2 .shed.yml --- a/.shed.yml Thu Jan 10 10:45:23 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,15 +0,0 @@ -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. -homepage_url: https://github.com/dePamphilis/PlantTribes -long_description: | - Contains a tool that is one of the PlantTribes collection of automated modular analysis pipelines that - 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/gregvonkuster/galaxy_tools/tree/master/tools/phylogenetics/plant_tribes/assembly_post_processor -type: unrestricted -categories: -- Phylogenetics |
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| diff -r 9c72c91d291f -r 4d73965d99a2 assembly_post_processor.xml --- a/assembly_post_processor.xml Thu Jan 10 10:45:23 2019 -0500 +++ b/assembly_post_processor.xml Wed Jun 09 20:26:55 2021 +0000 |
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| @@ -11,10 +11,7 @@ #set output_dir = 'assemblyPostProcessing_dir' AssemblyPostProcessor --transcripts '$input' ---prediction_method $prediction_method_cond.prediction_method -#if str($prediction_method_cond.prediction_method) == 'estscan': - --score_matrices '$score_matrices' -#end if +--prediction_method 'transdecoder' #if str($options_type.options_type_selector) == 'advanced': #set target_gene_family_assembly_cond = $options_type.target_gene_family_assembly_cond #if str($target_gene_family_assembly_cond.target_gene_family_assembly) == 'yes': @@ -68,16 +65,6 @@ fi]]></command> <inputs> <param name="input" format="fasta" type="data" label="Transcriptome assembly fasta file"/> - <conditional name="prediction_method_cond"> - <param name="prediction_method" type="select" label="Coding regions prediction method"> - <option value="transdecoder" selected="true">TransDecoder</option> - <option value="estscan">ESTScan</option> - </param> - <when value="transdecoder" /> - <when value="estscan"> - <param name="score_matrices" format="smat" type="data" label="Scores matrices"/> - </when> - </conditional> <conditional name="options_type"> <param name="options_type_selector" type="select" label="Options configuration"> <option value="basic" selected="true">Basic</option> @@ -133,32 +120,16 @@ <tests> <test> <param name="input" value="assembly.fasta" ftype="fasta"/> - <param name="prediction_method" value="transdecoder"/> <output name="output_cds" file="transcripts.cds" ftype="fasta"/> <output name="output_cleaned_cds" file="transcripts.cleaned.cds" ftype="fasta"/> <output name="output_cleaned_pep" file="transcripts.cleaned.pep" ftype="fasta"/> <output name="output_pep" file="transcripts.pep" ftype="fasta"/> </test> <test> - <param name="input" value="assembly.fasta" ftype="fasta"/> - <param name="prediction_method" value="estscan"/> - <param name="score_matrices" value="arabidopsis_thaliana.smat" ftype="smat"/> - <param name="options_type_selector" value="advanced"/> - <param name="dereplicate" value="yes"/> - <output name="output_cds" file="transcripts2.cds" ftype="fasta"/> - <output name="output_cleaned_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> - <output name="output_cleaned_nr_cds" file="transcripts.cleaned.nr.cds" ftype="fasta"/> - <output name="output_cleaned_nr_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> - <output name="output_cleaned_pep" file="transcripts.cleaned.nr.pep" ftype="fasta"/> - <output name="output_pep" file="transcripts2.pep" ftype="fasta"/> - </test> - <test> <param name="input" value="assembly_tgf.fasta" ftype="fasta"/> - <param name="prediction_method" value="transdecoder"/> <param name="options_type_selector" value="advanced"/> <param name="target_gene_family_assembly" value="yes"/> <param name="orthogroups" value="target_orthos.ids"/> - <param name="scaffold" value="22Gv1.1"/> <param name="method" value="orthomcl"/> <param name="dereplicate" value="yes"/> <output_collection name="output_targeted_gene_families" type="list"> @@ -186,7 +157,6 @@ * **Transcriptome assembly fasta file** - either de novo or reference-guided transcriptome assembly fasta file selected from your history. * **Coding regions prediction method** - method for finding coding regions within transcripts. Available methods are TransDecoder[3] and ESTScan[4]. - * **Scores matrices** - scores matrices, based on a related species, are required when ESTScan is used to find coding regions. Details of how to create species-specific scores matrices can be found on the ESTScan website (http://estscan.sourceforge.net). Matrices of some organisms are also available to download. **Other options** @@ -226,16 +196,6 @@ pages = {1494-1512},} </citation> <citation type="bibtex"> - @article{Iseli1999, - journal = {ISMB}, - author = {4. Iseli C, Jongeneel CV, Bucher P}, - title = {ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences}, - year = {1999}, - volume = {99}, - pages = {138-148}, - url = {http://estscan.sourceforge.net},} - </citation> - <citation type="bibtex"> @article{Huang1999, journal = {Genome Research}, author = {5. Huang X, Madan A}, |
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| diff -r 9c72c91d291f -r 4d73965d99a2 plant_tribes_scaffolds.loc --- a/plant_tribes_scaffolds.loc Thu Jan 10 10:45:23 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -## Plant Tribes scaffolds -#Value Name Path Description -22Gv1.1 22Gv1.1 ${__HERE__}/test-data/tool-data/plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1) |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/arabidopsis_thaliana.smat --- a/test-data/arabidopsis_thaliana.smat Thu Jan 10 10:45:23 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,8248 +0,0 @@\n-FORMAT: at.conf CODING REGION 6 3 1 s C+G: 0 42\n--2 1 4 -3 \n-1 1 0 -2 \n-1 0 2 -4 \n--3 1 4 -4 \n-1 -1 2 -3 \n-1 0 2 -4 \n-1 0 1 -2 \n--3 2 3 -2 \n-0 -1 3 -3 \n-1 -1 -2 0 \n-2 0 0 -3 \n--2 -1 3 -1 \n--1 0 2 -1 \n-1 0 1 -2 \n-0 -1 4 -4 \n--3 2 4 -3 \n--1 1 3 -4 \n-2 0 -1 -1 \n-2 1 -1 -2 \n--3 2 3 -2 \n-1 -1 2 -3 \n-2 -4 2 -3 \n-1 -2 4 -4 \n--2 1 3 -2 \n-0 -1 3 -3 \n-1 1 -1 -2 \n-2 0 -2 -1 \n--3 1 3 -1 \n-0 0 3 -3 \n-1 -1 0 -1 \n-2 -1 1 -4 \n--3 2 4 -4 \n--1 -1 5 -5 \n-2 -2 1 -2 \n-2 0 0 -3 \n--3 0 4 -2 \n-1 -2 3 -3 \n-3 -4 1 -3 \n-1 -3 2 -2 \n--2 1 3 -2 \n-1 -3 3 -3 \n-1 -1 0 -1 \n-3 -2 -2 -2 \n--3 0 3 -1 \n-0 -1 3 -3 \n-2 -1 0 -1 \n-2 -3 2 -3 \n--2 1 4 -2 \n-1 -1 1 -2 \n-2 -1 0 -2 \n-2 2 -3 -2 \n--3 1 4 -3 \n-1 -2 2 -2 \n-2 -2 2 -3 \n-2 -2 1 -3 \n--3 2 3 -2 \n-1 -4 1 1 \n-2 -1 -1 -1 \n-1 -1 2 -2 \n--3 0 4 -1 \n--2 1 3 -3 \n-1 -1 0 -1 \n-0 0 3 -4 \n--3 1 4 -4 \n--1 -1 4 -4 \n-3 -2 -1 -3 \n-2 -1 1 -3 \n--2 1 4 -4 \n-1 -2 2 -2 \n-3 -6 2 -4 \n-1 -2 2 -2 \n--2 1 3 -1 \n-0 -3 4 -3 \n-2 -1 -1 0 \n-2 -1 0 -2 \n--1 -1 3 -1 \n-0 -1 2 -1 \n-2 -1 0 -2 \n-1 -2 3 -2 \n--3 1 4 -3 \n-1 0 3 -4 \n-2 2 -1 -3 \n-2 1 -2 -3 \n--3 2 3 -2 \n-2 -1 -1 -2 \n-3 -5 1 -2 \n-2 -3 2 -3 \n-0 0 2 -1 \n-0 -2 3 -2 \n-1 0 1 -2 \n-2 -2 -2 0 \n--2 1 3 -2 \n-2 -1 2 -4 \n-2 -1 0 -1 \n-2 -1 1 -4 \n--2 2 3 -3 \n--1 -2 5 -4 \n-1 -2 3 -4 \n-2 -1 1 -3 \n--2 -1 4 -3 \n-1 -3 3 -3 \n-2 -7 3 -3 \n-1 -2 2 -2 \n--2 0 3 -1 \n-1 -3 3 -2 \n-0 -1 3 -2 \n-3 -2 -2 0 \n--3 -1 4 -1 \n-0 -1 3 -2 \n-1 -2 2 -2 \n-2 -3 3 -4 \n--3 0 4 -2 \n-0 2 0 -2 \n-2 -2 0 -2 \n-2 -2 -2 0 \n--2 0 4 -3 \n-1 -2 2 -2 \n-3 -4 0 -2 \n-1 -2 2 -3 \n--3 1 3 -1 \n--1 -2 0 2 \n-3 -2 -1 -2 \n-2 -1 1 -3 \n--2 -1 4 -1 \n-0 0 2 -2 \n-2 -1 -3 0 \n-1 -1 2 -2 \n--3 0 5 -3 \n--1 1 3 -4 \n-2 0 -1 -2 \n-3 1 -1 -4 \n--3 3 3 -3 \n-1 -1 1 -2 \n-3 -3 1 -4 \n-2 -2 1 -4 \n--2 1 2'..b' -3 -1 \n--1 1 -1 1 \n-1 0 -4 1 \n-1 -1 -4 2 \n--1 1 0 0 \n--4 2 -3 3 \n-0 -2 0 1 \n-1 0 -4 1 \n-0 1 -2 1 \n--3 0 -1 3 \n-0 1 -2 1 \n--1 -1 -4 3 \n--1 2 -1 0 \n--4 2 -1 2 \n-1 -1 0 0 \n-1 1 -3 1 \n-2 -1 -1 -1 \n--3 1 -2 3 \n-2 -2 -1 0 \n-1 -2 -1 1 \n-1 -3 2 0 \n--3 1 -1 3 \n-2 -4 -1 1 \n--1 0 -4 3 \n-2 -4 -1 1 \n--4 -1 -2 4 \n-2 -2 -1 1 \n-0 -1 -3 2 \n-1 -4 1 1 \n--3 -1 -1 3 \n-1 -1 -3 1 \n-2 -1 -5 1 \n-1 0 -4 1 \n-0 0 -1 1 \n-1 0 -3 1 \n-1 -1 -3 1 \n-1 -2 -1 2 \n--4 2 -1 2 \n-1 -2 -1 1 \n-1 -1 -5 2 \n-1 -2 -2 2 \n--1 -3 1 2 \n-0 0 -2 2 \n-0 -1 -5 3 \n--1 -2 -2 3 \n--3 0 0 2 \n-2 -1 -1 -1 \n-1 1 -3 1 \n-2 -1 -2 0 \n--1 0 -1 2 \n-1 -1 -2 1 \n-2 -2 -2 1 \n-1 -1 -1 1 \n--2 1 -2 3 \n-0 -3 0 1 \n--1 0 -6 3 \n-0 -3 2 0 \n--2 -2 0 3 \n-1 -2 -3 2 \n-1 -2 -4 3 \n-0 -3 -2 3 \n--1 -2 -1 2 \n-1 -1 -1 0 \n-1 1 -4 1 \n-2 -1 -2 0 \n--2 2 -2 1 \n-1 0 -2 1 \n-1 0 -3 1 \n-1 -3 1 0 \n--5 3 -4 2 \n-1 -3 -1 2 \n--1 2 -4 2 \n-1 -2 -2 2 \n--3 2 -2 2 \n-0 0 -2 2 \n--2 0 -5 4 \n-0 -1 -1 2 \n--5 4 -2 1 \n-1 -3 1 0 \n-0 0 -3 2 \n-2 -1 -1 0 \n--3 0 0 2 \n-1 -4 1 1 \n-1 -2 -2 2 \n-0 -4 0 2 \n--3 0 -1 3 \n-1 -4 0 1 \n--1 -1 -4 3 \n-1 -3 -1 1 \n--3 -1 0 3 \n-1 -2 -2 2 \n--1 -2 -3 3 \n-0 -4 -1 3 \n--3 -1 1 3 \n-1 -2 -1 1 \n-1 -1 -5 2 \n-0 -1 -1 1 \n--2 0 -1 2 \n-0 -1 -1 1 \n-0 0 -3 2 \n-1 -2 -2 2 \n--5 2 -3 3 \n-0 -3 -1 2 \n-0 -1 -5 3 \n-0 -3 -1 3 \n--1 -3 -1 3 \n-0 -1 -1 2 \n--1 -1 -5 3 \n--1 -3 0 2 \n--4 -1 -1 3 \n-FORMAT: at.conf START PROFILE 1 12 7 s C+G: 42 100\n-2 -3 0 0 \n-1 4 -4 -2 \n-6 -4 -1 -6 \n-8 -9 1 -9 \n-5 6 -14 -6 \n-6 -1 0 -11 \n-18 -100 -100 -100 \n--38 -38 -39 18 \n--49 -46 21 -44 \n--3 -13 12 -10 \n-1 9 -4 -8 \n--4 -7 6 2 \n-FORMAT: at.conf STOP PROFILE 1 12 6 s C+G: 42 100\n-0 0 2 -2 \n-1 1 -3 1 \n--4 2 -1 3 \n--59 -62 -50 18 \n-10 -66 10 -68 \n-15 -64 -2 -70 \n-4 -8 -1 1 \n-2 -2 -2 0 \n-3 -1 -4 0 \n-2 -2 -3 1 \n-2 -3 -3 2 \n-2 -2 -3 2 \n' |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/plant_tribes_scaffolds.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/plant_tribes_scaffolds.loc Wed Jun 09 20:26:55 2021 +0000 |
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| @@ -0,0 +1,3 @@ +## Plant Tribes scaffolds +#Value Name Path Description +22Gv1.1 22Gv1.1 ${__HERE__}/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1) |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/target_orthos.ids --- a/test-data/target_orthos.ids Thu Jan 10 10:45:23 2019 -0500 +++ b/test-data/target_orthos.ids Wed Jun 09 20:26:55 2021 +0000 |
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| @@ -1,5 +1,3 @@ -213 9300 -752 4632 4732 |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/tool-data/plant_tribes/scaffolds/README.txt --- a/test-data/tool-data/plant_tribes/scaffolds/README.txt Thu Jan 10 10:45:23 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,3 +0,0 @@ -For functional tests to work, this directory must contain symlinks to the scaffolds data -installed into the Galaxy instance to which planemo points via the --galaxy_root parameter. -This would typically be something like ~/galaxy/tool-data/plant_tribes/scaffolds/22Gv1.1. |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/transcripts.cds --- a/test-data/transcripts.cds Thu Jan 10 10:45:23 2019 -0500 +++ b/test-data/transcripts.cds Wed Jun 09 20:26:55 2021 +0000 |
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| @@ -1,8 +1,8 @@ ->Gene.1::contig_1::g.1::m.1 type:internal len:115 contig_1:344-3(-) +>contig_1.p1 type:internal len:115 contig_1:344-3(-) AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAAT ->Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 contig_2:2-511(+) +>contig_2.p1 type:5prime_partial len:170 contig_2:2-511(+) CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA ->Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 contig_3:463-86(-) +>contig_3.p1 type:5prime_partial len:126 contig_3:463-86(-) GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAACTAG ->Gene.4::contig_9::g.4::m.4 type:internal len:132 contig_9:2-394(+) +>contig_9.p1 type:internal len:132 contig_9:2-394(+) CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/transcripts.pep --- a/test-data/transcripts.pep Thu Jan 10 10:45:23 2019 -0500 +++ b/test-data/transcripts.pep Wed Jun 09 20:26:55 2021 +0000 |
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| @@ -1,8 +1,8 @@ ->Gene.1::contig_1::g.1::m.1 type:internal len:115 gc:universal contig_1:344-3(-) +>contig_1.p1 type:internal len:115 gc:universal contig_1:344-3(-) KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN ->Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 gc:universal contig_2:2-511(+) +>contig_2.p1 type:5prime_partial len:170 gc:universal contig_2:2-511(+) LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD* ->Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 gc:universal contig_3:463-86(-) +>contig_3.p1 type:5prime_partial len:126 gc:universal contig_3:463-86(-) VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN* ->Gene.4::contig_9::g.4::m.4 type:internal len:132 gc:universal contig_9:2-394(+) +>contig_9.p1 type:internal len:132 gc:universal contig_9:2-394(+) LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV |
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| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/transcripts2.cds --- a/test-data/transcripts2.cds Thu Jan 10 10:45:23 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,54 +0,0 @@ ->contig_1; 91 1 346 minus strand -XTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTAC -ACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGAT -GCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGT -CTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA -GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAA -CAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAATCGX ->contig_2 218 1 511 -XXCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCC -CCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATC -ATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGG -CCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA -TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTT -CCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGT -ACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCT -TGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA -CAACTGTTAAATTATGTGCGCTTTGATGATTAA ->contig_3; 134 1 379 minus strand -XXTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCT -GAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCAT -TCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATG -GATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC -ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAAC -CATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCA -CCATTTTCACAGATCAACTAG ->contig_5; -67 1 418 minus strand -XXCGGTGGTCCGCCACAAACACACGTCAAGCGGGATCCCGCATCCCGCGGGCTCTTCCAC -GCGGTCGTCCCGGCGCTCGGCCCTCTCCGTGACGCACGTCGAGAGGGACGATTTGGCCGA -TGCCGCGTGATGCCAGGCCCCGACATCATgCAAGGAGCACTCCGTTGTGCCGACCCTCGC -CTTCGATGACGTCCTCGGGCGTCTAGCGAAGTATCGAAGAAGGGCGAGCTAAGGAGCCAT -GAATCCTGGAGATGCGAGCCAGGTCACGAGAGGCGCGGCAGGCGAGTCTTTGCTCGCTCT -CGCACCGTCTGCTCTCGTGCTTGGAGAAGAAGGACCGACTGCTGACGTCGAACCGGATGA -TGGAAGGTTCGAACAAGTCAGATCTGGAAAGGGGTAGCATGGAAAAGGCGACACTCTCAC -X ->contig_7 103 1 296 -GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAAT -AAATCCAATGAAAACGGAACCGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATG -TTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCATCATCCAATGAAACATGTAGC -AACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGcG -AAACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGXX ->contig_9 34 1 396 -XXACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATT -TTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGC -CCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGT -AGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA -ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATT -AAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAG -GCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAX ->contig_10; 78 87 343 minus strand -ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAAC -TCAAGCGACGATAGCGAACCTTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAA -GATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCCGCCACAGAAATCATAGGTGG -CGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA -ATCGGCGGCAATGCCCCX |
| b |
| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/transcripts2.pep --- a/test-data/transcripts2.pep Thu Jan 10 10:45:23 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ ->contig_1; 91 1 346 minus strand; translated -XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCS -LRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR ->contig_2 218 1 511 ; translated -XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMG -PDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAG -TTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD ->contig_3; 134 1 379 minus strand; translated -XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYM -DYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRA -PFSQIN ->contig_5; -67 1 418 minus strand; translated -XGGPPQTHVKRDPASRGLFHAVVPALGPLRDARREGRFGRCRVMPGPDIIKEHSVVPTLA -FDDVLGRLAKYRRRASXGAMNPGDASQVTRGAAGESLLALAPSALVLGEEGPTADVEPDD -GRFEQVRSGKGXHGKGDTLT ->contig_7 103 1 296 ; translated -ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCS -NSNKRNSIESSSANFRPENGNESGEISGKKNTRKGKGDX ->contig_9 34 1 396 ; translated -XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEG -RIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDE -APMTQYFVFEAVX ->contig_10; 78 87 343 minus strand; translated -MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRW -RSLWRQIPIPPDTRNLALELIGGNAP |
| b |
| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/transcripts_tgf.cds --- a/test-data/transcripts_tgf.cds Thu Jan 10 10:45:23 2019 -0500 +++ b/test-data/transcripts_tgf.cds Wed Jun 09 20:26:55 2021 +0000 |
| b |
| b'@@ -1,34 +1,34 @@\n->Gene.1::contig_1::g.1::m.1 type:internal len:115 contig_1:344-3(-)\n+>contig_1.p1 type:internal len:115 contig_1:344-3(-)\n AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGGTCATGTTGTACACATGGTTAAT\n->Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 contig_2:2-511(+)\n+>contig_2.p1 type:5prime_partial len:170 contig_2:2-511(+)\n CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA\n->Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 contig_3:463-86(-)\n+>contig_3.p1 type:5prime_partial len:126 contig_3:463-86(-)\n GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAACTAG\n->Gene.4::contig_9::g.4::m.4 type:internal len:132 contig_9:2-394(+)\n+>contig_9.p1 type:internal len:132 contig_9:2-394(+)\n CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT\n->Gene.5::contig_11::g.5::m.5 type:5prime_partial len:108 contig_11:2-325(+)\n+>contig_11.p1 type:5prime_partial len:108 contig_11:2-325(+)\n ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGGCGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCCAAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCATGATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTATTGA\n->Gene.6::contig_11::g.6::m.6 type:5prime_partial len:100 contig_11:443-144(-)\n+>contig_11.p2 type:5prime_partial len:100 contig_11:443-144(-)\n GCTGCTAAAGTCACGGTTGCTCCCGGATCTCGCGTCGCTGCTGCTGGAAGCGGCGTTGCCTCAGAATCTCCGGCGACTGCTGAAGCCGGCGTTGCCCCAGGATCTCCCGCGGTCGACTTCAATAGCCACAGCGGGAGTTTCTGGAGCAACACCGACTGCAGCAGCAACAACGGGAGATTCGGAGCAACTCCGACGGGATATCATGGAGCAACCCCGACTTCAACAGTGGCGACGGGAGATTTTGGAACAACGCCGACTTCAGGAGCCGCGGTGGGAGAGCTTGGAGTAAATCCGACTTAA\n->Gene.7::contig_18::g.7::m.7 type:internal len:143 contig_18:426-1(-)\n+>contig_18.p1 type:internal len:143 contig_18:426-1(-)\n ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAAAATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGTACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTGGAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTTGCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGCTTTGGTTGGCATTGGATGAGGTTACC\n->Gene.8::contig_20::g.8::m.8 type:internal len:104 contig_20:1-309(+)\n+>contig_20.p1 type:internal len:104 contig_20:1-309(+)\n GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCA'..b'ATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAAACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAAATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAATTTACTTAAC\n->Gene.13::contig_29::g.13::m.13 type:3prime_partial len:267 contig_29:52-849(+)\n+>contig_29.p1 type:3prime_partial len:267 contig_29:52-849(+)\n ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCTGAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCACAGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCATATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGACCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGCAATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTGGTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGTTAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGAAGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCATAGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG\n->Gene.14::contig_30::g.14::m.14 type:internal len:160 contig_30:1-477(+)\n+>contig_30.p1 type:internal len:160 contig_30:1-477(+)\n AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTTATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGTCTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAAGTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGCTACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTGGTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT\n->Gene.15::contig_31::g.15::m.15 type:3prime_partial len:263 contig_31:787-2(-)\n+>contig_31.p1 type:3prime_partial len:263 contig_31:787-2(-)\n ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAGAACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCTCTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAATGAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAAGAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTGAAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTGGATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAAATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCAGTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAGAAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG\n->Gene.16::contig_33::g.16::m.16 type:internal len:206 contig_33:615-1(-)\n+>contig_33.p1 type:internal len:206 contig_33:615-1(-)\n GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGTTCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTGAAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCACGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAAAAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGATGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAGCGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGTCGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA\n->Gene.17::contig_35::g.17::m.17 type:internal len:131 contig_35:2-391(+)\n+>contig_35.p1 type:internal len:131 contig_35:2-391(+)\n ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAGGAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTGACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAGGAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGACAGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA\n' |
| b |
| diff -r 9c72c91d291f -r 4d73965d99a2 test-data/transcripts_tgf.pep --- a/test-data/transcripts_tgf.pep Thu Jan 10 10:45:23 2019 -0500 +++ b/test-data/transcripts_tgf.pep Wed Jun 09 20:26:55 2021 +0000 |
| b |
| @@ -1,34 +1,34 @@ ->Gene.1::contig_1::g.1::m.1 type:internal len:115 gc:universal contig_1:344-3(-) +>contig_1.p1 type:internal len:115 gc:universal contig_1:344-3(-) KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN ->Gene.2::contig_2::g.2::m.2 type:5prime_partial len:170 gc:universal contig_2:2-511(+) +>contig_2.p1 type:5prime_partial len:170 gc:universal contig_2:2-511(+) LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD* ->Gene.3::contig_3::g.3::m.3 type:5prime_partial len:126 gc:universal contig_3:463-86(-) +>contig_3.p1 type:5prime_partial len:126 gc:universal contig_3:463-86(-) VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGTIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN* ->Gene.4::contig_9::g.4::m.4 type:internal len:132 gc:universal contig_9:2-394(+) +>contig_9.p1 type:internal len:132 gc:universal contig_9:2-394(+) LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV ->Gene.5::contig_11::g.5::m.5 type:5prime_partial len:108 gc:universal contig_11:2-325(+) +>contig_11.p1 type:5prime_partial len:108 gc:universal contig_11:2-325(+) IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLHDIPSELLRISRCCCCSRCCSRNSRCGY* ->Gene.6::contig_11::g.6::m.6 type:5prime_partial len:100 gc:universal contig_11:443-144(-) +>contig_11.p2 type:5prime_partial len:100 gc:universal contig_11:443-144(-) AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGDFGTTPTSGAAVGELGVNPT* ->Gene.7::contig_18::g.7::m.7 type:internal len:143 gc:universal contig_18:426-1(-) +>contig_18.p1 type:internal len:143 gc:universal contig_18:426-1(-) TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMVEKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT ->Gene.8::contig_20::g.8::m.8 type:internal len:104 gc:universal contig_20:1-309(+) +>contig_20.p1 type:internal len:104 gc:universal contig_20:1-309(+) GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGHLHWFRHSYPLHVGLVSLDQLLGS ->Gene.9::contig_20::g.9::m.9 type:internal len:103 gc:universal contig_20:2-307(+) +>contig_20.p2 type:internal len:103 gc:universal contig_20:2-307(+) AYASMLTDMPYKIGNAICFNLILYFMTNLRREPGAFFFFLLISFTLTLVMSMLFRTIGSVSRTLSQAMAPAAILILALVIYTGFVIPTRYMLGWSRWINYLD ->Gene.10::contig_20::g.10::m.10 type:internal len:103 gc:universal contig_20:307-2(-) +>contig_20.p3 type:internal len:103 gc:universal contig_20:307-2(-) IQVVDPTRPAQHVAGRNDETSVNDQRKDKDSCGSHGLRQCTRNGSNSAEEHRHDKRQRERYQQEEEECSWFAAKVRHEVQDQVETDRVANLVGHIREHRCVS ->Gene.11::contig_21::g.11::m.11 type:5prime_partial len:168 gc:universal contig_21:519-16(-) +>contig_21.p1 type:5prime_partial len:168 gc:universal contig_21:519-16(-) VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLKNAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVGTQRLAFE* ->Gene.12::contig_24::g.12::m.12 type:internal len:111 gc:universal contig_24:331-2(-) +>contig_24.p1 type:internal len:111 gc:universal contig_24:331-2(-) KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKEIEELTQKLASEGQKLQSQISSIMEENNLLN ->Gene.13::contig_29::g.13::m.13 type:3prime_partial len:267 gc:universal contig_29:52-849(+) +>contig_29.p1 type:3prime_partial len:267 gc:universal contig_29:52-849(+) MKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEVQLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAAYDLLDIYCELVVARLPVIESQKNCPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRMLVEKLSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPPHFEAVQVQAHPSNNTLHSSPSNSSQQDDRTSVFVETSTFKTPS ->Gene.14::contig_30::g.14::m.14 type:internal len:160 gc:universal contig_30:1-477(+) +>contig_30.p1 type:internal len:160 gc:universal contig_30:1-477(+) KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQVCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN ->Gene.15::contig_31::g.15::m.15 type:3prime_partial len:263 gc:universal contig_31:787-2(-) +>contig_31.p1 type:3prime_partial len:263 gc:universal contig_31:787-2(-) MTRSRPHIEKLESRVSQDDLLEGTCARTRPLSYDEIMLGRNNKGDAGKEVASGSGVADSASGHGDIEKISNFPEYHRQINEVSERMDVRHTSNDFQKVSCRRKVDSKNDNLVQDKDEKYRESGVKLKSIWEKTEGSKRVREGENERRHYSNRKRDGHLGVDSYNGSNKRQARESYRKGKTSERGRVKSEIDRKQLVNDEGQVHRKRKTERRMSSDSEKEYKRRDERNVMHTERLTNRGSQKSEKENRRKRHNEEDKTKSLST ->Gene.16::contig_33::g.16::m.16 type:internal len:206 gc:universal contig_33:615-1(-) +>contig_33.p1 type:internal len:206 gc:universal contig_33:615-1(-) EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAARDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQRLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK ->Gene.17::contig_35::g.17::m.17 type:internal len:131 gc:universal contig_35:2-391(+) +>contig_35.p1 type:internal len:131 gc:universal contig_35:2-391(+) IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEEEITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ |
| b |
| diff -r 9c72c91d291f -r 4d73965d99a2 tool-data/plant_tribes_scaffolds.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/plant_tribes_scaffolds.loc.sample Wed Jun 09 20:26:55 2021 +0000 |
| b |
| @@ -0,0 +1,4 @@ +## Plant Tribes scaffolds +#Value Name Path Description +#22Gv1.0 22Gv1.0 /plant_tribes/scaffolds/22Gv1.0 22 plant genomes (Angiosperms clusters, version 1.0; 22Gv1.0) +#22Gv1.1 22Gv1.1 /plant_tribes/scaffolds/22Gv1.1 22 plant genomes (Angiosperms clusters, version 1.1; 22Gv1.1) |
| b |
| diff -r 9c72c91d291f -r 4d73965d99a2 tool_data_table_conf.xml.test --- a/tool_data_table_conf.xml.test Thu Jan 10 10:45:23 2019 -0500 +++ b/tool_data_table_conf.xml.test Wed Jun 09 20:26:55 2021 +0000 |
| b |
| @@ -1,6 +1,6 @@ <tables> <table name="plant_tribes_scaffolds" comment_char="#"> <columns>value, name, path, description</columns> - <file path="${__HERE__}/plant_tribes_scaffolds.loc" /> + <file path="${__HERE__}/test-data/plant_tribes_scaffolds.loc" /> </table> </tables> |