# HG changeset patch # User greg # Date 1496940249 14400 # Node ID fcc5585680206bf4272bd3f822e01b6143a989cb Uploaded diff -r 000000000000 -r fcc558568020 .shed.yml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/.shed.yml Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,15 @@ +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/plant_tribes/assembly_post_processor +type: unrestricted +categories: +- Phylogenetics diff -r 000000000000 -r fcc558568020 assembly_post_processor.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/assembly_post_processor.py Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,69 @@ +#!/usr/bin/env python +import argparse +import os +import shutil + +import utils + +OUTPUT_DIR = 'assemblyPostProcessing_dir' + +parser = argparse.ArgumentParser() +parser.add_argument('--dereplicate', dest='dereplicate', default=None, help='Remove duplicate sequences') +parser.add_argument('--gap_trimming', dest='gap_trimming', type=float, default=0, help='Trim alignments') +parser.add_argument('--gene_family_search', dest='gene_family_search', default=None, help='Targeted gene families') +parser.add_argument('--method', dest='method', default=None, help='Protein clustering method') +parser.add_argument('--min_length', dest='min_length', type=int, default=0, help='Minimum sequence length') +parser.add_argument('--num_threads', dest='num_threads', type=int, help='Number of processors') +parser.add_argument('--output_pttgf', dest='output_pttgf', default=None, help='Primary targeted gene families dataset') +parser.add_argument('--output_cds', dest='output_cds', help='Output transcripts.cds') +parser.add_argument('--output_cleaned_cds', dest='output_cleaned_cds', help='Output transcripts.cleaned.cds') +parser.add_argument('--output_cleaned_nr_cds', dest='output_cleaned_nr_cds', default=None, help='Output transcripts.cleaned.nr.cds') +parser.add_argument('--output_cleaned_nr_pep', dest='output_cleaned_nr_pep', default=None, help='Output transcripts.cleaned.nr.pep') +parser.add_argument('--output_cleaned_pep', dest='output_cleaned_pep', help='Output transcripts.cleaned.pep') +parser.add_argument('--output_pep', dest='output_pep', help='Output transcripts.pep') +parser.add_argument('--output_pttgf_dir', dest='output_pttgf_dir', default=None, help='Directory hierarchy of targeted gene family datasets') +parser.add_argument('--prediction_method', dest='prediction_method', help='Coding regions prediction method') +parser.add_argument('--scaffold', dest='scaffold', default=None, help='Gene family scaffold') +parser.add_argument('--score_matrices', dest='score_matrices', default=None, help='Scores matrices') +parser.add_argument('--strand_specific', dest='strand_specific', default=None, help='Strand-specific assembly') +parser.add_argument('--transcripts', dest='transcripts', help='Transcriptome assembly fasta file') + +args = parser.parse_args() + +# Build the command line. +cmd = 'AssemblyPostProcessor' +if args.dereplicate is not None: + cmd += ' --dereplicate' +if args.gap_trimming > 0: + cmd += ' --gap_trimming %4f' % args.gap_trimming +if args.gene_family_search is not None: + cmd += ' --gene_family_search %s' % args.gene_family_search +if args.method is not None: + cmd += ' --method %s' % args.method +if args.min_length > 0: + cmd += ' --min_length %d' % args.min_length +cmd += ' --num_threads %d' % args.num_threads +cmd += ' --prediction_method %s' % args.prediction_method +if args.scaffold is not None: + cmd += ' --scaffold %s' % args.scaffold +if args.score_matrices is not None: + cmd += ' --score_matrices %s' % args.score_matrices +if args.strand_specific is not None: + cmd += ' --strand_specific' +cmd += ' --transcripts %s' % args.transcripts +# Run the command. +utils.run_command(cmd) + +# Handle outputs. +shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cds'), args.output_cds) +shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.cds'), args.output_cleaned_cds) +if args.output_cleaned_nr_cds is not None: + shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.cds'), args.output_cleaned_nr_cds) +if args.output_cleaned_nr_pep is not None: + shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.nr.pep'), args.output_cleaned_nr_pep) +shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.cleaned.pep'), args.output_cleaned_pep) +shutil.move(os.path.join(OUTPUT_DIR, 'transcripts.pep'), args.output_pep) +if args.output_pttgf is not None and args.output_pttgf_dir is not None: + src_output_dir = os.path.join(OUTPUT_DIR, 'targeted_gene_families') + utils.move_directory_files(src_output_dir, args.output_pttgf_dir) + utils.write_html_output(args.output_pttgf, 'Targeted gene families', args.output_pttgf_dir) \ No newline at end of file diff -r 000000000000 -r fcc558568020 assembly_post_processor.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/assembly_post_processor.xml Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,288 @@ + + post-processes de novo transcriptome assembly + + macros.xml + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + options_type['options_type_selector'] == 'advanced' and options_type['target_gene_family_assembly_cond']['target_gene_family_assembly'] == 'yes' + + + + + options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes' + + + options_type['options_type_selector'] == 'advanced' and options_type['dereplicate'] == 'yes' + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and +evolutionary analyses of genome-scale gene families and transcriptomes. This tool post-processes de novo +assembled transcripts into putative coding sequences and their corresponding amino acid translations and +optionally assigns transcripts to circumscribed gene families ("orthogroups")[2]. After transcripts have been +assigned to gene families, overlapping contigs can be identified and merged to reduce fragmentation in the +de novo assembly. + +----- + +**Required options** + + * **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** + + * **Perform targeted gene assembly?** - selecting 'Yes' enables local assembly of one or more targeted gene families in a specific scaffold. Scaffolds are defined in PlantTribes as clusters of paralogous/orthologous sequences from a specified set of proteomes[5-7]. + + * **Targeted gene families** - select a history item containing a list of targeted orthogroup identifiers corresponding to the gene family classification from a specified scaffold. Gene family identifiers can be obtained from the function annotation table ("Orthogroup ID" field of .summary file) of scaffold data installed into Galaxy via the PlantTribes Scaffolds Download Data Manager tool, and also available at the PlantTribes github repository (https://github.com/dePamphilis/PlantTribes/tree/master/config). + * **Gene family scaffold** - one of the PlantTribes gene family scaffolds (installed into Galaxy by the PlantTribes Scaffolds Download Data Manager tool) whose orthogroup(s) are targeted for the localized assembly. + * **Protein clustering method** - gene family scaffold protein clustering method. Each PlantTribes scaffold data has up to three sets of clusters - GFam[8] (clusters of consensus domain architecture), OrthoFinder[9] (broadly defined clusters) or OrthoMCL[10] (narrowly defined clusters). You can also install your own data scaffold created using a different clustering method as long as it conforms to the PlantTribes scaffold data format. + * **Trim alignments** - trim gene family multiple sequence alignments that include scaffold backbone genes and locally assembled transcripts to remove non-conserved regions (gappy sites)[11]. The trimmed alignments are used in assigning scores to locally assembled transcripts to determine how well they compare to the backbone gene models. The default setting of 0.1 removes sites that have gaps in 90% or more of the sequences in the multiple sequence alignment. This option is restricted to the range 0.0 - 1.0. + + * **Strand-specific assembly?** - select 'Yes' if transcriptome library sequences were strand-specific. If 'Yes" is selected, transcripts from the minority strand (antisense) are removed. + * **Remove duplicate sequences?** - select 'Yes' to remove duplicated and exact subsequences[12]. + * **Minimum sequence length** - set the minimum sequence length of predicted coding regions. The default is 200 bp. + + + + + + @article{Honaas2016, + journal = {PloS one}, + author = {2. Honaas LA, Wafula EK, Wickett NJ, Der JP, Zhang Y, Edger PP, Altman NS, Pires JC, Leebens-Mack JH}, + title = {Selecting superior de novo transcriptome assemblies: lessons learned by leveraging the best plant genome}, + year = {2016}, + volume = {11}, + number = {1}, + pages = {e0146062},} + + + @article{Haas2013, + journal = {Nature Protocols}, + author = {3. Haas BJ, Papanicolaou A, Yassour M, Grabherr M, Blood PD, Bowden J, Couger MB, Eccles D, Li B, Lieber M, MacManes MD}, + title = {De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis}, + year = {2013}, + volume = {8}, + number = {8}, + pages = {1494-1512},} + + + @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},} + + + @article{Huang1999, + journal = {Genome Research}, + author = {5. Huang X, Madan A}, + title = {CAP3: A DNA sequence assembly program}, + year = {1999}, + volume = {9}, + number = {9}, + pages = {868-877}, + url = {http://seq.cs.iastate.edu/cap3.html},} + + + @article{Eddy2009, + journal = {Genome Inform}, + author = {6. Eddy SR}, + title = {A new generation of homology search tools based on probabilistic inference}, + year = {2009}, + volume = {23}, + number = {1}, + pages = {205-211},} + + + @article{Katoh2013, + journal = {Molecular biology and evolution}, + author = {7. Katoh K, Standley DM}, + title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability}, + year = {2013}, + volume = {30}, + number = {4}, + pages = {772-780},} + + + @article{Sasidharan2012, + journal = {Nucleic Acids Research}, + author = {8. Sasidharan R, Nepusz T, Swarbreck D, Huala E, Paccanaro A}, + title = {GFam: a platform for automatic annotation of gene families}, + year = {2012}, + pages = {gks631},} + + + @article{Li2003, + journal = {Genome Research} + author = {9. Li L, Stoeckert CJ, Roos DS}, + title = {OrthoMCL: identification of ortholog groups for eukaryotic genomes}, + year = {2003}, + volume = {13}, + number = {9}, + pages = {2178-2189},} + + + @article{Emms2015, + journal = {Genome Biology} + author = {10. 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},} + + + @article{Capella-Gutierrez2009, + journal = {Bioinformatics,}, + author = {11. Capella-Gutierrez S, Silla-Martínez JM, Gabaldón T}, + title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses}, + year = {2009}, + volume = {25}, + number = {15}, + pages = {1972-1973},} + + + @article{Gremme2013, + journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, + author = {12. Gremme G, Steinbiss S, Kurtz S}, + title = {GenomeTools: a comprehensive software library for efficient processing of structured genome annotations}, + year = {2013}, + volume = {10}, + number = {3}, + pages = {645-656},} + + + diff -r 000000000000 -r fcc558568020 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,130 @@ + + + 1.0 + + + plant_tribes_assembly_post_processor + + + + + plant_tribes_gene_family_aligner + + + + + plant_tribes_gene_family_classifier + + + + + plant_tribes_gene_family_integrator + + + + + plant_tribes_kaks_analysis + + + + + r-optparse + + + + + plant_tribes_gene_family_phylogeny_builder + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @misc{None, + journal = {None}, + author = {1. Wafula EK}, + title = {Manuscript in preparation}, + year = {None}, + url = {https://github.com/dePamphilis/PlantTribes},} + + + diff -r 000000000000 -r fcc558568020 plant_tribes_scaffolds.loc --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,3 @@ +## 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) diff -r 000000000000 -r fcc558568020 plant_tribes_scaffolds.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/plant_tribes_scaffolds.loc.sample Thu Jun 08 12:44:09 2017 -0400 @@ -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) diff -r 000000000000 -r fcc558568020 test-data/arabidopsis_thaliana.smat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/arabidopsis_thaliana.smat Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,8248 @@ +FORMAT: at.conf CODING REGION 6 3 1 s C+G: 0 42 +-2 1 4 -3 +1 1 0 -2 +1 0 2 -4 +-3 1 4 -4 +1 -1 2 -3 +1 0 2 -4 +1 0 1 -2 +-3 2 3 -2 +0 -1 3 -3 +1 -1 -2 0 +2 0 0 -3 +-2 -1 3 -1 +-1 0 2 -1 +1 0 1 -2 +0 -1 4 -4 +-3 2 4 -3 +-1 1 3 -4 +2 0 -1 -1 +2 1 -1 -2 +-3 2 3 -2 +1 -1 2 -3 +2 -4 2 -3 +1 -2 4 -4 +-2 1 3 -2 +0 -1 3 -3 +1 1 -1 -2 +2 0 -2 -1 +-3 1 3 -1 +0 0 3 -3 +1 -1 0 -1 +2 -1 1 -4 +-3 2 4 -4 +-1 -1 5 -5 +2 -2 1 -2 +2 0 0 -3 +-3 0 4 -2 +1 -2 3 -3 +3 -4 1 -3 +1 -3 2 -2 +-2 1 3 -2 +1 -3 3 -3 +1 -1 0 -1 +3 -2 -2 -2 +-3 0 3 -1 +0 -1 3 -3 +2 -1 0 -1 +2 -3 2 -3 +-2 1 4 -2 +1 -1 1 -2 +2 -1 0 -2 +2 2 -3 -2 +-3 1 4 -3 +1 -2 2 -2 +2 -2 2 -3 +2 -2 1 -3 +-3 2 3 -2 +1 -4 1 1 +2 -1 -1 -1 +1 -1 2 -2 +-3 0 4 -1 +-2 1 3 -3 +1 -1 0 -1 +0 0 3 -4 +-3 1 4 -4 +-1 -1 4 -4 +3 -2 -1 -3 +2 -1 1 -3 +-2 1 4 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+-1 0 -1 2 +1 -1 -2 1 +2 -2 -2 1 +1 -1 -1 1 +-2 1 -2 3 +0 -3 0 1 +-1 0 -6 3 +0 -3 2 0 +-2 -2 0 3 +1 -2 -3 2 +1 -2 -4 3 +0 -3 -2 3 +-1 -2 -1 2 +1 -1 -1 0 +1 1 -4 1 +2 -1 -2 0 +-2 2 -2 1 +1 0 -2 1 +1 0 -3 1 +1 -3 1 0 +-5 3 -4 2 +1 -3 -1 2 +-1 2 -4 2 +1 -2 -2 2 +-3 2 -2 2 +0 0 -2 2 +-2 0 -5 4 +0 -1 -1 2 +-5 4 -2 1 +1 -3 1 0 +0 0 -3 2 +2 -1 -1 0 +-3 0 0 2 +1 -4 1 1 +1 -2 -2 2 +0 -4 0 2 +-3 0 -1 3 +1 -4 0 1 +-1 -1 -4 3 +1 -3 -1 1 +-3 -1 0 3 +1 -2 -2 2 +-1 -2 -3 3 +0 -4 -1 3 +-3 -1 1 3 +1 -2 -1 1 +1 -1 -5 2 +0 -1 -1 1 +-2 0 -1 2 +0 -1 -1 1 +0 0 -3 2 +1 -2 -2 2 +-5 2 -3 3 +0 -3 -1 2 +0 -1 -5 3 +0 -3 -1 3 +-1 -3 -1 3 +0 -1 -1 2 +-1 -1 -5 3 +-1 -3 0 2 +-4 -1 -1 3 +FORMAT: at.conf START PROFILE 1 12 7 s C+G: 42 100 +2 -3 0 0 +1 4 -4 -2 +6 -4 -1 -6 +8 -9 1 -9 +5 6 -14 -6 +6 -1 0 -11 +18 -100 -100 -100 +-38 -38 -39 18 +-49 -46 21 -44 +-3 -13 12 -10 +1 9 -4 -8 +-4 -7 6 2 +FORMAT: at.conf STOP PROFILE 1 12 6 s C+G: 42 100 +0 0 2 -2 +1 1 -3 1 +-4 2 -1 3 +-59 -62 -50 18 +10 -66 10 -68 +15 -64 -2 -70 +4 -8 -1 1 +2 -2 -2 0 +3 -1 -4 0 +2 -2 -3 1 +2 -3 -3 2 +2 -2 -3 2 diff -r 000000000000 -r fcc558568020 test-data/assembly.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly.fasta Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,73 @@ +>contig_1 +CGATTAACCATGTGTACAACATGACCAATTATGGCCGATCTTGCTTGTTCAGGAGTCTCA +CTCATCATTCCAAAATCAAGAAAAGCAAGCTTCCCGTCAGGTGTAGCTAAGAGATTCCCT +GGGTGAGGATCTGCATGAAAATAGCCGTACTCAAGCAGCTGTCGAAGACTGCACTGTATG +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 000000000000 -r fcc558568020 test-data/assembly_tgf.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/assembly_tgf.fasta Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,271 @@ +>contig_1 +CGATTAACCATGTGTACAACATGACCAATTATGGCCGATCTTGCTTGTTCAGGAGTCTCA +CTCATCATTCCAAAATCAAGAAAAGCAAGCTTCCCGTCAGGTGTAGCTAAGAGATTCCCT +GGGTGAGGATCTGCATGAAAATAGCCGTACTCAAGCAGCTGTCGAAGACTGCACTGTATG +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 +>contig_11 +CATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATC +TCCCGTCGTTGTTGTTGGAGGCGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGT +TCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCCAAGCTCTCCCACCGCGGCT +CCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCA +TGATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTC +CAGAAACTCCCGCTGTGGCTATTGAAGTCGACCGCGGGAGATCCTGGGGCAACGCCGGCT +TCAGCAGTCGCCGGAGATTCTGAGGCAACGCCGCTTCCAGCAGCAGCGACGCGAGATCCG +GGAGCAACCGTGACTTTAGCAGCG +>contig_12 +GAATAATATTTTCCCACATAAACCTGATGCCTTGAATCTGATGGGGCTTTAATTTTATAC +AGATGCTTGGAGGGATTCTTACTGGCTCTTCACCTTCCTCTCTCACCACATTAATTATGT +AACCTGCAGAAATATCGCCCAGCAATTCTACACCAGTGCCATCAAATGAGCTCCTATTAC +TGACTGTAGATCTCATGATTACGGACTTGGTAGAAAACCGTGCTTCCAAAGATTTCAGCC +GCTCTTGACGTTCCTTTTCAATTGCAATTTTCTTCTTGGTCTCTTCCCCCCGCGATTTTG +ATCGCTATAGAGAACGTTTGGATGAGGATG +>contig_13 +AGCGACACATATCGCGCTCTCTCTCTCTCTTCAATAAATACGCAAACCCTACTACCATAG +TTTTCACGCCTTAAAATGTTTTCGCCTTATCGTTGATTGCTTCACGAGACGACACCTTGA +TTAGTTATTATTCCCGATCCATCCGCCTGTTTGTTTTTTACTGATTTAGTTGAGCGAAAG +CTTAATTGGGGGTGATCATCGGTCGCCGCGGAAAATGATGTCGTCTGGAAGGTACATGTC +ATACTCACCGTCTCCTTCCGCCCCTCACTCACCTCACATTGGCATCGCCGGCAGCGGCGG +GGGTATGCGTACTGCCGCCTCTGTGCTCATCGAGCAAGAAAAATACCTCTCAGAGTTGCT +GTCTGAACGCAACAAACTCAGTCCCTTCGTGGCTGTGCTGCCAAATAGTTATCGTTTGCT +GAACCAGG +>contig_14 +TGCTTGCCGCAACTATAAATAAATACCAAGAGGAAAAAATACAGAGAATGAAGAAGCTTA +AAGTACTAGTAACCACCATGTTGGAGCTATGGACTTTCTTGGACACACATAGTGAAGAGC +AACAATCGTTTGAACACGTTAAGTGTTATGTAGCCGCTGCTGCTGTTGATGAGCATGCAC +AAAAGGCATACGAGTTACCCGGAATTCTTTCTTTGGACTGCCTTAACAATGTTGAGACAG +AAGTTTCTCG +>contig_15 +TGTGTTTTCGGTTCGTGAAGTGTGTGTGTACAAAATTGCCGGATCTAATACTATCGTAGG +AGGAATGGGATATTGACGAGGAAGGAGGTGAAAAAGGTGTTAAAATGGAGGAGAAATTGG +TTTTTATGTGGGGGTACTTACCGGGGGCGCTGCCGCAGAGGATGCCGATTTTGTCTCCGA +TGGTGGTGCGGCTGCCGCATGGCGGCGGTTCATGGAAGGATGTATGTGGTGGAGGCTGTG +GTTTCGCCATGGCTATATCGGATTCTGGTAAGCTCATTACATGGGGGTCTACTGATGATT +TAGGTCAAAGCTACGTGACCTCTGGGAAACATGGGGAAATGCCAGAGCCTTTTCCACTAC +CC +>contig_16 +GGGGTTTTCCCACGGCGGCCACGATGGGTGGAAGCGGATGGGGTGGAGGATTCCGGTGTA +GGGTCCATAGAAGCAGATAGCTCAGCAATGGGATAGCCGGGAGAGATCGAATTGGTATTG +AAGGCAGTGGTAACAGCGGCAGCAGGTGTGGAGGAGGGACGGGAGCGTTTGGTGGCGCGT +GTGGTTGGGCCGGGAGAGGCTGATGAGGTGGATGCCTCTGTCCGCTTACGGCACCGAGTT +TCCATACAACCTACAAAATCGGAAATAGACGTCGCCGATTAATCGGCGGACATGCGCAAT +ATCAATCCCCAACTTCGTTGCATTTCAATTTCAC +>contig_17 +TGAGCGGCTACGGACAGGCCGAACTTTGGGTGGCTGCTATGCCATTATACATGCACGGTA +TACCTAAGCATCAGAAATTAGGATACACGTTGAACTTGTAAGCTCCAATCGAGGATTTAT +GTGATGATGAGATCGAGGGTTTCGCGCCACGAATAAGGGCTCCGATCACTCGGGGTTGTG +CTGCTGAATAAGGAAGAATTTTGATTTGATG +>contig_18 +GGTAACCTCATCCAATGCCAACCAAAGCGGGCACTTCTCTCCATCAATGGAAACGGGGTC +TAATTCCTTTATACTAACCATTTCAAGTGCCGAAGCATCAAGAAGCAAGCCCTGGTGAGG +CCTATTATCAACGACCATGTTGAGGTCGTGTTTGGATACCTCTTTTTTGCTTAATCCAAT +CTTTTCCACCATTTTCAAAACTCTCTCGAACCGTTTCTTGTCCTTCTTCTTACTGTTACT +ACTCAAATCCAAACCTTCCTGAACGTACAACGCGTAGAGTTCTCTTCGCCCGGATGAGAG +TGCAGCTAAAATGGGACCAACTCCATAGATCCCTTCACCTACTATTTTCGGCAATGTGGA +TTCCTTAGCTTCTTTCCATGTCTTTCTACCCCAATCTTCCTGCTTGTTCCATCTTCTCAC +CTCTGTTC +>contig_19 +ATACAAGAAAAGATACCCAGTCGTTCCAACTCTTCTTACAAGAATTCTGTGGTGGAGAAT +ATGTTTGGATGAAGCTCAAATGGTGGAGGGTAATGCTGCTGCAGCAACAGAACTGGCTGT +GCGTCTACATGCAAAACATCGTTGGTGTATAACAGGGACTCCCATACAACGGAAACTTGA +CGACCTGTATGGGCTTTTGAGATTCCTTCAATCAAGTCCATTCAATGTCCTCCGCTNG +>contig_20 +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAA +CTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCT +GCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGT +TTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCAT +TTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTA +CTTGGATCA +>contig_21 +CGCCATATTAATGTGTCACTCGAATGCAAGTCTTTGGGTGCCAACCAGTGAGGCATAAAG +ACCCTTTTGCTCTAACAACTCAGAGTGTGTCCCCAGTTCTGAAATCTTCCCATCAGAGCA +TAAAGCAATTTGATCAGCATTTTGAACGGTGCTCAGCCTGTGAGCAATCACTAAAGTCGT +TCTTCCTTTCATCAAACGGTTCAAAGCATCCTGAACCAGACGTTCACTGACTGCGTCCAA +AGCACTGGTAGCCTCATCAAGAATCAAGATTGGAGCATTCTTGAGCAGAGCCCTTGCAAT +GGCTACCCTCTGTCTTTGTCCTCCACTTAACAACCCACCACGCTCACCAACTAATGTGTC +ATAACCCTGTGGCAACGCAATGATAAATTCATGAGCATTAGCTGCTTTAGCAGCTTTTAT +CACATCGACCTTGGAAACATAATCATCTGGGAGTCCGTAAGCAATATTTTCTCCAATGGA +AACCGAGAATAGAACAGGTTCCTGATTCACTATGGAAACC +>contig_22 +CCAGTTTCAATTATATTACATATGTAACCATGCACCACAGAGTGGGTATGGATGTCGCTA +ATATCAACAGGGAGCTGCTGAGTTGAGTTAACTAGTGAACACTTGGCACTAAGTACAAGA +TTGTTTCCTTCAACATCAAGAACCAATAATTCATCAAAATGATATCCTGGCTTCAAGACA +GACATCAATAGAGCAGCAAGTCCATGGTGGTCTGCCAAATGTTCAAGAG +>contig_23 +ATCCGTGATTCTTCAGGGTCGCCGGCGGCAAAGCTGGGGACTTTTTCGTCAGTTGGTTTG +GCTCCGGTTCAGGATCGGAATCGGATGAGGCATCTTCGAACGACGCGTTTTCTTCTGGGT +CGGATTCTGAATCCAACACGATTGGCTTCACCGGCTCCACATTATTGGACATTTTTTGTT +TCAAAACGGCGCAGTTTTTGCATGAGACTAGCA +>contig_24 +CGTTAAGTAAATTGTTCTCTTCCATTATAGAAGATATCTGAGACTGCAGCTTTTGTCCTT +CAGAAGCAAGCTTCTGAGTCAGCTCTTCTATTTCTTTTCTTGCACTAGTTAGTTCTTCAA +CAGTGCCGTCTTTCTCAGATGAAACAACGTTCAATTTCATCTGTATATCGTTTAGCTCGG +ATTTAAATGCACCCAACTCCTGACTGAGTTTCGAGTTTTCTGCAACAAGTGCCTCAGTCT +CCTTTATAAACATACTACCCTTGCTCTCCAATTCGCTTTCCAAATCCTTGGATTTTAACA +AGATTTGTTCGATTTCTAATTCACGGGTTTTC +>contig_25 +AGAAAATCAATCAGTACGAAAATCTCCATTAACCCAATCATCCCCCTTCCTTGCCTTTAT +CGATTTGTGATCAAAGTCGCCTTTTATCAATTTGTCCCCGTGCTCAGTTTCTTCCTCTCC +AGTTCATTCCCCCACCAATCGTTGCTAATTGATACCTAATCGCCTTTTTAACACCTCCTT +TTTTTGACTTAGTGCTTGATTTTCCTCGATCATAATCATTTCCAA +>contig_26 +AGAGGAAAGAAGGGGCGTCGGCAACAAAATTTGAAATTGAAAATATCTTCCCCGTCCGTC +ACTCCTTCTTGCGATCCCAAGAAAAAAGAGGAAAGAGGGGAGGCTACAACTTTTAGAGAG +AGGAAGCATAACGGTTGTGGCTTCTTGTTCTTGGAAGAAGAAACAATCGTTGTCGACAGG +TAGAGGGGATAATAATTGTTTAAAAAAATTGTTGGCAAAAAAAAAGTGAAAAATGAGAGA +AATAATAAGCATACA +>contig_27 +CCCACAACCCGGGCCCAAGACCCGGGCTATCCCGATAGCAAGTGCCCCACTTCCAGTCCC +TAAATCGGCCCACAAACCATTTTTCAGTTCCCCATTTTTCTTCACTGCATCTTCAACCAA +ATCCAAAATAACCTCCGTCTCAGGCCTGGGTATCAAAACACCTTCCTCAACACTCAATAT +CAAATCCCGCCAGTGTTCACAGCCCACCACGTACTGAAACGGCCTTCTTTCCTCAATCCT +CTGCTTCCACAGCTTGTAGAG +>contig_28 +CTTGGCTTTGATTAGGTGTTGTAGTTTGAGATCGCGCTGAATTATTGTTTGCTGTCACAA +GAACTGTTGGGGAGGAGGAGGAGCTGTCAAGGTGCGACGATCCTTGACGTTTTTCTTTAT +TCAGCACACTTTCTTCGAGTAATAGCATGGTCTGCGTGGATTCTAGGTCGGGTAATTTTT +CGCGATGCTTAATGATGCACGCATTTGGAGAAAATTGTG +>contig_29 +TGCTGGTAAATAGCTAGCAAAGTTAGGAGTAGTGATCGCAATTTCCGGACGATGAAGAAA +TCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGC +AAAACGTCTCTGAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTG +CAACTGAAGCAGATGAAGCGGGAAATAGCACAGTTGCTCGAGTCTGGACAGGATCAGACC +GCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCATATGATCTC +CTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAAT +TGCCCCATTGACCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGA +GATGTACCCGAGTTTCTTGATGCAAGGAAGCAATTTTCAGCTAAATATGGAAAAGATTTC +ACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTGGTTGAAAAA +TTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAG +GAGCACAATGTTAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAAT +GACCGACTGACTGGACCAAGTTCCTTTACGAAGGAGAGAGAACAGTACCCTGAACCTCCT +CATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCATAGCTCGCCA +TCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAG +ACACCATCG +>contig_30 +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAA +AATGTATGCTCTGATATTTTATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGC +CATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGTCTGGAGCTGCTACAAATGTA +ATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAA +GTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGA +TTTAAGGATGCTGAGGTTGCTACCAATATAACACATGATTATTGTCATGTATCTCATCTG +TTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTGGTAATGGTTCAGCCACTGTT +GATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAATT +>contig_31 +CCGTACTCAAGCTTTTAGTTTTATCCTCCTCATTATGACGTTTGCGTCTGTTTTCTTTTT +CAGACTTCTGGCTGCCTCTGTTAGTTAATCTTTCTGTATGCATCACATTTCTTTCGTCTC +TTCTTTTGTACTCTTTCTCAGAGTCACTGCTCATTCGCCGTTCTGTTTTCCTTTTCCTGT +GGACCTGTCCTTCATCGTTAACAAGCTGTTTTCTATCTATTTCGGATTTGACTCTGCCTC +TTTCAGAAGTTTTACCCTTTCTATATGACTCTCTGGCTTGCCTCTTATTTGATCCATTAT +ATGAATCCACACCTAAATGGCCATCTCTTTTTCTGTTGCTGTAATGTCGTCTTTCATTTT +CTCCTTCTCTCACTCTCTTGCTGCCTTCAGTCTTTTCCCATATACTCTTTAACTTGACAC +CACTTTCCCTATACTTTTCATCCTTATCCTGGACTAAATTGTCATTCTTACTATCCACTT +TTCTCCGGCAACTTACCTTCTGAAAATCATTTGAAGTATGTCTAACATCCATACGTTCAG +AAACCTCATTTATTTGCCGATGGTATTCTGGAAAATTAGAAATCTTTTCAATGTCACCAT +GCCCTGATGCACTATCAGCCACTCCAGAGCCACTGGCAACTTCTTTACCTGCATCTCCCT +TGTTATTTCTTCCGAGCATTATCTCATCATAGCTTAATGGCCTCGTTCTTGCACAAGTGC +CCTCCAAAAGATCATCCTGAGACACTCTACTTTCTAATTTCTCTATGTGTGGGCGGGATC +TAGTCATGGCGCTAACGGACTTCTACTATGTTTACGAGCATGAGGAACTGCCAGAGCGCG +GCCGGAGAGAATAAGCGTCGCCTGGTGGTTTTAC +>contig_32 +CACCGACACATCACAGAAATGGGGCTTTCCATGTTACTTCATTCACGAATGCCTTTGTCA +TATTGGGATGATGCTTTTTCTGCTGCAATTCACACAATCAACCGCCTACCTACTCTGATT +CTCAACAAAGTTTCTCCTTTTGAAGTACTCTTTGGACGCGCACCGGTGTATTCTAACTTT +CATCCTTTCGGCTGCAGAGTTTTTCCCTATGTTCGACCCACTGCTGAACACAAACTTGCT +CCACGCAGTCTGCCTTGTATCTTCATCGGCTACAGCGCTCACTATAAAGGC +>contig_33 +TTTTAATTCTATAGGGCGAAGTAATGCTGTCTTTTCAGCAACCTTTTGCCAATCGACAAA +GTCAATGAGCTCTTCATCCATTGATTCTTTTGCAGCAAGAAGAAGGATTTTCCTCCTTTC +TGCTTGAGTTAGTCGCTGAAGATGAAATATTCGATCCATTCTACCAGGACGCAGTAAAGC +CCCATCGATTTGTTTAAGATTCCGAGTAGTAGCCATCAAAACTACCCCATCTTGTTTCTC +AAACCCATCAAGCTCCACCAGAAGTTGATTGATGAAAGATTCGTGATCCAGCTTTTTGGT +CTGAAGGTCCTTCCCGCGGACACCAGCAAAGAGGTCAAAGTCTTCCACAAATATAATGAC +AGGAGCCAGATCCCGTGCTGCTTGAAACAATTCTCTAACGTTTGATGCACCTTGGCCCAC +AAACAGACCAGCTTCCAGCTGTTGGGCTTTTACTTCAACTAAAGGAACCTTCGCTTCCGC +TGCTATAGCCATTGCTAGGGATGTTTTACCTGTTCCTATCTCACCAACAATAAGAACACC +CCGAGGTGCCCGAGCTCCCATTTCTTGGAATGCACGAGGATTTTGTAGAAATGCCACAAC +TTCATTAATTTCTTC +>contig_34 +ACCCGTTGGACCCTCTCGTGATTCAAACTCAACTTGTTTCATAAAATAGCACAACACTGC +TCGGTACTGAAAACTGGAGGATCTTGTAGGTCAATAATACAAGTTACAACTCTTGTAATT +CCTCAACTGAGTGCACAGTCCAAAGTGGCCAATGGCATCAAGTAACAGATTACCAATAAG +ATAACAGTAGAAGTCAGATGAATATTCCTGTCTTGATTTTGTTTTCTCAACTGCTTCTAC +TTCCAATTAAGGAGAGACACAGTCGAAAATAGAATAAACCAAATATTTATCTGTAGGCTT +CCGGCAGGCGGTAACCACTGATCACTAAATTGTCGGCGAACATCTTGCCAGTTTTGGGCA +TCACATGCCAATGCATTGTTAAGTTGAAGTCTTTACCACGTAGATTGCTTCCTTGGTCAA +TAAAACGATACTTGTTAGTTGTCTGGATCTGAAATATTGCTTGCTCTTTGGAGGGTATAA +TAAGATCCCACAAGGAGACCTGATTCAGCGCATTTGTTGGGGTTTCA +>contig_35 +AATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGAT +GCTTTACAGAGGGATATCGAGGAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCA +ACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTGACACCGATGGATCTGGAAC +TATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGA +GGAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGA +CGAGTTTTGTCACATGATGACAGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTAC +CAAGGCTTTTCAGATTATCGACAAAGATCAAAA diff -r 000000000000 -r fcc558568020 test-data/output.pttgf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.pttgf Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,6 @@ +

Targeted gene families: 1 items

+

+Directories + +
752 +
diff -r 000000000000 -r fcc558568020 test-data/target_orthos.ids --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/target_orthos.ids Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,5 @@ +213 +9300 +752 +4632 +4732 diff -r 000000000000 -r fcc558568020 test-data/transcripts.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,8 @@ +>Gene.1::contig_1::g.1::m.1 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(+) +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA +>Gene.3::contig_3::g.3::m.3 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(+) +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT diff -r 000000000000 -r fcc558568020 test-data/transcripts.cleaned.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,26 @@ +>contig_1 +AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT +GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA +CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT +ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG +TCATGTTGTACACATGGTTAAT +>contig_2 +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA +CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA +TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG +GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA +GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG +GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA +CTGTTAAATTATGTGCGCTTTGATGAT +>contig_3 +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGC +TCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTT +TCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACA +ATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTAC +AGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_9 +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT +GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA +AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA +GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA +ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT diff -r 000000000000 -r fcc558568020 test-data/transcripts.cleaned.nr.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned.nr.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,43 @@ +>contig_1 +NTTAAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAAC +AATGGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGA +ATACCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTA +GCTACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAAT +TGGTCATGTTGTACACATGGTTAATCGN +>contig_10 +ATGGCAGAAGAGAACACCACTACAATGAACCTCGATCTCAATTTGGGCCCCATCAATAACTCAAGCGACGATAGCGAACC +TTCATCACGCCCTTATACTGATGTCGCAATGAACTTGGAAGATTGGTTAGATAGTCCCGTCCGAGTTCGTGAAGTCGTCC +GCCACAGAAATCATAGGTGGCGCTCTTTGTGGCGCCAAATCCCAATTCCGCCTGATACGCGAAACCTCGCGCTCGAATTA +ATCGGCGGCAATGCCCCN +>contig_2 +NNCCTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGA +CTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACC +TCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAA +TGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTC +GGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGC +CGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCA +CAACTGTTAAATTATGTGCGCTTTGATGAT +>contig_3 +NNTGTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAG +AGCTCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATA +CTTTCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGC +ACAATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGT +TACAGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_5 +NNCGGTGGTCCGCCACAAACACACGTCAAGCGGGATCCCGCATCCCGCGGGCTCTTCCACGCGGTCGTCCCGGCGCTCGG +CCCTCTCCGTGACGCACGTCGAGAGGGACGATTTGGCCGATGCCGCGTGATGCCAGGCCCCGACATCATCAAGGAGCACT +CCGTTGTGCCGACCCTCGCCTTCGATGACGTCCTCGGGCGTCTAGCGAAGTATCGAAGAAGGGCGAGCGGAGCCATGAAT +CCTGGAGATGCGAGCCAGGTCACGAGAGGCGCGGCAGGCGAGTCTTTGCTCGCTCTCGCACCGTCTGCTCTCGTGCTTGG +AGAAGAAGGACCGACTGCTGACGTCGAACCGGATGATGGAAGGTTCGAACAAGTCAGATCTGGAAAGGGGCATGGAAAAG +GCGACACTCTCACN +>contig_7 +GAGAATGAGTGGTCTGGGGCTGAGTTTTTGAATGAAATGGCGGCAATGATGACTCAAAATAAATCCAATGAAAACGGAAC +CGGAACTTTTGAAGAACTGCAACAATTGTTCGATGAAATGTTTCAGAGCGACATCGAGTCCTTCAATGGTTGTTCTTCAT +CATCCAATGAAACATGTAGCAACTCGAACAAGAGGAATTCCATTGAGTCGAGCTCGGCTAATTTCAGACCCGAAAATGGA +AACGAAAGCGGCGAGATTAGCGGGAAGAAGAATACTAGGAAAGGTAAAGGTGACGNN +>contig_9 +NNACTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCA +TGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCT +CAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGA +ACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGC +TGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTTGAN diff -r 000000000000 -r fcc558568020 test-data/transcripts.cleaned.nr.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned.nr.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,22 @@ +>contig_1 +XKKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLL +ATPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVNR +>contig_10 +MAEENTTTMNLDLNLGPINNSSDDSEPSSRPYTDVAMNLEDWLDSPVRVREVVRHRNHRWRSLWRQIPIPPDTRNLALEL +IGGNAP +>contig_2 +XLSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEK +WVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAAS +QLLNYVRFDD +>contig_3 +XVDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKG +TIESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_5 +XGGPPQTHVKRDPASRGLFHAVVPALGPLRDARREGRFGRCRVMPGPDIIKEHSVVPTLAFDDVLGRLAKYRRRASGAMN +PGDASQVTRGAAGESLLALAPSALVLGEEGPTADVEPDDGRFEQVRSGKGHGKGDTLT +>contig_7 +ENEWSGAEFLNEMAAMMTQNKSNENGTGTFEELQQLFDEMFQSDIESFNGCSSSSNETCSNSNKRNSIESSSANFRPENG +NESGEISGKKNTRKGKGDX +>contig_9 +XLRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGR +TAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAVX diff -r 000000000000 -r fcc558568020 test-data/transcripts.cleaned.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,13 @@ +>contig_1 +KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA +TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_3 +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT +IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV diff -r 000000000000 -r fcc558568020 test-data/transcripts.cleaned_tgf.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned_tgf.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,102 @@ +>contig_1 +AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT +GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA +CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT +ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG +TCATGTTGTACACATGGTTAAT +>contig_11 +ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGG +CGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCC +AAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCAT +GATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTA +T +>contig_18 +ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAA +AATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGT +ACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTG +GAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTT +GCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGC +TTTGGTTGGCATTGGATGAGGTTACC +>contig_2 +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA +CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA +TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG +GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA +GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG +GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA +CTGTTAAATTATGTGCGCTTTGATGAT +>contig_20 +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGA +CGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTC +TTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCAT +TTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA +>contig_21 +GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTA +TGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATG +ACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAG +AATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAA +CCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTAT +GCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGC +ACCCAAAGACTTGCATTCGAG +>contig_24 +AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTAT +GTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAA +ACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAA +ATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAA +TTTACTTAAC +>contig_29 +ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCT +GAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCAC +AGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCA +TATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGA +CCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGC +AATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTG +GTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGT +TAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGA +AGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCAT +AGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG +>contig_3 +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGC +TCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTT +TCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACA +ATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTAC +AGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_30 +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTT +ATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGT +CTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAA +GTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGC +TACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTG +GTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT +>contig_31 +ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAG +AACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCT +CTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAAT +GAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAA +GAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTG +AAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTG +GATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAA +ATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCA +GTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAG +AAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG +>contig_33 +GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGT +TCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTG +AAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCA +CGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAA +AAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGA +TGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAG +CGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGT +CGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA +>contig_35 +ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAG +GAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTG +ACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAG +GAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGAC +AGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA +>contig_9 +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT +GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA +AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA +GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA +ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT diff -r 000000000000 -r fcc558568020 test-data/transcripts.cleaned_tgf.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.cleaned_tgf.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,49 @@ +>contig_1 +KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA +TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>contig_11 +IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLH +DIPSELLRISRCCCCSRCCSRNSRCGY +>contig_18 +TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMV +EKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_20 +GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGH +LHWFRHSYPLHVGLVSLDQLLGS +>contig_21 +VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLK +NAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVG +TQRLAFE +>contig_24 +KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKE +IEELTQKLASEGQKLQSQISSIMEENNLLN +>contig_29 +MKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEVQLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAA +YDLLDIYCELVVARLPVIESQKNCPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRML +VEKLSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPPHFEAVQVQAHPSNNTLH +SSPSNSSQQDDRTSVFVETSTFKTPS +>contig_3 +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT +IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_30 +KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQ +VCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN +>contig_31 +MTRSRPHIEKLESRVSQDDLLEGTCARTRPLSYDEIMLGRNNKGDAGKEVASGSGVADSASGHGDIEKISNFPEYHRQIN +EVSERMDVRHTSNDFQKVSCRRKVDSKNDNLVQDKDEKYRESGVKLKSIWEKTEGSKRVREGENERRHYSNRKRDGHLGV +DSYNGSNKRQARESYRKGKTSERGRVKSEIDRKQLVNDEGQVHRKRKTERRMSSDSEKEYKRRDERNVMHTERLTNRGSQ +KSEKENRRKRHNEEDKTKSLST +>contig_33 +EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAA +RDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQ +RLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK +>contig_35 +IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEE +EITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV diff -r 000000000000 -r fcc558568020 test-data/transcripts.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,8 @@ +>Gene.1::contig_1::g.1::m.1 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(+) +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD* +>Gene.3::contig_3::g.3::m.3 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(+) +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV diff -r 000000000000 -r fcc558568020 test-data/transcripts2.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts2.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,54 @@ +>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 diff -r 000000000000 -r fcc558568020 test-data/transcripts2.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts2.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,25 @@ +>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 diff -r 000000000000 -r fcc558568020 test-data/transcripts_tgf.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,34 @@ +>Gene.1::contig_1::g.1::m.1 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(+) +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTACGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCATGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGGGTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGAGATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGGGTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAACTGTTAAATTATGTGCGCTTTGATGATTAA +>Gene.3::contig_3::g.3::m.3 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(+) +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGTGGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAAAACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACAGCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGAACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT +>Gene.5::contig_11::g.5::m.5 type:5prime_partial len:108 contig_11:2-325(+) +ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGGCGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCCAAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCATGATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTATTGA +>Gene.6::contig_11::g.6::m.6 type:5prime_partial len:100 contig_11:443-144(-) +GCTGCTAAAGTCACGGTTGCTCCCGGATCTCGCGTCGCTGCTGCTGGAAGCGGCGTTGCCTCAGAATCTCCGGCGACTGCTGAAGCCGGCGTTGCCCCAGGATCTCCCGCGGTCGACTTCAATAGCCACAGCGGGAGTTTCTGGAGCAACACCGACTGCAGCAGCAACAACGGGAGATTCGGAGCAACTCCGACGGGATATCATGGAGCAACCCCGACTTCAACAGTGGCGACGGGAGATTTTGGAACAACGCCGACTTCAGGAGCCGCGGTGGGAGAGCTTGGAGTAAATCCGACTTAA +>Gene.7::contig_18::g.7::m.7 type:internal len:143 contig_18:426-1(-) +ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAAAATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGTACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTGGAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTTGCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGCTTTGGTTGGCATTGGATGAGGTTACC +>Gene.8::contig_20::g.8::m.8 type:internal len:104 contig_20:1-309(+) +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCATTTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA +>Gene.9::contig_20::g.9::m.9 type:internal len:103 contig_20:2-307(+) +GCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGACGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTCTTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCATTTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGAT +>Gene.10::contig_20::g.10::m.10 type:internal len:103 contig_20:307-2(-) +ATCCAAGTAGTTGATCCAACGAGACCAGCCCAACATGTAGCGGGTAGGAATGACGAAACCAGTGTAAATGACCAGCGCAAGGATAAGGATAGCTGCGGGAGCCATGGCCTGCGACAGTGTACGCGAAACGGATCCAATAGTGCGGAAGAGCATCGACATGACAAGCGTCAGCGTGAACGATATCAGCAGGAAGAAGAAGAATGCTCCTGGTTCGCGGCGAAGGTTCGTCATGAAGTACAAGATCAAGTTGAAACAGATCGCGTTGCCAATCTTGTAGGGCATATCCGTGAGCATCGATGCGTAAGC +>Gene.11::contig_21::g.11::m.11 type:5prime_partial len:168 contig_21:519-16(-) +GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTATGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATGACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAGAATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAACCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTATGCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGCACCCAAAGACTTGCATTCGAGTGA +>Gene.12::contig_24::g.12::m.12 type:internal len:111 contig_24:331-2(-) +AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTATGTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAAACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAAATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAATTTACTTAAC +>Gene.13::contig_29::g.13::m.13 type:3prime_partial len:267 contig_29:52-849(+) +ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCTGAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCACAGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCATATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGACCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGCAATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTGGTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGTTAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGAAGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCATAGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG +>Gene.14::contig_30::g.14::m.14 type:internal len:160 contig_30:1-477(+) +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTTATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGTCTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAAGTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGCTACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTGGTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT +>Gene.15::contig_31::g.15::m.15 type:3prime_partial len:263 contig_31:787-2(-) +ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAGAACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCTCTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAATGAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAAGAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTGAAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTGGATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAAATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCAGTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAGAAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG +>Gene.16::contig_33::g.16::m.16 type:internal len:206 contig_33:615-1(-) +GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGTTCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTGAAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCACGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAAAAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGATGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAGCGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGTCGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA +>Gene.17::contig_35::g.17::m.17 type:internal len:131 contig_35:2-391(+) +ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAGGAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTGACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAGGAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGACAGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA diff -r 000000000000 -r fcc558568020 test-data/transcripts_tgf.cleaned.nr.cds --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.cleaned.nr.cds Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,102 @@ +>contig_1 +AAAAAATTATATGGAGACAAGGAAGATATCCTTGTCCCAGATATTTTCTGGGATTACACGAGTGGAAAGGTGCTAACAAT +GGAGTGGGTTGAAGGTGTTAAATTAAATGAGCAAGATGCCGTTGAGAGTCAAGGGCTCAGTGTTCTGGATCTGGTGAATA +CCGGCATACAGTGCAGTCTTCGACAGCTGCTTGAGTACGGCTATTTTCATGCAGATCCTCACCCAGGGAATCTCTTAGCT +ACACCTGACGGGAAGCTTGCTTTTCTTGATTTTGGAATGATGAGTGAGACTCCTGAACAAGCAAGATCGGCCATAATTGG +TCATGTTGTACACATGGTTAAT +>contig_11 +ATTTATGGAAAGGGGATTCAAAATATGAGAACACTCTGGGGTGGCGTTGCTCCCGAATCTCCCGTCGTTGTTGTTGGAGG +CGGTGTTACTCCAGAATCTCCCGTCGTCGGAGGCATTGTTCTAGGATCTCCCGCAGTGCTGCTTAAGTCGGATTTACTCC +AAGCTCTCCCACCGCGGCTCCTGAAGTCGGCGTTGTTCCAAAATCTCCCGTCGCCACTGTTGAAGTCGGGGTTGCTCCAT +GATATCCCGTCGGAGTTGCTCCGAATCTCCCGTTGTTGCTGCTGCAGTCGGTGTTGCTCCAGAAACTCCCGCTGTGGCTA +T +>contig_18 +ACAGAGGTGAGAAGATGGAACAAGCAGGAAGATTGGGGTAGAAAGACATGGAAAGAAGCTAAGGAATCCACATTGCCGAA +AATAGTAGGTGAAGGGATCTATGGAGTTGGTCCCATTTTAGCTGCACTCTCATCCGGGCGAAGAGAACTCTACGCGTTGT +ACGTTCAGGAAGGTTTGGATTTGAGTAGTAACAGTAAGAAGAAGGACAAGAAACGGTTCGAGAGAGTTTTGAAAATGGTG +GAAAAGATTGGATTAAGCAAAAAAGAGGTATCCAAACACGACCTCAACATGGTCGTTGATAATAGGCCTCACCAGGGCTT +GCTTCTTGATGCTTCGGCACTTGAAATGGTTAGTATAAAGGAATTAGACCCCGTTTCCATTGATGGAGAGAAGTGCCCGC +TTTGGTTGGCATTGGATGAGGTTACC +>contig_2 +CTTTCCAAGGTACCCATCCCATCCAACAACATATATGCTATAAATGATAAGAAGTCCCCGGAAGATGCAGCAGACGACTA +CGAAAACCGCCTCAAGGAACTCGTCTCCGAAAAAATCATACCCGTTTCAACCATTAGCGGGTTCCCGAAGTTCGACCTCA +TGTTGCTTGGAATGGGGCCCGACGGCCATGTGGCCTCTCTTTTCCCTTCTCACATGCAACGCTATGAGAAGGAGAAATGG +GTCACTTTCATAACTGACTCTCCCAAACCGCCTCCGTCGAGAATCACTTTTACGTTTCCGATGATCAACTCGGCTTCGGA +GATCGCTATGGTGGTTACCGGGGCTGATTTGGCTGGTACAACTAAGATAGCATTGGGTACTACGGGCAATGTTAAGCCGG +GTGAGACTCCTTTGCCTTGTACTGAAGTTTCGGCTGAGGGAGAGGTTACTTGGTTCTTGGACAAAGATGCTGCTTCACAA +CTGTTAAATTATGTGCGCTTTGATGAT +>contig_20 +GGCTTACGCATCGATGCTCACGGATATGCCCTACAAGATTGGCAACGCGATCTGTTTCAACTTGATCTTGTACTTCATGA +CGAACCTTCGCCGCGAACCAGGAGCATTCTTCTTCTTCCTGCTGATATCGTTCACGCTGACGCTTGTCATGTCGATGCTC +TTCCGCACTATTGGATCCGTTTCGCGTACACTGTCGCAGGCCATGGCTCCCGCAGCTATCCTTATCCTTGCGCTGGTCAT +TTACACTGGTTTCGTCATTCCTACCCGCTACATGTTGGGCTGGTCTCGTTGGATCAACTACTTGGATCA +>contig_21 +GTTTCCATAGTGAATCAGGAACCTGTTCTATTCTCGGTTTCCATTGGAGAAAATATTGCTTACGGACTCCCAGATGATTA +TGTTTCCAAGGTCGATGTGATAAAAGCTGCTAAAGCAGCTAATGCTCATGAATTTATCATTGCGTTGCCACAGGGTTATG +ACACATTAGTTGGTGAGCGTGGTGGGTTGTTAAGTGGAGGACAAAGACAGAGGGTAGCCATTGCAAGGGCTCTGCTCAAG +AATGCTCCAATCTTGATTCTTGATGAGGCTACCAGTGCTTTGGACGCAGTCAGTGAACGTCTGGTTCAGGATGCTTTGAA +CCGTTTGATGAAAGGAAGAACGACTTTAGTGATTGCTCACAGGCTGAGCACCGTTCAAAATGCTGATCAAATTGCTTTAT +GCTCTGATGGGAAGATTTCAGAACTGGGGACACACTCTGAGTTGTTAGAGCAAAAGGGTCTTTATGCCTCACTGGTTGGC +ACCCAAAGACTTGCATTCGAG +>contig_24 +AAAACCCGTGAATTAGAAATCGAACAAATCTTGTTAAAATCCAAGGATTTGGAAAGCGAATTGGAGAGCAAGGGTAGTAT +GTTTATAAAGGAGACTGAGGCACTTGTTGCAGAAAACTCGAAACTCAGTCAGGAGTTGGGTGCATTTAAATCCGAGCTAA +ACGATATACAGATGAAATTGAACGTTGTTTCATCTGAGAAAGACGGCACTGTTGAAGAACTAACTAGTGCAAGAAAAGAA +ATAGAAGAGCTGACTCAGAAGCTTGCTTCTGAAGGACAAAAGCTGCAGTCTCAGATATCTTCTATAATGGAAGAGAACAA +TTTACTTAAC +>contig_29 +ATGAAGAAATCGAAGCTTCTGCAGAATTCGAAGGACTTACTTTCTAGGAGCTTCAATCCTGCTAAATGCAAAACGTCTCT +GAGGCTGGCGGGTTCAAGGTTGAAGCTATTGAGAAACAAGAAAGAGGTGCAACTGAAGCAGATGAAGCGGGAAATAGCAC +AGTTGCTCGAGTCTGGACAGGATCAGACCGCTCGAATTCGAGTCGAACATCTGATTAGGGAAGAGAAGATGATGGCTGCA +TATGATCTCCTCGATATATACTGCGAGCTTGTTGTTGCACGTCTTCCAGTAATTGAGTCACAAAAGAATTGCCCCATTGA +CCTGAAAGAAGCAATTGCAAGTTTAGTATTTGCAGCACCAAGATGTGGAGATGTACCCGAGTTTCTTGATGCAAGGAAGC +AATTTTCAGCTAAATATGGAAAAGATTTCACTACTGCAGCCACAGAACTTCGTCCACAGTGCGGTGTAGGCCGCATGTTG +GTTGAAAAATTATCTGCAACAGCGCCTGATGTACAGAGCAAAACTAAAATCTTGAATGCAATAGCTGAGGAGCACAATGT +TAAATGGGAACCCACATCATTTGGAGAGAACGACTCTGCACCTCTCAATGACCGACTGACTGGACCAAGTTCCTTTACGA +AGGAGAGAGAACAGTACCCTGAACCTCCTCATTTTGAAGCTGTACAAGTCCAAGCTCACCCGAGCAACAACACCTTGCAT +AGCTCGCCATCAAATTCTTCCCAGCAGGATGATAGAACCTCAGTTTTTGTTGAAACTTCTACTTTCAAGACACCATCG +>contig_3 +GTGGATGAAGGAGTTGTTGTTGCTGGCTTGTCAGAGCAGGAGAAGGCATCTGTTTCTGAAATTCTGACAACTGCTAGAGC +TCATTCAGAAACAATTGAGAACCTTAAGAGAGATCATTCCCAGCAGGTATCCTGTATCGAACAGCACACGAATGATACTT +TCAGGCAAAAATACATGGATTACGAGCCTACAGGGTCCACGCCAGTTAGGAGCGAGCCGGATATTCCCAGCAAAGGCACA +ATAGAGTCACTTCGTGCCATGCCTATAGATGCACTTGAAGAAGAATTTCGAGAAAACCATTCATACGAATCTGCTGTTAC +AGGAAAGGAACTAATGCCGTCTGTTACGACTCGTGCACCATTTTCACAGATCAAC +>contig_30 +AAGGCTAGTGGACTTTTTTCAAGTAAAGATTCTGTTGATTCAACAGATAGCCACATGGAAAATGTATGCTCTGATATTTT +ATCAATGAGCATCAACAAAAACCAAATTTTAGAGAATGGCCATGTTCATAACAATAGAGGAGCAGCAATATTTGAGTTGT +CTGGAGCTGCTACAAATGTAATTGAGGACGTTGGTTTGTCAGATGTCCAGTCTGACACCAGATTGGGAATGGCAAGTCAA +GTTTGCCAAGTTGATATGCATGAACCAGAGGGCGGTTTGTTGTCTTTTAAGAACCAAAGATTTAAGGATGCTGAGGTTGC +TACCAATATAACACATGATTATTGTCATGTATCTCATCTGTTAAAGCATTCTAACGTTCAAGTTCCTAAGTACATTAGTG +GTAATGGTTCAGCCACTGTTGATCTGAATAGGCAGACTGTAGATAGGAATAACAATTTTAAAGTTTCAACATCTAAT +>contig_31 +ATGACTAGATCCCGCCCACACATAGAGAAATTAGAAAGTAGAGTGTCTCAGGATGATCTTTTGGAGGGCACTTGTGCAAG +AACGAGGCCATTAAGCTATGATGAGATAATGCTCGGAAGAAATAACAAGGGAGATGCAGGTAAAGAAGTTGCCAGTGGCT +CTGGAGTGGCTGATAGTGCATCAGGGCATGGTGACATTGAAAAGATTTCTAATTTTCCAGAATACCATCGGCAAATAAAT +GAGGTTTCTGAACGTATGGATGTTAGACATACTTCAAATGATTTTCAGAAGGTAAGTTGCCGGAGAAAAGTGGATAGTAA +GAATGACAATTTAGTCCAGGATAAGGATGAAAAGTATAGGGAAAGTGGTGTCAAGTTAAAGAGTATATGGGAAAAGACTG +AAGGCAGCAAGAGAGTGAGAGAAGGAGAAAATGAAAGACGACATTACAGCAACAGAAAAAGAGATGGCCATTTAGGTGTG +GATTCATATAATGGATCAAATAAGAGGCAAGCCAGAGAGTCATATAGAAAGGGTAAAACTTCTGAAAGAGGCAGAGTCAA +ATCCGAAATAGATAGAAAACAGCTTGTTAACGATGAAGGACAGGTCCACAGGAAAAGGAAAACAGAACGGCGAATGAGCA +GTGACTCTGAGAAAGAGTACAAAAGAAGAGACGAAAGAAATGTGATGCATACAGAAAGATTAACTAACAGAGGCAGCCAG +AAGTCTGAAAAAGAAAACAGACGCAAACGTCATAATGAGGAGGATAAAACTAAAAGCTTGAGTACG +>contig_33 +GAAGAAATTAATGAAGTTGTGGCATTTCTACAAAATCCTCGTGCATTCCAAGAAATGGGAGCTCGGGCACCTCGGGGTGT +TCTTATTGTTGGTGAGATAGGAACAGGTAAAACATCCCTAGCAATGGCTATAGCAGCGGAAGCGAAGGTTCCTTTAGTTG +AAGTAAAAGCCCAACAGCTGGAAGCTGGTCTGTTTGTGGGCCAAGGTGCATCAAACGTTAGAGAATTGTTTCAAGCAGCA +CGGGATCTGGCTCCTGTCATTATATTTGTGGAAGACTTTGACCTCTTTGCTGGTGTCCGCGGGAAGGACCTTCAGACCAA +AAAGCTGGATCACGAATCTTTCATCAATCAACTTCTGGTGGAGCTTGATGGGTTTGAGAAACAAGATGGGGTAGTTTTGA +TGGCTACTACTCGGAATCTTAAACAAATCGATGGGGCTTTACTGCGTCCTGGTAGAATGGATCGAATATTTCATCTTCAG +CGACTAACTCAAGCAGAAAGGAGGAAAATCCTTCTTCTTGCTGCAAAAGAATCAATGGATGAAGAGCTCATTGACTTTGT +CGATTGGCAAAAGGTTGCTGAAAAGACAGCATTACTTCGCCCTATAGAATTAAAA +>contig_35 +ATTCACAGCCTTCTCTTTCATCTCGAGATTGTCTACCTTCTGCAGATCGATATGTCGATGCTTTACAGAGGGATATCGAG +GAAGGATAAACCTAGAGGACGTCAGCACGGGTTGACTCAACAGAAAAGGCAAGAGATAAAGGAAGCTTTTGAACTGTTTG +ACACCGATGGATCTGGAACTATTGATGCGAAAGAGTTGAACGTAGCAATGAGGGCTCTCGGTTTTGAAATGTCAGAAGAG +GAAATTACGAGAATGATAGCTGAAGTAGACAAAGACGGGAGTGGGGCGATTGACTTTGACGAGTTTTGTCACATGATGAC +AGCCAAATTCGGAGAAAGGGACACCAAAGAGGAGCTTACCAAGGCTTTTCAGATTATCGACAAAGATCAA +>contig_9 +CTTCGGTTAAAGGCAGATGAGGAGGCACAATGTTTGAATCAGATGCAGCGTATCATTTTTGATGAAATTATGGAGCATGT +GGAGTTAGAAAAGGGGGGCTTCTATTTCGTATATCGCCCTGGGGGCAACGGAAAGACCTTGTGGTTGGCTATTATCTCAA +AACTGAGAAGCGAGGGTAGAATAGTTCTCGCAGTGGCTTCATCAGGTATAGCATTGCTTTTGGTTGAGGGTGGTAGAACA +GCCCATTCTCGATTTAAAATACCCATAGATGTCAATGAATATAACAATTGTGAAATTAAACAGAACATCTACCTCGCTGA +ACTTATATGTCACACCAATTTGGTCATTTGGGATGAGGCACCTATGACTCAATATTTTGTCTTTGAGGCGGTT diff -r 000000000000 -r fcc558568020 test-data/transcripts_tgf.cleaned.nr.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.cleaned.nr.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,49 @@ +>contig_1 +KKLYGDKEDILVPDIFWDYTSGKVLTMEWVEGVKLNEQDAVESQGLSVLDLVNTGIQCSLRQLLEYGYFHADPHPGNLLA +TPDGKLAFLDFGMMSETPEQARSAIIGHVVHMVN +>contig_11 +IYGKGIQNMRTLWGGVAPESPVVVVGGGVTPESPVVGGIVLGSPAVLLKSDLLQALPPRLLKSALFQNLPSPLLKSGLLH +DIPSELLRISRCCCCSRCCSRNSRCGY +>contig_18 +TEVRRWNKQEDWGRKTWKEAKESTLPKIVGEGIYGVGPILAALSSGRRELYALYVQEGLDLSSNSKKKDKKRFERVLKMV +EKIGLSKKEVSKHDLNMVVDNRPHQGLLLDASALEMVSIKELDPVSIDGEKCPLWLALDEVT +>contig_2 +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKW +VTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQ +LLNYVRFDD +>contig_20 +GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGH +LHWFRHSYPLHVGLVSLDQLLGS +>contig_21 +VSIVNQEPVLFSVSIGENIAYGLPDDYVSKVDVIKAAKAANAHEFIIALPQGYDTLVGERGGLLSGGQRQRVAIARALLK +NAPILILDEATSALDAVSERLVQDALNRLMKGRTTLVIAHRLSTVQNADQIALCSDGKISELGTHSELLEQKGLYASLVG +TQRLAFE +>contig_24 +KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKE +IEELTQKLASEGQKLQSQISSIMEENNLLN +>contig_29 +MKKSKLLQNSKDLLSRSFNPAKCKTSLRLAGSRLKLLRNKKEVQLKQMKREIAQLLESGQDQTARIRVEHLIREEKMMAA +YDLLDIYCELVVARLPVIESQKNCPIDLKEAIASLVFAAPRCGDVPEFLDARKQFSAKYGKDFTTAATELRPQCGVGRML +VEKLSATAPDVQSKTKILNAIAEEHNVKWEPTSFGENDSAPLNDRLTGPSSFTKEREQYPEPPHFEAVQVQAHPSNNTLH +SSPSNSSQQDDRTSVFVETSTFKTPS +>contig_3 +VDEGVVVAGLSEQEKASVSEILTTARAHSETIENLKRDHSQQVSCIEQHTNDTFRQKYMDYEPTGSTPVRSEPDIPSKGT +IESLRAMPIDALEEEFRENHSYESAVTGKELMPSVTTRAPFSQIN +>contig_30 +KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQ +VCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN +>contig_31 +MTRSRPHIEKLESRVSQDDLLEGTCARTRPLSYDEIMLGRNNKGDAGKEVASGSGVADSASGHGDIEKISNFPEYHRQIN +EVSERMDVRHTSNDFQKVSCRRKVDSKNDNLVQDKDEKYRESGVKLKSIWEKTEGSKRVREGENERRHYSNRKRDGHLGV +DSYNGSNKRQARESYRKGKTSERGRVKSEIDRKQLVNDEGQVHRKRKTERRMSSDSEKEYKRRDERNVMHTERLTNRGSQ +KSEKENRRKRHNEEDKTKSLST +>contig_33 +EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAA +RDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQ +RLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK +>contig_35 +IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEE +EITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ +>contig_9 +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRT +AHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV diff -r 000000000000 -r fcc558568020 test-data/transcripts_tgf.pep --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/transcripts_tgf.pep Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,34 @@ +>Gene.1::contig_1::g.1::m.1 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(+) +LSKVPIPSNNIYAINDKKSPEDAADDYENRLKELVSEKIIPVSTISGFPKFDLMLLGMGPDGHVASLFPSHMQRYEKEKWVTFITDSPKPPPSRITFTFPMINSASEIAMVVTGADLAGTTKIALGTTGNVKPGETPLPCTEVSAEGEVTWFLDKDAASQLLNYVRFDD* +>Gene.3::contig_3::g.3::m.3 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(+) +LRLKADEEAQCLNQMQRIIFDEIMEHVELEKGGFYFVYRPGGNGKTLWLAIISKLRSEGRIVLAVASSGIALLLVEGGRTAHSRFKIPIDVNEYNNCEIKQNIYLAELICHTNLVIWDEAPMTQYFVFEAV +>Gene.5::contig_11::g.5::m.5 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(-) +AAKVTVAPGSRVAAAGSGVASESPATAEAGVAPGSPAVDFNSHSGSFWSNTDCSSNNGRFGATPTGYHGATPTSTVATGDFGTTPTSGAAVGELGVNPT* +>Gene.7::contig_18::g.7::m.7 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(+) +GLRIDAHGYALQDWQRDLFQLDLVLHDEPSPRTRSILLLPADIVHADACHVDALPHYWIRFAYTVAGHGSRSYPYPCAGHLHWFRHSYPLHVGLVSLDQLLGS +>Gene.9::contig_20::g.9::m.9 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(-) +IQVVDPTRPAQHVAGRNDETSVNDQRKDKDSCGSHGLRQCTRNGSNSAEEHRHDKRQRERYQQEEEECSWFAAKVRHEVQDQVETDRVANLVGHIREHRCVS +>Gene.11::contig_21::g.11::m.11 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(-) +KTRELEIEQILLKSKDLESELESKGSMFIKETEALVAENSKLSQELGAFKSELNDIQMKLNVVSSEKDGTVEELTSARKEIEELTQKLASEGQKLQSQISSIMEENNLLN +>Gene.13::contig_29::g.13::m.13 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(+) +KASGLFSSKDSVDSTDSHMENVCSDILSMSINKNQILENGHVHNNRGAAIFELSGAATNVIEDVGLSDVQSDTRLGMASQVCQVDMHEPEGGLLSFKNQRFKDAEVATNITHDYCHVSHLLKHSNVQVPKYISGNGSATVDLNRQTVDRNNNFKVSTSN +>Gene.15::contig_31::g.15::m.15 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(-) +EEINEVVAFLQNPRAFQEMGARAPRGVLIVGEIGTGKTSLAMAIAAEAKVPLVEVKAQQLEAGLFVGQGASNVRELFQAARDLAPVIIFVEDFDLFAGVRGKDLQTKKLDHESFINQLLVELDGFEKQDGVVLMATTRNLKQIDGALLRPGRMDRIFHLQRLTQAERRKILLLAAKESMDEELIDFVDWQKVAEKTALLRPIELK +>Gene.17::contig_35::g.17::m.17 type:internal len:131 gc:universal contig_35:2-391(+) +IHSLLFHLEIVYLLQIDMSMLYRGISRKDKPRGRQHGLTQQKRQEIKEAFELFDTDGSGTIDAKELNVAMRALGFEMSEEEITRMIAEVDKDGSGAIDFDEFCHMMTAKFGERDTKEELTKAFQIIDKDQ diff -r 000000000000 -r fcc558568020 tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,6 @@ + + + value, name, path, description + +
+ diff -r 000000000000 -r fcc558568020 tool_data_table_conf.xml.test --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.test Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,6 @@ + + + value, name, path, description + +
+ diff -r 000000000000 -r fcc558568020 utils.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/utils.py Thu Jun 08 12:44:09 2017 -0400 @@ -0,0 +1,80 @@ +import os +import shutil +import subprocess +import sys + +FSTDERR = 'stderr.txt' +FSTDOUT = 'stdout.txt' + + +def check_execution_errors(rc, fstderr, fstdout): + if rc != 0: + fh = open(fstdout, 'rb') + out_msg = fh.read() + fh.close() + fh = open(fstderr, 'rb') + err_msg = fh.read() + fh.close() + msg = '%s\n%s\n' % (str(out_msg), str(err_msg)) + stop_err(msg) + + +def get_response_buffers(): + fstderr = os.path.join(os.getcwd(), FSTDERR) + fherr = open(fstderr, 'wb') + fstdout = os.path.join(os.getcwd(), FSTDOUT) + fhout = open(fstdout, 'wb') + return fstderr, fherr, fstdout, fhout + + +def move_directory_files(source_dir, destination_dir, copy=False): + source_directory = os.path.abspath(source_dir) + destination_directory = os.path.abspath(destination_dir) + if not os.path.isdir(destination_directory): + os.makedirs(destination_directory) + for dir_entry in os.listdir(source_directory): + source_entry = os.path.join(source_directory, dir_entry) + if copy: + shutil.copy(source_entry, destination_directory) + else: + shutil.move(source_entry, destination_directory) + + +def run_command(cmd): + fstderr, fherr, fstdout, fhout = get_response_buffers() + proc = subprocess.Popen(args=cmd, stderr=fherr, stdout=fhout, shell=True) + rc = proc.wait() + # Check results. + fherr.close() + fhout.close() + check_execution_errors(rc, fstderr, fstdout) + + +def stop_err(msg): + sys.exit(msg) + + +def write_html_output(output, title, dir): + with open(output, 'w') as fh: + dir_items = sorted(os.listdir(dir)) + # Directories can only contain either files or directories, + # but not both. + if len(dir_items) > 0: + item_path = os.path.join(dir, dir_items[0]) + if os.path.isdir(item_path): + header = 'Directories' + else: + header = 'Datasets' + else: + header = '' + fh.write('

%s: %d items

\n' % (title, len(dir_items))) + fh.write('

\n') + fh.write('%s\n' % header) + for index, fname in enumerate(dir_items): + if index % 2 == 0: + bgcolor = '#D8D8D8' + else: + bgcolor = '#FFFFFF' + link = '%s\n' % (fname, fname) + fh.write('\n' % (bgcolor, link)) + fh.write('
%s
\n')