|
Commit message:
planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty |
|
added:
README.rst macros.xml pairwise.xml scripts/S01_run_first_blast.py scripts/S02_04_keep_one_hit_from_blast.py scripts/S03_run_second_blast.py scripts/S05_find_rbh.py static/images/adaptsearch_picture_helps.png test-data/inputs_diamond/AcAcaud_Trinity.fasta test-data/inputs_diamond/AmAmphi_Trinity.fasta test-data/inputs_diamond/ApApomp_Trinity.fasta test-data/inputs_diamond/PfPfiji_Trinity.fasta test-data/inputs_tblastx/AcAcaud_trinity.fasta test-data/inputs_tblastx/AmAmphi_trinity.fasta test-data/inputs_tblastx/ApApomp_trinity.fasta test-data/inputs_tblastx/PfPfiji_trinity.fasta test-data/outputs_diamond_dna/RBH_AcAcaudAmAmphi test-data/outputs_diamond_dna/RBH_AcAcaudApApomp test-data/outputs_diamond_dna/RBH_AcAcaudPfPfiji test-data/outputs_diamond_dna/RBH_AmAmphiPfPfiji test-data/outputs_diamond_dna/RBH_ApApompPfPfiji test-data/outputs_dna_tblastx/RBH_AcAcaud_AmAmphi_dna test-data/outputs_dna_tblastx/RBH_AcAcaud_ApApomp_dna test-data/outputs_dna_tblastx/RBH_AcAcaud_PfPfiji_dna test-data/outputs_dna_tblastx/RBH_AmAmphi_ApApomp_dna test-data/outputs_dna_tblastx/RBH_AmAmphi_PfPfiji_dna test-data/outputs_dna_tblastx/RBH_ApApomp_PfPfiji_dna test-data/outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta test-data/outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta test-data/outputs_prot/ReciprocalBestHits_ApApomp_AmAmphi.fasta test-data/outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta test-data/outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta test-data/outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta test-data/pairwise.out |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,14 @@ +Changelog +--------- + +**Version 2.0 - 18/04/2017** + + - NEW: Replace the zip between tools by Dataset Collection + + +**Version 1.0 - 13/04/2017** + + - TEST: Add funtional test with planemo + + - IMPROVEMENT: Use conda dependencies for blast, samtools and python + |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +<macros> + + <xml name="python_required"> + <requirement type="package" version="2.7">python</requirement> + </xml> + + <token name="@HELP_AUTHORS@"> +.. class:: infomark + +**Authors** Eric Fontanillas created the version 1 of this pipeline. Victor Mataigne developped version 2. + +.. class:: infomark + +**Galaxy integration** Julie Baffard and ABiMS TEAM, Roscoff Marine Station + + | Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool. + | Credits : Gildas le Corguillé, Misharl Monsoor + +--------------------------------------------------- + + </token> + + <xml name="citations"> + <citations> + <citation type="bibtex">Credits : ABIMS team, Roscoff Marine Station</citation> + <citation type="bibtex">Contact support.abims@sb-roscoff.fr for any questions or concerns about the Galaxy implementation of this tool.</citation> + <citation type="bibtex">Version 1 : Scripts by Eric Fontanillas -- Galaxy integration by Julie Baffard</citation> + <citation type="bibtex">Version 2 : improvments by Victor Mataigne, Gildas le Corguillé, Misharl Monsoor</citation> + </citations> + </xml> + +</macros> |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d pairwise.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pairwise.xml Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| b'@@ -0,0 +1,243 @@\n+<tool name="Pairwise" id="pairwise" version="2.1.1">\n+\n+ <description>\n+ Find homologous couples by blast with RBH\n+ </description>\n+\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+\n+ <requirements>\n+ <expand macro="python_required" />\n+ <requirement type="package" version="1.65">biopython</requirement>\n+ <requirement type="package" version="0.9.22">diamond</requirement>\n+ <requirement type="package" version="2.2.22">blast-legacy</requirement> \n+ </requirements>\n+\n+ <command><![CDATA[\n+ #set $infiles = ""\n+ #for $input in $inputs\n+ ln -s \'$input\' \'$input.element_identifier\';\n+ #set $infiles = $infiles + $input.element_identifier + ","\n+ #end for\n+ #set $infiles = $infiles[:-1]\n+ \n+ ln -s $__tool_directory__/scripts/S02_04_keep_one_hit_from_blast.py . &&\n+ ln -s $__tool_directory__/scripts/S03_run_second_blast.py . &&\n+ ln -s $__tool_directory__/scripts/S05_find_rbh.py . && \n+\n+ python -W ignore $__tool_directory__/scripts/S01_run_first_blast.py $infiles ${e_value} $method\n+ > ${output};\n+ ]]></command>\n+\n+ <inputs>\n+ <param name="inputs" type="data" format="fasta" multiple="true" label="Input fasta files" />\n+ <param name="method" type="select" label="Alignment tool to use" help="tblastx is slow and sensitive, diamond is a lot quicker and less sensitive">\n+ <option value="tblastx">tblastx</option>\n+ <option value="diamond">Diamond</option>\n+ </param>\n+ <param name="e_value" type="float" value="1e-5" label="e_value" help="e-value for blast." />\n+ </inputs>\n+\n+ <outputs>\n+ <data format="txt" name="output" label="Pairwise" />\n+ <collection name="output_fasta_dna" type="list" label="Pairwise_DNA">\n+ <discover_datasets pattern="__name_and_ext__" directory="outputs_RBH_dna" />\n+ </collection>\n+ </outputs>\n+\n+ <tests>\n+ <test>\n+ <param name="inputs" ftype="fasta" value="inputs_tblastx/AcAcaud_trinity.fasta,inputs_tblastx/AmAmphi_trinity.fasta,inputs_tblastx/ApApomp_trinity.fasta,inputs_tblastx/PfPfiji_trinity.fasta" />\n+ <param name="e-value" value="1e-5" />\n+ <param name="method" value="tblastx" />\n+ <output_collection name="output_fasta_dna" type="list">\n+ <element name="RBH_AcAcaud_AmAmphi_dna">\n+ <assert_contents>\n+ <has_text text=">Ac5_1/1_1.000_160"/>\n+ <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>\n+ <has_text text=">Am1_1/1_1.000_160"/>\n+ <has_text text=">Ac7_1/1_1.000_160"/>\n+ <has_text text="GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGG"/>\n+ <has_text text=">Am3_1/1_1.000_160"/>\n+ <has_text text=">Ac6_1/1_1.000_160"/>\n+ <has_text text="CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTA"/>\n+ <has_text text=">Am2_1/1_1.000_160"/>\n+ </assert_contents>\n+ </element>\n+ <element name="RBH_AcAcaud_PfPfiji_dna">\n+ <assert_contents>\n+ <has_text text=">Ac8_1/1_1.000_160"/>\n+ <has_text text="ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTG"/>\n+ <has_text text=">Pf8_1/1_1.000_160"/>\n+ <has_text text=">Ac5_1/1_1.000_160"/>\n+ <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>\n+ <has_text text=">Pf7_1/1_1.000_160"/>\n+ </assert_contents>\n+ </element>\n+ '..b' <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCAC"/>\n+ <has_text text=">Pf7_1/1_1.000_160"/>\n+ </assert_contents>\n+ </element>\n+ <element name="RBH_AmAmphi_PfPfiji_dna">\n+ <assert_contents>\n+ <has_text text=">Am8_1/1_1.000_160"/>\n+ <has_text text="GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCAT"/>\n+ <has_text text=">Pf9_1/1_1.000_160"/>\n+ <has_text text=">Am1_1/1_1.000_160"/>\n+ <has_text text="GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCA"/>\n+ <has_text text=">Pf7_1/1_1.000_160"/>\n+ </assert_contents>\n+ </element>\n+ <element name="RBH_ApApomp_PfPfiji_dna">\n+ <assert_contents>\n+ <has_text text=">Ap2_1/1_1.000_160"/>\n+ <has_text text="ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTA"/>\n+ <has_text text=">Pf5_1/1_1.000_160"/>\n+ <!--\n+ <has_text text=">Ap1_1/1_1.000_160"/>\n+ <has_text text="GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAA"/>\n+ <has_text text=">Pf4_1/1_1.000_160"/>\n+ <has_text text=">Ap4_1/1_1.000_160"/>\n+ <has_text text="CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGA"/>\n+ <has_text text=">Pf10_1/1_1.000_160"/>\n+ <has_text text=">Ap3_1/1_1.000_160"/>\n+ <has_text text="GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCT"/>\n+ <has_text text=">Pf6_1/1_1.000_160"/>\n+ -->\n+ </assert_contents>\n+ </element>\n+ </output_collection>\n+ </test>\n+ </tests>\n+\n+ <help>\n+\n+ @HELP_AUTHORS@\n+ \n+<![CDATA[\n+\n+**Description**\n+\n+This tool searches for different homologous genes from pairwise comparisons between a set of fasta files (one file per species).\n+ \n+--------\n+\n+**Parameters**\n+\n+ - \'Input files\' : a collection of fasta files (one file per species)\n+ - \'e_value\' : the blast e-value. By default it\'s 1e-5.\n+ - \'Alignment tool\' : choose the sequences alignment tool between tblastx and Diamond. tblastx is more sensitive and Diamond is much faster.\n+\n+--------\n+\n+**Outputs**\n+\n+ - \'Pairwise\' : the general output. It gives the information about what the tool has done for each pairwise.\n+\n+ - \'Pairwise_DNA\' : the output which contains nucleic sequences (of the pairwise) that are homologous. The sequences are in nucleic format. There are one file per couple of species, and homologous pairs are written by sets of 4 lines : \n+\n+Exemple for two homologous pairs for the output file for species X/Y :\n+\n+| >Gene_A_species_X_homologous_to_Gene_B_species_Y\n+| Nucleic_sequence_from_filter_assemblies\n+| >Gene_B_species_Y_homologous_to_Gene_A_species_X\n+| Nucleic_sequence_from_filter_assemblies\n+| >Gene_C_species_X_homologous_to_Gene_D_species_Y\n+| Nucleic_sequence_from_filter_assemblies\n+| >Gene_D_species_Y_homologous_to_Gene_C_species_X\n+| Nucleic_sequence_from_filter_assemblies\n+\n+\n+--------\n+\n+**The AdaptSearch Pipeline**\n+\n+.. image:: adaptsearch_picture_helps.png\n+\n+---------\n+\n+Changelog\n+---------\n+\n+**Version 2.1 - 03/07/2018**\n+\n+ - Add the possibility to use Diamond instead of tblastx\n+\n+**Version 2.0 - 18/04/2017**\n+\n+ - NEW: Replace the zip between tools by Dataset Collection\n+\n+\n+**Version 1.0 - 13/04/2017**\n+\n+ - TEST: Add functional test with planemo\n+\n+ - IMPROVEMENT: Use conda dependencies for blast, samtools and python\n+\n+ ]]>\n+ </help>\n+\n+</tool>\n' |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d scripts/S01_run_first_blast.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01_run_first_blast.py Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| b'@@ -0,0 +1,170 @@\n+#!/usr/bin/env python\n+# coding: utf-8\n+# Author : Victor Mataigne\n+\n+import itertools, argparse, os\n+\n+"""\n+IMPROVMENTS :\n+ - Maybe a bit of code factoring\n+ - See if it possible to avoid build several times the same db\n+"""\n+\n+# The script (and S03_run_second_blast.py as well) must be launched with the python \'-W ignore\' option if tested with planemo\n+\n+def main():\n+ parser = argparse.ArgumentParser()\n+ parser.add_argument(\'files\', help=\'fasta files separated by commas\')\n+ parser.add_argument(\'evalue\', help=\'evalue for blast\')\n+ parser.add_argument(\'method\', choices=[\'tblastx\', \'diamond\'], help=\'alignment tool (tblastx or diamond)\')\n+ args = parser.parse_args()\n+\n+ in_files = args.files.split(\',\')\n+\n+ if args.method == \'diamond\':\n+ in_files_translated = []\n+ from Bio.Seq import Seq\n+ from Bio.Alphabet import IUPAC\n+\n+ # From every sequence, make three sequences (translations in the three reading frames)\n+ print \'Translating every sequence in all reading frames ...\'\n+ for file in in_files:\n+ name = \'translated_%s\' %file\n+ in_files_translated.append(name)\n+ translated_file = open(name, \'w\')\n+ with open(file, \'r\') as file:\n+ for name, seq in itertools.izip_longest(*[file]*2):\n+ s = Seq(seq.strip(\'\\n\').upper(), IUPAC.ambiguous_dna)\n+ translated_file.write(name.strip(\'\\n\')+\'_orf_1\\n\')\n+ translated_file.write(s.translate()._data+\'\\n\')\n+ translated_file.write(name.strip(\'\\n\')+\'_orf_2\\n\')\n+ translated_file.write(s[1:].translate()._data+\'\\n\')\n+ translated_file.write(name.strip(\'\\n\')+\'_orf_3\\n\')\n+ translated_file.write(s[2:].translate()._data+\'\\n\')\n+ translated_file.close()\n+\n+ # Make the list of all pairwise combinations\n+ list_pairwise = itertools.combinations(in_files_translated, 2)\n+\n+ elif args.method == \'tblastx\':\n+ list_pairwise = itertools.combinations(in_files, 2)\n+\n+ else :\n+ print \'Mispecified alignment tool\'\n+ exit()\n+\n+ os.mkdir(\'outputs_RBH_dna\')\n+\n+ # Main loop\n+\n+ if args.method == \'diamond\':\n+ for pairwise in list_pairwise:\n+ print "Pair of species:"\n+ print pairwise\n+\n+ sp1, sp2 = pairwise[0].split(\'_\')[1], pairwise[1].split(\'_\')[1] #rename \'translated_Xx_transcriptom.fasta\'\n+ sub_directory_name = sp1 + \'_\' + sp2\n+ os.mkdir(\'./blast_%s\' %sub_directory_name)\n+\n+ print \'Running first blast with Diamond ...\'\n+\n+ # Run diamond\n+ os.system(\'diamond makedb --in %s -d %s >> log_diamond.log\' %(pairwise[1], sp2))\n+ os.system(\'diamond blastp -q %s -d %s --max-target-seqs 1 -o matches_blast1_%s -e %s --more-sensitive >> log_diamond.log\' %(pairwise[0], sp2, sub_directory_name, args.evalue))\n+\n+ # tabular output :\n+ # qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n+ \n+ a = pairwise[1].replace(\'translated_\', \'\')\n+ b = pairwise[0].replace(\'translated_\', \'\')\n+\n+ # There is a chance to have no hits returned\n+ if os.path.getsize(\'matches_blast1_%s\' %sub_directory_name) == 0:\n+ print \'No hits found. Processing next species pair ...\'\n+ else :\n+\n+ # Record only one best_hit per transcript (best of the 6 orfs)\n+ os.system(\'python S02_04_keep_one_hit_from_blast.py matches_blast1_%s %s %s %s %s %s\' %(sub_directory_name, a, b, sub_directory_name, \'1\', args.method))\n+\n+ # 2d blast with only best hits as db\n+ print \'Running second blast with Diamond ... \'\n+\n+ os.system(\'python -W ignore S03_run_second_blast.py best_hits_db_blast1_%s %s %s %s %s\' %(sub_directory_name, pairwise[0], sub_director'..b'keep_one_hit_from_blast.py matches_blast2_%s %s %s %s %s %s\' %(sub_directory_name, b, a, sub_directory_name, \'2\', args.method))\n+\n+ # Find Reciprocical Best Hits\n+ name1 = \'best_hits_q_blast1_{}\'.format(sub_directory_name)\n+ name2 = \'best_hits_q_blast2_{}\'.format(sub_directory_name)\n+ os.system(\'python S05_find_rbh.py %s %s \' %(name1, name2))\n+\n+ os.system(\'mv log_diamond.log ./blast_%s\' %sub_directory_name) \n+ os.system(\'rm -f *.dmnd\')\n+\n+ # Those files exist obly if hits were found during the first blast\n+ if os.path.getsize(\'matches_blast1_%s\' %sub_directory_name) != 0:\n+ os.system(\'mv *best_hits* ./blast_%s\' %sub_directory_name)\n+ os.system(\'mv RBH* outputs_RBH_dna\')\n+\n+ os.system(\'mv matches_blast* ./blast_%s\' %(sub_directory_name))\n+\n+ os.mkdir(\'translated_seqs\')\n+ os.system(\'mv translated*.fasta ./translated_seqs\')\n+\n+ elif args.method == \'tblastx\':\n+ for pairwise in list_pairwise:\n+ print "Pair of species:"\n+ print pairwise\n+\n+ sp1, sp2 = pairwise[0].split(\'_\')[0], pairwise[1].split(\'_\')[0]\n+ sub_directory_name = sp1 + \'_\' + sp2\n+ os.mkdir(\'./blast_%s\' %sub_directory_name)\n+\n+ print \'Running first tblastx ...\'\n+\n+ # Run diamond\n+ os.system(\'formatdb -i %s -p F -o T >> log_tblastx.log\' %(pairwise[1]))\n+ os.system(\'blastall -p tblastx -d %s -i %s -o matches_blast1_%s -T F -e %s -F "mS" -b1 -v1 -K 1 -m 8 >> log_tblastx.log\' %(pairwise[1], pairwise[0], sub_directory_name, args.evalue))\n+\n+ # tabular output :\n+ # qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore\n+ \n+ # There is a chance to have no hits returned\n+ if os.path.getsize(\'matches_blast1_%s\' %sub_directory_name) == 0:\n+ print \'No hits found. Processing next species pair ...\'\n+ else:\n+\n+ # Record only one best_hit per transcript (best of the 6 orfs)\n+ os.system(\'python S02_04_keep_one_hit_from_blast.py matches_blast1_%s %s %s %s %s %s\' %(sub_directory_name, pairwise[1], pairwise[0], sub_directory_name, \'1\', args.method))\n+\n+ # 2d blast with only best hits as db\n+ print \'Running second blast with Diamond ... \'\n+\n+ os.system(\'python S03_run_second_blast.py best_hits_db_blast1_%s %s %s %s %s\' %(sub_directory_name, pairwise[0], sub_directory_name, args.evalue, args.method))\n+\n+ # Record only one best_hit per transcript (best of the 6 orfs)\n+ os.system(\'python S02_04_keep_one_hit_from_blast.py matches_blast2_%s %s %s %s %s %s\' %(sub_directory_name, pairwise[0], pairwise[1], sub_directory_name, \'2\', args.method))\n+\n+ # Find Reciprocical Best Hits\n+ name1 = \'best_hits_q_blast1_{}\'.format(sub_directory_name)\n+ name2 = \'best_hits_q_blast2_{}\'.format(sub_directory_name)\n+ os.system(\'python S05_find_rbh.py %s %s \' %(name1, name2))\n+\n+ os.system(\'mv log_tblastx.log ./blast_%s\' %sub_directory_name) \n+ os.system(\'rm -f *.nhr\')\n+ os.system(\'rm -f *.nin\')\n+ os.system(\'rm -f *.nsd\')\n+ os.system(\'rm -f *.nsi\')\n+ os.system(\'rm -f *.nsq\')\n+\n+ # Those files exist obly if hits were found during the first blast\n+ if os.path.getsize(\'matches_blast1_%s\' %sub_directory_name) != 0:\n+ os.system(\'mv *best_hits* ./blast_%s\' %sub_directory_name)\n+ os.system(\'mv RBH* outputs_RBH_dna\') \n+\n+ os.system(\'mv matches_blast* ./blast_%s\' %(sub_directory_name))\n+ #os.system(\'mv matches_blast2_%s ./blast_%s\' %(sub_directory_name, sub_directory_name)) \n+\n+if __name__ == "__main__":\n+ main()\n' |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d scripts/S02_04_keep_one_hit_from_blast.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S02_04_keep_one_hit_from_blast.py Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,140 @@ +#!/usr/bin/env python +# coding: utf-8 +# Author : Victor Mataigne + +import argparse, itertools, pickle + +def list_with_max_score(list_of_hits): + """ Among a list of blast hits of the same query, returns the one which has the highest score """ + max_score = 0 + ind_max_score = 0 + i = 0 + + for hit in list_of_hits: + if float(hit[11]) > max_score: + max_score, ind_max_score = hit[11], i + i += 1 + + return list_of_hits[ind_max_score] + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('matches', help='diamond blastp output file (tabular) between two species') + parser.add_argument('nucleic_file_db', help='Sequence file used as DB for the first blast') + parser.add_argument('nucleic_file_q', help='Sequence used as query for the first blast') + parser.add_argument('file_subname', help='keyword for output file name') + parser.add_argument('step', help='1 or 2 according to which blast has been performed') + parser.add_argument('method', choices=['tblastx', 'diamond'], help='alignment tool (tblastx or diamond)') + args = parser.parse_args() + + print 'Keeping best hits in {}'.format(args.matches) + + # read tab file in a list (a line = a list elem) + list_hits = [] + dic_hits_common = {} # unique matches for query + dic_hits_common_db = {} # unique matches for db + with open(args.matches, 'r') as hits: + for hit in hits.readlines(): + h = hit.strip('\n') + h2 = h.split('\t') + list_hits.append(h2) + + if args.method == 'diamond': + if h2[0][0:-6] not in dic_hits_common.keys(): + dic_hits_common[h2[0][0:-6]] = [] + if h2[1][0:-6] not in dic_hits_common_db.keys(): + dic_hits_common_db[h2[1][0:-6]] = [] + + elif args.method == 'tblastx': + if h2[0] not in dic_hits_common.keys(): + dic_hits_common[h2[0]] = [] + if h2[1] not in dic_hits_common_db.keys(): + dic_hits_common_db[h2[1]] = [] + + # Gather in a list of lists elems with common query + for hit in list_hits: + if args.method == 'diamond': + dic_hits_common[hit[0][0:-6]].append(hit) + dic_hits_common_db[hit[1][0:-6]].append(hit) + + elif args.method == 'tblastx': + dic_hits_common[hit[0]].append(hit) + dic_hits_common_db[hit[1]].append(hit) + + # Keep only the best hits in queries + list_best_hits_q = [] + for list_hits in dic_hits_common.values(): + list_best_hits_q.append(list_with_max_score(list_hits)) + + # Keep only the best hits in db + list_best_hits_db = [] + for list_hits in dic_hits_common_db.values(): + list_best_hits_db.append(list_with_max_score(list_hits)) + + del list_hits + + # This dict (exported then with pickle) stores the best hit in the db for the query + # A similar dict is built after the second blast, in which query and db are switched + # The comparison of the dicts allow to spot RBH + dico_best_hits_q = {} + for hit in list_best_hits_q: + if args.method == 'diamond': + dico_best_hits_q[hit[0][0:-6]] = hit[1][0:-6] + elif args.method == 'tblastx': + dico_best_hits_q[hit[0]] = hit[1] + + n = 'dict_best_hits_from_blast_{}'.format(args.step) + pickle_dic_besthits_q = open(n, 'w') + pickle.dump(dico_best_hits_q, pickle_dic_besthits_q) + pickle_dic_besthits_q.close() + + ## Other temp files : + + # Make big dictionary with initial query fasta file + initial_seqs_q = {} + with open(args.nucleic_file_q, 'r') as nf : + for h, s in itertools.izip_longest(*[nf]*2): + header = h.strip('\n') + sequence = s.strip('\n') + initial_seqs_q[header] = sequence + + # Make big dictionary with initial DB fasta file + initial_seqs_db = {} + with open(args.nucleic_file_db, 'r') as nf : + for h, s in itertools.izip_longest(*[nf]*2): + header = h.strip('\n') + sequence = s.strip('\n') + initial_seqs_db[header] = sequence + + # Write best_hits from query with nucleic sequence in output file + name = 'best_hits_q_blast{}_{}'.format(args.step, args.file_subname) + output = open(name, 'w') + for hit in list_best_hits_q: + if args.method == 'diamond': + output.write('>'+hit[0][0:-6]+'\n') + output.write(initial_seqs_q['>'+hit[0][0:-6]]+'\n') + elif args.method == 'tblastx': + output.write('>'+hit[0]+'\n') + output.write(initial_seqs_q['>'+hit[0]]+'\n') + output.close() + + # Write best_hits on db with nucleic sequence in output file + name = 'best_hits_db_blast{}_{}'.format(args.step, args.file_subname) + output = open(name, 'w') + for hit in list_best_hits_db: + if args.method == 'diamond': + output.write('>'+hit[1][0:-6]+'\n') + output.write(initial_seqs_db['>'+hit[1][0:-6]]+'\n') + elif args.method == 'tblastx': + output.write('>'+hit[1]+'\n') + output.write(initial_seqs_db['>'+hit[1]]+'\n') + + output.close() + + del initial_seqs_q + del initial_seqs_db + + print 'Done' + +if __name__ == "__main__": + main() \ No newline at end of file |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d scripts/S03_run_second_blast.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S03_run_second_blast.py Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,45 @@ +#!/usr/bin/env python +# coding: utf-8 +# Author : Victor Mataigne + +import itertools, argparse, os + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('query_file', help='fasta file (to translate) for query') + parser.add_argument('db_file', help='fasta files (already translated) for db') + parser.add_argument('file_subname', help='keyword for output file name') + parser.add_argument('evalue', help='evalue for blast') + parser.add_argument('method', choices=['tblastx', 'diamond'], help='alignment tool (tblastx or diamond)') + args = parser.parse_args() + + if args.method == 'diamond': + from Bio.Seq import Seq + from Bio.Alphabet import IUPAC + # Traduire les best hits + f_name = 'translated_{}'.format(args.query_file) + translated_file = open(f_name, 'w') + with open(args.query_file, 'r') as file: + for name, seq in itertools.izip_longest(*[file]*2): + s = Seq(seq.strip('\n').upper(), IUPAC.ambiguous_dna) + translated_file.write(name.strip('\n')+'_orf_1\n') + translated_file.write(s.translate()._data+'\n') + translated_file.write(name.strip('\n')+'_orf_2\n') + translated_file.write(s[1:].translate()._data+'\n') + translated_file.write(name.strip('\n')+'_orf_3\n') + translated_file.write(s[2:].translate()._data+'\n') + translated_file.close() + + os.system('diamond makedb --in %s -d %s >> log_diamond.log' %(args.db_file, args.db_file.split('_')[1])) + os.system('diamond blastp -q %s -d %s --max-target-seqs 1 -o matches_blast2_%s -e %s --more-sensitive >> log_diamond.log' %(f_name, args.db_file.split('_')[1], args.file_subname, args.evalue)) + + elif args.method == 'tblastx': + os.system('formatdb -i %s -p F -o T >> log_tblastx.log' %(args.db_file)) + os.system('blastall -p tblastx -d %s -i %s -o matches_blast2_%s -T F -e %s -F "mS" -b1 -v1 -K 1 -m 8 >> log_tblastx.log' %(args.db_file, args.query_file, args.file_subname, args.evalue)) + + else : + print 'Mispecified alignment tool' + exit() + +if __name__ == "__main__": + main() |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d scripts/S05_find_rbh.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S05_find_rbh.py Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,53 @@ +#!/usr/bin/env python +# coding: utf-8 +# Author : Victor Mataigne + +import argparse, pickle, itertools + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('besthits_file1', help='') + parser.add_argument('besthits_file2', help='') + args = parser.parse_args() + + # Open dict of best hits + file_best_hit_dict_q = open('dict_best_hits_from_blast_1') + file_best_hit_dict_db = open('dict_best_hits_from_blast_2') + best_hit_dict_q = pickle.load(file_best_hit_dict_q) + best_hit_dict_db = pickle.load(file_best_hit_dict_db) + file_best_hit_dict_q.close() + file_best_hit_dict_db.close() + + best_h1 = {} + with open(args.besthits_file1, 'r') as bh1 : + for h, s in itertools.izip_longest(*[bh1]*2): + header = h.strip('>\n') + sequence = s.strip('\n') + best_h1[header] = sequence + + best_h2 = {} + with open(args.besthits_file2, 'r') as bh2 : + for h, s in itertools.izip_longest(*[bh2]*2): + header = h.strip('>\n') + sequence = s.strip('\n') + best_h2[header] = sequence + + # Find RBH: + reverse_best_hit_dict_db = dict((v,k) for k,v in best_hit_dict_db.iteritems()) + + rbh = set(best_hit_dict_q.items()).intersection(set(reverse_best_hit_dict_db.items())) + + s = args.besthits_file1.split('_') + suffix = s[4] + '_' + s[5] + out_name = 'RBH_{}_dna.fasta'.format(suffix) + output = open(out_name, 'w') + + for pairwise_couple in rbh : + output.write('>'+pairwise_couple[0]+'\n') + output.write(best_h1[pairwise_couple[0]]+'\n') + output.write('>'+pairwise_couple[1]+'\n') + output.write(best_h2[pairwise_couple[1]]+'\n') + output.close() + +if __name__ == "__main__": + main() \ No newline at end of file |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d static/images/adaptsearch_picture_helps.png |
| b |
| Binary file static/images/adaptsearch_picture_helps.png has changed |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_diamond/AcAcaud_Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_diamond/AcAcaud_Trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| b'@@ -0,0 +1,500 @@\n+>Ac1_1/1_1.000_151\n+TCGCTCTCCTCCGCCTTTTCTCTAAGCTTAAAAATTATGAAGAGTCTGCACCAGAGACAACTCCTTAGCACATCGACCGACCAGCTGGCCATAAAATGTCTTATTTATACCTTTGTCATGAGCCTTGATAATCCTTTGTGCCAGTGGTGGC\n+>Ac2_1/1_1.000_160\n+ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTG\n+>Ac3_1/1_1.000_160\n+ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGC\n+>Ac4_1/1_1.000_160\n+AAACAATGCAATCCTCTACCATTGCCAAGATATGAAGAACAAGTAAATGGCACATCAACAACAATGATAATAATAAGTGCTAATAACAATAAGAGTAATACAATTACCACAATATCTGAGAACAAGGGGCTTAAGCATAGCTATCATTATTTGGGAGGGG\n+>Ac5_1/1_1.000_160\n+GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT\n+>Ac6_1/1_1.000_160\n+CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA\n+>Ac7_1/1_1.000_160\n+GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG\n+>Ac8_1/1_1.000_160\n+ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT\n+>Ac9_1/1_1.000_160\n+GCCATTCGTCTTAGGAGAAGTTTGTCGTCAGGAAAGATACATGAGGCCTGGATTCTTTCTGACACCGACTCGACGATGTCATTACCTTGTCCACCTGGAACCAACCCCTCATCGACTTCAGCGGATCCATATCTGGTGATCACCAGAAAAACGAACACTA\n+>Ac10_1/1_1.000_160\n+GCCTGGGTATTATTTACCACAGTAACCTTTCATCAGTTTGTGGTGAAAGTACGTGACGTTATGCATTGGCAAGATTGGACATTTTGGTTCGCCCTGTTTTGTACGCATAATAATGTATGTAGTTGTATTTTCCAAAATAATTGTTATATTAGCTATCCAA\n+>Ac11_1/1_1.000_160\n+ACAATTACACAGGTATCAACAAATGTTCACTGCACCTGTCAGTTCCACAAACATAAAGATTACACACATGTACACATCTTTACAAAATATTTACAATTTTGTATTCTTAATTCTATCCACTTGGCTCTGGAAGGCCTTCAGCCATCAGATGATGTGTTTA\n+>Ac12_1/1_1.000_160\n+CAATCCAGCACTAGCAGGAGTGTTGGCCGGAAGGTTGATGATATTTTTCAGTCAAAGAATCTGCATGCTCCAGATGATCGCCTATCAGACAAGGATAACCGTGACAAGTCCAAGAACCCTTTACTTAACAATGAGATGACTCCTCAGTCATTTTCTCGAG\n+>Ac13_1/1_1.000_141\n+GATTACATGCAAAACATAATAGAAATGTTTGTCCCAAGGTCTTACCAGTTTATAGTTTTACATTCGTGTCTTGAAATAAGAAAATGCCTTTATGAGAGTGTATTATTACTCAGTAGATGGAAATTAGCTTACCGGGGGATA\n+>Ac14_1/1_1.000_160\n+CCTGTTGTGACTCGTTCCCTGACGTCGTGCACGCAAGCGCACGCGCGTGCGCGCCGGGTTAGGCACACATACGCGGCACAGGTGCGCAGTATTAGACAGACGCAGACGCAGGCGTCCAGACACGCCAGCCAGCACGGTTACAATGTCCATATCACAATGA\n+>Ac15_1/1_1.000_147\n+CTGAATGTCAACCAGTCACTGACCATCAGCTACATGTCTCTAATGGTCACTAGCATGAAACATGAAATGCCTGCTTATAGTGGGTCTGTAACTGGTAGGATACTGATTACATGTGGAGGCTTATTAAAGGGGTATCCTATTATTTTT\n+>Ac16_1/1_1.000_160\n+CTATGTTGGCTACTGCTAAGGATGTGCTACTTGCCTGATGTAAACAATTCCCAGAATGAATATAAACCAATCATAAGGAGAACTATGGAACCATCCTTAAATGTATTAATCTTATTTAAAATTATGTGCACATCTTGTTTGGCAGAAGGTACATTAAAGC\n+>Ac17_1/1_1.000_160\n+ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGC\n+>Ac18_1/1_1.000_160\n+ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTG\n+>Ac19_1/1_1.000_160\n+GCCAGTGAACTCATTAGGCTCTGTCTGCGCCGATATGATAAGAACGAGTTTGACAGCGATGGTTATATTATGAACAGCGAGCTCGCCTACGATGATGACTCTGAAATGCCTGATGACCTAATTGACCGTTTAGAAGCTGGAAATATTACAAGCTTTGTGC\n+>Ac20_1/1_1.000_168\n+CACGAGACTAGAAAGATTACTCAAATAAACAAAACCAAATTATGGAAATCATTAAACATCTTTCTTATTTCATCACCTGTAACCATATTTATTAAATACATTCTGCTCTTAGTTGTGTTGAGAATATTCTTGCAGTCTTCTCATTCCTATGTCTTTCAGCTAGTCCAT\n+>Ac21_1/1_1.000_309\n+AATCCCGCCATGTTGAATGCAATGCTCAAGCGTCAGGCCGAGCTGTACGGCAGCAAGCTGGTGGAGCGAGCACACTCCATGCCTCACACCAGCCCGTGGACTATCTCCCACTACATCCAGCTCCGCGTCGTGCGCGAGTTCGGCCTGCCCGACTCCATGATCCAAGTGCTGCAGTCACAGCGTACGCCGTCTGAGGAAGAGCTGCTGTCCGAGGCCAGGTATCACACGCCGAGACGAGAACGTCACAAGAACGCCACGTACTACCATCACACCATGCCCTGTCAGCATCATCATCATCACCATCATCAT\n+>Ac22_1/1_1.000_201\n+AAATCCGAC'..b'ATGACGGCACCGAAGATGATGAGCACTGTAACGGCGATGGACGCTGTCCATCGAATCAATCTAGAAAGCAATCGGAAAATGCTAAGAGTCCGGAGGAAGGACTCGCCGGCAGCGGAACCCGCATAGCCGTGGAAGATGCGGTTTCGCCCTACGAGAGAACGAATCAGATGTCATTTGTCAAGGGCGGTACATTCCAAATGGGTTTGGAGAAGCCCATCATACCACCCGACGGCGAGGGTCCAACTCGTATGGTCACCGTCAAGTCGTTCTACATGGACCGTTATGAAGTGAGCAACGCCGAATTTGAGCTATTTGTTAACAGTACTGGCTACATCACTGAAGCTGAGAAGTTTGGTGATTCGTTCGTAATGGAAGCCATGCTTAGTGATAAAGTCAAGTCGGAGATCACTCAGGCAGTAGCTGCTGCCCCCTGGTGGTTGCCCGTAAAAGGTGCTGATTGGAGACATCCTTTTGGACCAGAT\n+>Ac238_1/1_1.000_168\n+AGCACTAAACAGATACTCGGATATGACTTGGTCAGCGCCACTGGTTCCTGTCCATGTCGTGTATTATTCAACTATGGTCCAACTATATACCACATTACAAACGTGGCTGAAGTACTGACGTCCTTCTCTGTTTGTTTTTATTTAAACATGATTTCGAACAATTTTTCT\n+>Ac239_1/1_1.000_406\n+GTGACGTTGATACCTGGTGACGGTGTAGGACCCGAACTACTGTCCAGTGTCAAGGACGTCTTCTCATCCTGTGGGGTTCCCATTGAATTTGAGGAATTCTATGTCAGTGAAACGAACCCAGCTCAGAGTGTTAGCGTCAAGGATGTGGCAGAGTCGTGTCGGAAGAATGGCATCTGTCTGAAGGGCATCATTTCTTCACCACTTTCATTCCAAGGTGGAATCCTTCAGACTCTGAACATGCAGATACGACGTGAGTTGGATTTGTTTGCCAATGTAGTCCGCGTCCACAGCCTGCCTGGCATACACACAAGACATAACGACCTCGACCTTGTCATTATCCGTGAATCAACAGAGGGCGAGTATAGTGCATTGGAGCATGAGGCAAGTTTCTGTTTCAGTCTTTGCC\n+>Ac240_1/1_1.000_213\n+TTTGCCAAGTTCCAGAAGAAATCCAATGCAAAAGGCACTCCCAGTCAGTCACCTGTCAAGGCATCAACTTCTAATTCAAACAACGTCACATCAGCAGTGAATGGTTACCGAGAGACTTCTGGGGCTTCAGAGACTGTCAAACCTTCATCACATTCTAAAAGCACAGCCAAAACAAAGAACTCACCTAGTCCCACTAGTGAAGTGGTGCATCTG\n+>Ac241_1/1_1.000_129\n+AGAATGTACCTTTTTAGAATATTTTTGAAGGCTAAGAAATGTATACATGATGGCACTTTAATGCCTGTTTATTTTGTAGATGAAATTTTGCACCAAGTTATTTGTTTTGTGTTTTTGTTGTTTTGTGAT\n+>Ac242_1/1_1.000_390\n+GTCAAGGTGACGGAAATACAACAGCTGATAGTAAAAAACCAGCACAGACTGCTACAGACTCTTTGGACATGTTTGCTGATGAAGAGGCCAGCTGTGAAAAAGCAGCTACTAATGGCAGCCATGTTAATGAAGCTGAGAACAAAACCACAGAAGAACACAGTGACGCTGGAGAGAAAGGTTCTCTTGGTCCGGAAGAATCAAATGAGGTTCATTGGGAGTATAAGTGGGAAAAGGGTGATGACAAAGAAATCCATGGTCCATTTACATCAAAGCAGATGTTACAGTGGACAGAGGAAGGTTTCTTTGATGAGGGAGTACTTGTCAGGAAGGTTGGCGCCACAGGACAGTTCTACAGTTCAAGAAGAATTGATTTTGATCTTTATACCTGAT\n+>Ac243_1/1_1.000_186\n+ATATCTGTGGCTGTGTATGCATACAGAAAAATATTCTGTCCTCCACTGGGACACATTACCATTTTGCATGATATGTTATATGTGTTTACAAAAGGCAAGTCATGTTACAACCACATTAATATTATGATACATGCTTTGTATTTAGTAAAAAAAACAACACTTATCATAATTAATGGCAGATTTATG\n+>Ac244_1/1_1.000_153\n+TATGAAGCTCATCTGTTCAGTGTGGGAGATAGCATGGGGTTTGATGGGCACAGCTACGACCATCTAAACAACAACAATAATAATACACGTGTTAGTAAAACACTGTCATGCAAGGTGCCTTACAGAATTGTAGCTCGGATCACAACACCCAAC\n+>Ac245_1/1_1.000_186\n+CAGCACGTCAACAACACAGTACTCAGCCTTTTTATTATTGAACCAAAAGACAACATATCTTCACGGGTTATTTCCTTCGTGTCAGGTGTCAGAATAAATGTATGCTCGAATTTTATCTCAACCATTAATTGTTACATGAGCAGATCTTTCAAAGACAAAAGTTCACTCATAATTATCCTTGATAAA\n+>Ac246_1/1_1.000_150\n+AAAGACATATTCTTATGGCCAACATCCAAATGCTCATTGTATGAAAGCTTGCAAAGTACAAACAACACATTTTCTTCACATATGAAATCATCCACTGCTGTAGCACCACCAGATATATCATACAATTTAATCAGTCTATTACAGTGCAAC\n+>Ac247_1/1_1.000_297\n+CCTCTGCCCCAAACGAAAATAACCAGCAATGCGTCGTGCCTCGTAAAACAACCAGATGTTGATTCTCACAGCCAGCTGGGTGGGGGTTTAATCAGTGATTTGGCGGGTGTAGCCGAGATGGATGCAGATCATTTGTTCATCCGATTCGACCAGAGAAATGAACGTGTGAATCTATTGTCGATTTCTTTCATTGGTTTCTACCACAGCACAAGTGGGGCCTTATCACAAGAAATGTTACTAGTTTTTACATGTCCACAGATTTATATCGACATCCTACAGAGAAGTGTACACATGCTT\n+>Ac248_1/1_1.000_225\n+CGATCTTGTCTCCGGCTTCTTCCATCCAGAATTCTACACTCGAGGACACACCGGACAACATTTGCCAGGTGGTACGAAAGCTCCTTGGCAGTAAACCACGGGACAGGTCATGTTGACACAGATGACGGTGCCAGTCAGTGCCTTCTCTCCCTGCCAAGGACAGTAACAGTAACTGCATGGTCCGAGGCGCACCCTCTCTCCAAGTCTGTATGTCATTCCATTAAA\n+>Ac249_1/1_1.000_291\n+ATGGGGCCACTACCTCAGCACAGCATACTGAGACATATCCACAGAGGTAAAGCTTTGGTGTTTTGCCGCAGAGATGTCCTGGACTGGCGAGTGTATCTTGATTTGTCTCATGTGTGTGTCACGGCCATTTCAATTAGAGTTGGCAATCACTTTAATGATCTGACAGAAGTGGAACAAGTTGATTTAAATGAACCCAGTGGTTGGGTGATGATCCCTGTGTTAGACATACATCAGAGGCCAGTCAGATCATTCATGATCCAGATAGCTGTTCTCTCCAACCATCAAAATGGC\n+>Ac250_1/1_1.000_410\n+GAGAAAAGCAAACAACAACAGATTATTGATGAACTGATGCAGAAACTTGCAGCCAGTGATGGCCGTGTGGAATCATTGACAGCACAAGTACAACAATTAAAGGCCCAAAACTCAGATCTTCAAAGACAGTTACAGGCCAGCGAAGACAAGGCAAAGATCATTGATGAAGATAGGGAAAAACTGGCACACCAGATTGAAGAGTTGATGAAACACTCTGGAGATAGCTCAGAGCAGCTATCTATCCTTGGAGAACAGCTTCATGACCGTGATAGAAAGCTAGCAGAGCTGCAGGCAGCTTTATCAAATTCTACACAAAAACTAGGTCAGCTGACAGAAAAACTTGAACAGGAACAAGAAATAAGAGAAAGAGAGTTAGAGGTGATGGCTGCTAAACATGAGGAGGATTTAAA\n' |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_diamond/AmAmphi_Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_diamond/AmAmphi_Trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| b'@@ -0,0 +1,450 @@\n+>Am1_1/1_1.000_160\n+GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT\n+>Am2_1/1_1.000_160\n+CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA\n+>Am3_1/1_1.000_160\n+GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG\n+>Am4_1/1_1.000_147\n+ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAAGTT\n+>Am5_1/1_1.000_160\n+TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTG\n+>Am6_1/1_1.000_160\n+ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAAT\n+>Am7_1/1_1.000_160\n+GGGGCCCGGGATGTCGAGGATGTTGTACTCGTAGTTGCTGTGGTTGACGTGGTATTGTTGTTCCTGGCTGTGGCTCCGTTACCACTTGACGTGGCTGTTGTGGTGCTGGTGGAAAAACGACTAGTGGTTGTGTCTGCAACTAATTCCTCGCCTCTAATCA\n+>Am8_1/1_1.000_160\n+GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAAAGAGCTTCTATGGTT\n+>Am9_1/1_1.000_160\n+AGCCATCAAAGGTTGCTAATCATGTTGAGTTGTATTGTCAAGCATTTCTACTCGAGGCAACCATTAATAATTGAAGTTATCAGTTATATTGTCAACTCAATGGAAAATCAAATGGATTTAATTAAGGAAGGAAGATTTTGTACTTGTAAATCTGCATTTT\n+>Am10_1/1_1.000_160\n+AGCAACTTTGCCACCACCACCACCACCAACAATAACAACAACAGCTGCAACACCGCGACCAATAACAACAACAACACTGGTAACACTAACCACGTCACCACCAGAAATAACATCTTCACAACCATCACCAACACTACCATTAACTCAACTTATAACAATA\n+>Am11_1/1_1.000_160\n+ATTTTTTGTAGATATTTTTATCTATTTACATTTCTATCTTTATTTCTCCCTACGACCGAAGGCCTCAAAGAGCATATGATTTATTTCTGTCCATTTATCGACCGTGCGTCTGTCTGTCCATCCGCCTCCCTTCCACAAACAGCTGCCGCTACTGTTATAT\n+>Am12_1/1_1.000_160\n+ATAAAGTGGGCCATACAAAGTGAGACCTTACACATATATGAATGTCTAAATTGTCCTATGTTGTCCCATTTAACATGTTTAGTTTGTGGTATTTTTCAAACAAATATAACATGGGGTTTGAATTGGCCGGAATCTAGCACATTAGTCTCTGAGGAAATTT\n+>Am13_1/1_1.000_160\n+ACAACTCCTCCAATAGTACTACCAGCTTGTCAGGGTGAACCAGATGGTAATGCACCTGATCCTGACTCGTGCTCACGATATGTAGTATGTCTCAATCAGGAACCGGTTAATGACTATCCATGTGATCCAAGTACCTTCTTCAACGACCTACCCGAGTACA\n+>Am14_1/1_1.000_160\n+TACTTTCCTGAAATTAGTTCTAATGGTTTCATTGTGATGACAAAGTTTAATATGTCAAGCATAATAAACTTGATTGTGTTTTTCCACCTCAGCAGTCATTTATACATTTTATTGAATGTAGAGGGTGTTGAGACATTCAGTGTTGTTATACTTGCAACAA\n+>Am15_1/1_1.000_160\n+ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAAT\n+>Am16_1/1_1.000_160\n+TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTG\n+>Am17_1/1_1.000_160\n+ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAAAACCAGTATGGCCAAA\n+>Am18_1/1_1.000_160\n+CGAACATCTCATGAAGTGACTCAGACCTCATTTACCCCTAAGGGCTCTATGTTAGGGGGACATGTCATTCCACAGATATGCATGGATGACTCGCATGCATCCAGGGCATTACGGTACAGTAAACGTCCAACAGATGCCCCTCAGATACGACCCATAGAGC\n+>Am19_1/1_1.000_160\n+TTTAGTGAAGAATTTATAATGACTCATGATGTTTGTGTCAATGTACTAAACTTAATGGCACAAATTGCGAACTCATTTTTTTTCTATTATATGTGGGTCTTTTCATTCAACCAGCATTTAGTATATAGACAATTTCTATCTATTCACTTGGATAAAGCAA\n+>Am20_1/1_1.000_160\n+ACCTGTCCCCAACCCCAATCATTAAATCTTTCCCCTTTCGCATGTTCACAGCCCAGCTGCAGCACAACTAGAAAATCCAGACATGCTGAAAATACATGTTATTTGTGTATCTGGCATGTAATTTGTTTCACTCAAAACAGTAACTCTTCTTCAGGAGGTA\n+>Am21_1/1_1.000_135\n+ATTAACCGCCTCTATTTGCTTCTAGCTACATGTTCTTCCTGTGTAAATACCTTCTTTCATTCCTTCGTTGTTATCAATGTTAGTTTTGTGTTACTATTTCCTTGGCTGTTATATTCTACAGGGTATGCTTTTAAA\n+>Am22_1/1_1.000_135\n+AGTGGTACAGCAGAAACATTAAAACCAGTTTTTTTGTGTTTGCAAACAATTCTCATGAATATTGTATTTGGTGCTTGGAATGTGTACAGACCCTATATAGATCATATTGAATGTGTAAATATGAATTTGTACAGT\n+>Am23_1/1_1.000_102\n+TCACT'..b'AGAAGGATTACTTTTTTTAATAGGTAATGTTTTATCAATGACAGGGCTCTTTTTGACACTGCTGACACACTGCATACTAAACAAACAATTATGGAGTCTCAAGGCCCAATGTCTGGTATCACTGGTTATCGCTCTGTTGTTGGCAAAACTTGCTTTCCAAGTGAATCCATATTTTAGCGAGAATGAACATCTATGCTCTTTAGTGGCTATGTTACAACATTATTTCTGTCTGTCCGCATTCTGCTGGGTCAGCGTTCTG\n+>Am210_1/1_1.000_180\n+CCTGGAGACATTATTTTTCATGGTTTTCCTACAGAGAATGCAAATCAATTTGCTACACTCTTTGGTTCATTCATCAGTGTGTTTATTTTGTATGCCTGTTTCATAAAATGTTCAAATAATGTTGTTCAGATGTATGCATTTTGTCACCATGTCACCAAGCAAGAAGTATTTAATAAACTT\n+>Am211_1/1_1.000_216\n+CAATGGGCTGGAGCCACCAGAGCAGGTCTCCCCGGGCTCGTTTATTGCCCCAGAGCCAGCCCACAATTAAAACAGTTATCAACTGTTGTGTCGTTACTGACTGGAAACAAGTATTCTGTTGCAGACCTGGTCCATGTCGTCTTCAATTACCTAGAGGACCGAGAGGAGTCTGGGACAACGGAAACGTTGTTTACGTACATTATTGAAAGGCTGGAG\n+>Am212_1/1_1.000_162\n+CCATATGTAATACACATCCATGAGTCACTATATCCAAGGGTATGCTGGTTGCAGGTTTATCGCATCTTGATATTTTTTCTCAGGGACCAAGTGTATCGGGGTAAAGTATATCAAGATATTTGGATAAAGGTGAAATACACAAGGTGGTTAAATAAGATTATT\n+>Am213_1/1_1.000_263\n+CTTTCCTTGTTCATGTACAGGGCGATAAAAAAGGCATTTATGTTTTTTTCTCTTGTTGACTTTCACAGTTTACTCTCTCATATTGGTCTTTATATAGTATTTATATCAGTTGATATTGTTGTACACCATGAATACATATATACAGGACTTTGTACTGGTGAACATATTATGATTTGTGACAATAAATTGGTGGACAAGTTCCTAGAGTTCCATGTGATTAGCTTCAATCAATCAATAAACGGATATTACACTCTGAAAAAAAA\n+>Am214_1/1_1.000_168\n+ATATTAAATTATAATAATGTATACATGTGTGTTATTATAATTATTACATTTGATTGTTATTATAATGATTGTTATTGGTTCAATGATTCATGTGATAGGAATTGTGTGTTATTTCTGCAATCCTTCTGGGGCATGTTACTGCAGAAAGAAATTTCAAAATGTGTTGTG\n+>Am215_1/1_1.000_214\n+CGCCGGTTTGTTCAAATGTTCTCCAAAATTAAAGAAACTCTTCGCGGTTTGTGGTCTGGGGGAACAGAAACCACAAAAAATAACAGAAAGCGACATTTAGAAGGAGATGTCCTGGTTTCCCCAGCCAAGAAACGTGCCAGATCCTATTCATCAGATCCTGAAGATGGTATAGGAAAGAAGAGCCCCTTGTCTAAAGTAGCTGATTGGGTTGGTC\n+>Am216_1/1_1.000_358\n+ATGTTCCAGGTTCATACAGGGTATAGGTCGTCCCTACCCCCAACAGGGTATAGGGGTAGGGTATCTGCCTCAGTAGACCGTGATGCAGGGTCGAGAGTGTACCCTAGCAGTTACTCATCATATGGCCCTGCGAGGCGTTACAGTCTATCAGTGGATCATGAGGTATCAAAATCGGTTCCTATAGAAAATGGCCAAGACTCGTATGTTCTTGGTTATGCATCTGTGAAGACTAGAAGTGATCCAGATGAACCAATACCCCATGCACATATTGAAGCACCTTCAATTGGACATGCCACTGTTCGCATCAAGTCCCCAGACAATGGTCCTAGAGTCACGGTCACCTCTTCGTATGTTCCAG\n+>Am217_1/1_1.000_388\n+CCTGTCAAACAAGAAGGAAATAAATTTCAGACCCCTCTGAAAAAGAAATCGTCTTTCCAAATGCCAACGAAAAATTCTTCAAATCAGATTGAAATGCCATCAGATACTGATGATTCAGCACTAGTTGCCGGCTTAGAACGTGCAGAAGAAATGGTTCCTTGTGAACATGGTGACGAACCTGAGAAAGAAAATTCTGTACCAAAAATTAGACAGAAACTCGAAGTCCCTGATGGTACCAAGAAGTCACGAATGAAAGCCAAAGTTAGTCAGGCGCAAAGAATATCGCAGAAGAAAAGGGACGGAAACGTGAAACCAATTATGGGAGAATTATACAGAAATAAAACGGGAGCTTCACAGATGACCTTCAGTGAACTGTTTGATGGTCAAC\n+>Am218_1/1_1.000_180\n+CAAGTTGTATCATTATGTCATTCAAAGAACAATTCAATACATGTATTGTATCTAGGCCAAACCAAACTCAATCTAGACAACAATGACAGTGTATCCAATCTATCTCTGCCCAAATATGTACAGTCAGTAGCAATTACTAAAACACTGGTTTCTGCAACAGGATATAGGCGTTTAGTTTTA\n+>Am219_1/1_1.000_144\n+ACTCACCATTTTATAAACACATATATATATATAGGTCAGTGGTTTCACCCAATCTTAACTCAAGCAATTGATGAGCTAATAGATCATTTGGCTGTTGAATTTATTGTCATGACCATACTAATTCATTCACTGGGTCTGGTGAAA\n+>Am220_1/1_1.000_141\n+CACAAAGGTTCTAATCTTACACTGCAACTTAACATGTGTTTCTCTGAAATAATTTTAAGGGTTCAATATCATGCTTTGAGGTCAAAACCCACCCTGTTACATCTTTCCCATGTGTGTACATATGATTACCAACACGTCATA\n+>Am221_1/1_1.000_175\n+GTTATTGACAAAAACCTACAAGATGAGTCTTCAGTCATTGAATCGTTGAACGTAAACTTTGGTTGCCAATGGATCACCAGTTCACCAGTAGTTGCCTTTCTTGCCTTTGCCTTTCTTTCCTCCTTTCTTTCCTTTCTTTCCGCTTTTCTTCCCTTTCTTTCCTTTCTTGCCTTTC\n+>Am222_1/1_1.000_166\n+GAACTGGATATCATATCTGTTTCATTGAATTTGATTGTTGTTGCCATATCAAGTGTCTTTGTTATCATTCTGTTTATTGTGTATTGCCAGAAAATCTTTAGTTACAATAAGATAAGATTGCAAATAAAATGGTTTACAGACATGTGGCAGAGCACTATTGTTCAGC\n+>Am223_1/1_1.000_239\n+GGACATTGCAAAAAATTGGCACCCTTTTACGAAGAAGCAGCCAAAATATTGAGTGATAAGGGGTCTAGGGTTAAGCTTGCCAAGGTTGACGCAACTCAGGATCCAGAATTGGCAGAACGATATTCAGTTCGTGGTTATCCCACATTAAAGCTTTTCCGTGGCAAAAATGCTGAAGATTATAACGGTGGACGCACGACCGATACTATTGTCAGCTGGTTGGATAGTATGACCGGTCCTTC\n+>Am224_1/1_1.000_149\n+ACCAATATTAAACTTAGAAAAAATATTTCCCTAACTTTCAATGGGACAAATTTATATTTTGGGTTTCAAACTTATTTATTTGGGGGACAAGTAAACCAGACAAGATCCGAGCCTGCCCTAATTTGGTATAGGAGGTTTTTTTGGATTCC\n+>Am225_1/1_1.000_212\n+GAGTGGCTCTTGCATAATGTTAATACAGATGCAGCATGGATTGTTTTCCCAAAAATATTAATTCTTCTGTATCTCATGATAACATGTTGGGTTTATTCTTCTGTTTCTCAGGGTCAAATTTTGGGTTTATTCATGGTAACAAAATACTATACAACAAAATACAATAACTTAATATTGGTTTTTGAACTAAATCACTGGAAATTGTTATTATG\n' |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_diamond/ApApomp_Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_diamond/ApApomp_Trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| b'@@ -0,0 +1,400 @@\n+>Ap1_1/1_1.000_160\n+GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT\n+>Ap2_1/1_1.000_160\n+ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT\n+>Ap3_1/1_1.000_160\n+GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA\n+>Ap4_1/1_1.000_160\n+CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA\n+>Ap5_1/1_1.000_160\n+AATCTACTGACAGATACCTGGAACGAGATGCAGGTCAAGTGGTCGTGTTGTGGTGTGGATGGCTACTCCGACTGGACGCAAGCTGAAGGTCTGGCCACGGGTCACTACGTGCCGCAGTCCTGCTGTCAGAACACGATGAGTACAAGCTGCACGTCACAGA\n+>Ap6_1/1_1.000_160\n+TGGCGAAATGTAGTGGTCATTGATGGATTTTATTGCAATCAGTGTTACATATTACAAGCATTTCTTAATAAACAAAAAGTTGCACGAGATATTTTTTACTTAAAGGTTTTATGGGATGAACACAGTCAATTATATTCATGTAAAAGGCCTTATCCGAGAA\n+>Ap7_1/1_1.000_160\n+TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCT\n+>Ap8_1/1_1.000_160\n+GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAA\n+>Ap9_1/1_1.000_160\n+TGTCTTTACTTCTATCCTTCTCATCATGTTTTACATCATTTTTATTGCTGCCTCTCTTCTCAGCCCTTTCCACACTTTCATGTTTATCTTTTGATTTTTCAACTTCAACTCCATCTTCATCATCATTCTCATGCATTAATTCTTCTATTTCTTCTTCCAA\n+>Ap10_1/1_1.000_160\n+GCAGTGGTGGGAAGTTGTTCACCCTGGCTTGGTGTCCCATGTTTCTCTGTAATTCCTGTTCCTTTCTCTGTAGTTCCTCAGCCTTCCTCTCCAGTTCTTCCTGACGTCTCTTCAGGTCATCTGTGGCAGCCTGGGCCGTGGTCTTGGCGGCTGAGTATGG\n+>Ap11_1/1_1.000_160\n+ACGACAGAGGTCCTCTGCTTGATGAATATGGTTACACCAGAGGATTTGGAAGATGAAGAGGAATATGAAGAAATTTTGGAGGATGTCAAAGAAGAGTGCAGCAAATATGGTTATGTGAAGAGTATAGAGATCCCACGGCCCATTAAGGGTGTGGAAGTGC\n+>Ap12_1/1_1.000_160\n+TGTCTTTACTTCTATCCTTCTCATCATGTTTTACATCATTTTTATTGCTGCCTCTCTTCTCAGCCCTTTCCACACTTTCATGTTTATCTTTTGATTTTTCAACTTCAACTCCATCTTCATCATCATTCTCATGCATTAATTCTTCTATTTCTTCTTCCAA\n+>Ap13_1/1_1.000_160\n+GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAA\n+>Ap14_1/1_1.000_160\n+TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCT\n+>Ap15_1/1_1.000_160\n+GTTGTCAGTGGATCTCGTGATGCAACACTGAGGCTATGGAATGTCGATACTGGCCAGTGTCTGCATGTTCTGATGGGACATATGGCAGCTGTACGGTGTGTGCAGTATGATGGCAAGCGTGTTGTTAGTGGTGCCTATGATTATACAGTTAGAGTGTGGG\n+>Ap16_1/1_1.000_160\n+AGATTTATATTTGAGAATGTTTTGAGTACGACTTCTGTACAGACACACAGCAGAATGACCCTTGTATTGTTTAACAACGTTCAAAATTTCCTGATTCTTCTACCGAAAAAAATACATAAGAAGAGCCACCAAGACGATCAGATCACGGAGGTACTGGCAT\n+>Ap17_1/1_1.000_160\n+GCAGACTCGGCTGGCACGGCCACCGCCTTCCTCTGTGGAGTGAAGGCTCGCTACGGAACGCTGGGTCTGGGACCGAGAGCCACACGATCTGACTGTAGACAGAGTCACATCAACAAACTGAAGTGTATAGGAGACATGGCACAACAAGCAGGTATGAGGA\n+>Ap18_1/1_1.000_160\n+CCGGCCTGCAAGACGCCATTTTACTTCGTCTGTCAATCGAGGTCAAAGGTCACTACCGTTGTCTCCGAGAAGCACACAGACGCCGAGCTGGTTCACACGCTGTGTATTCGGCACAGATCTACTGTTGCTTGGGATATTTTAGCCGGCGAACGAGCGAAAT\n+>Ap19_1/1_1.000_160\n+CCGGCGATCGTTCAGAGGGCCAGCGGTCTGGCCATGTCAGAGATCTATCACCTGCGCTTCTGCGATGGGGATCGGCTGAACGTCAGCTGCCCGGACAACTGGCAGATCCACATCTCGTCCAGCTACTTCGTCTACGTCAGCGGCGTCGACGGCCGCGGCG\n+>Ap20_1/1_1.000_160\n+CATGAAGGACCTGTGTGGCAGGTGGCTTGGGCACATCCAATGTTTGGTAATCTGATAGCATCATGTAGTTATGACAGAAAGGTGATTATTTGGAAGGAGACTGGAGGGACATGGGCAAAGCTTTATGAATACAACAATCATGATTCCTCAGTTAATTCAG\n+>Ap21_1/1_1.000_468\n+GCAGCCATACAGAATGCTAAATATATAATAGCCCAAGTTAACCCTAACATGCCCCGTACATTTGGTGATGGTGTAATACACATGTCTCACTGTGATGCCATGGTACAAGTTACTGATCCACTGCCTGAGATTCATGTGTCTAAATGTACAGAGGTTGAGACCAAGATAGGCAAATTTATTGCTGATAATCTTGTCCATGACGGTGCCACTTTGCAGATGGGCATTGGGTCTATTCCTGATGCTGTTTTGGCTCAGCTTGGAGAACACAGAGATATTGGGATCCACACAGAAATGTTTAGTGATGGAGT'..b'3_1/1_1.000_269\n+GTCGGATATCACTGCTGTACGTCTTTCCGCGTGTACTGTACACGTCTGTATGTGTTCCGGTGTATTGTACACGTGGCGTATGCGGTGGTTGTACAAGCCAGGCCACCCTGTCGTCGGTATCACCGTGTACACACACACACACGCCGTATCCGGAAGGAATGTGTCCCCTCGTCGGCTGTAAAGTGCCCTAACAATCCGTCTGTCTATCCGCCTTCCGCCTACCCGAGCCACCTCAGACACAGACAACTAGCCGTATGCCAGAAGTCCGG\n+>Ap194_1/1_1.000_221\n+GCCAGATGTCAGAAAAATAATGAAGAATTTGATCAAGAAGATGATGAACAATGGAGCCAAGGTGGTGCAGAAGAGGATGTGCAAAGACCAGAAGTTTCAGTGGCACACAGGGGAAGAGGAAGAGGGCAAGGTCGAGGAGGTCAGAGAGGAAGAGGTGGAAAATCACTTAATAAGGATAATAGGCAGCTCCAGCCAGCCAGATGTCAGGAAAATAATCAAGA\n+>Ap195_1/1_1.000_335\n+GCAGTTGTCGTAGAAGCGGTCGTCGTTGTCTCGGTCGTACGTCGAGAACGGCTGGCCGTCGTGGTTGCTCCAGGCCGGCGTCAGCGAGTCGCCGGCGTCGCCGCGGTAGCCGTGCACGTGTATCCGGTAGTCCTGCGACTCGTCCAGCAGCCGGAAGTGCTCGTACTCGGCGTAGTGGTGCCGGCCGTCGAAGTCCGACATCTCGATGCGCAGCATGTAGTCATCTTGATTGGTGAGCTGATAGATCCGGTCGTTGCCAAGCCAGAACTCTCCTCTCGGATCCCCGAATCCACGCTTGTACTGCTCCCAGTTCCGGTAGAAGTCGACCGACCCGT\n+>Ap196_1/1_1.000_201\n+ACAGGTAAGAGTGATAATGGCTCTGAGTGGGACTTGGTCTGTGATATTCCTTGGATAGAGACATTGGCATCAGACAAAGACAGGATGAATCAGAGCTGGATATATTCTGATAGTAAAGTTGGTGTGTATAGTCCAAGTGGCAAAGGACACTGTAACATTATCTCAGCACAGAGAATCCTCATGGACAAAATCAAGGAAATC\n+>Ap197_1/1_1.000_759\n+GATGCTGGAGAATCCTGCTTATTCGACAACGGCCCGTGTACAAGAATAGTTGGAGGGATTGGCGCTAGAGAAAATGAATTTCCATATATGGTTTCCTTGATCCGTAACGAAGAAGGCGTCTGGAATCACTTCTGTGGGGGTGTACTTATCAATGAGTACTGGGTTCTGACGCTTGGTCTGTGTTCAGTTGGCACTCAGGATCCTTCGGTCAACATGAGAGCGGTACTCGGAGCTCATCTTCTGTCGACGCCGTCAGTCAGCGAGGTTGTCTTGAATGTTGTCGACACTATAACCCACGAAGACTACGTACCCGAGCTCGGTGATGACAACGATATCGGTCTGGTAAAACTGGCATCGCCTGCCCCGATCAGCGACGCCATCCGACCAGTCTGTCCACCGGATCCAGAGAACAGTTACACGGCGGCCAGCTGCGTGGTTAGTGGATGGGGCTCCACCGTCAACAATGGACCGTTCCAAGATCAACTGACGTATACTAATATTTCCGTAAATTCCCAGTCGTTCTGTGTTGACCAGATATTTGGTTACACACCCGAAGGAAAGCTCTGCGCTTCAAACGGCGATTATACGAGGGACACTTGCGATGGAGATGCAGGGAATCCGCTTGTAGATAAGATTGCCGGTCAGTTTACGGTCGTAGGATTAGCTGCAGGTTCATTGAGATGTGGCGAAGACAAGCCTGGAATTTATACCCGAGTTGGCGACTTCGCTGATTGGATCACACTAAAACTGGAAAAGAAC\n+>Ap198_1/1_1.000_218\n+TGGCCAAGTTATCGGTTGGTTAAAGGAAAAGAATCGCTAATCGTATTGAGTGATGTGGTTTTGAAATCGGAAACGTTTTACTGCTTTGACTGTGGTCCGGTCGCTGGACCGCTTCTCCGTCTGCAGCGTCACGGAAGTCGTGTTAGGCGTGATTCCGGCCATCGGAGTGGTGCGATGGGACGCAGACACCGAGTGACCTCGTCCGTTGCACACCTCTG\n+>Ap199_1/1_1.000_1407\n+AATTTTCTAGCCATGAGACGCTTCCTCTCGTGGACGCTGCTTGCATGCCTCCTGCTGGCATCCGAGGCTCGAATCGACAACGCGTTCGGCACCGAAATAGAAAAGCACGGCCACCAGAAGAAGGAGGCCCAGCATCTGGATCCAAATCCCGAACAAGCGATCGAAGGCGGTAAGGTCAGAAGCGTGGATCATCACAATATCGTGGATTATGGTGGCCAAAGCCGCCGTACCACGAAGGAATCTCAGAGTGAATCGGACAGAAATGTCAAACAACAGAATTCACACAACAATGAAGGCCAGAGAAGGAAATGGAGCTTGTCTAAATATGCTTCTGAAGGAAAGGCTGCGGGGAAATGGAAGGCGTGGAAGAACCAATCCAAAGGCAAACACAAACAAGACGCGGGCAAGTGTAGTCAGATGAAGTGCACCCGGAAACAAGTTTGTCTTGTTAATGGGGAAACTGGGGTCGCTGAGTGCATTCCTAAGAGGATACTGCGCCAGAGCCGGAAAACCGACAAATCCGCAAAAGGACGCATCAACCGGAAACAGAATTCAAAAAAGAAACATCCATCCGCAGTGAAGCTGACCAACAGCAAAAAGGGTTCAGCTGATAAGCACAAAAAAGCACATAGAATAGCAAAGAAAATAAAGAACAAGGCCGAGAAGTTCCAGAACAAATACCAAGAGAAGAAGAGACACCATCTTCACCATCTGAAGGATGTCAGCAACCAAAAGAGGGCACCACTGCATTCTGCTAGCAGTATTAACAGTCTGCCTCTGAAACCTGCTGATACTACAACACTGAAATACTGCAGCCAGAAGGAATTAGATGTGATGGGAAAACGTCTGCTGGATTGGTTCAAGGTTCTTCAGGATCAATCACAACAACCTCACATTATCCAGAAGAGAAACTCCAAGAAGAAAGAGCTCCATGAACAAGATGAATGCATCTGCCAAGCCCCTGTCAGATCGGAGTTTCTAAGGTTGGATAAAGACCAGGATGATAAGTTGTCTGTGAAGGAATTAGAAGAGTTGAAAACAGACAGCTATGAACATTGTATGAAGCCATTTATCAAATCGTGTGACCACAACAGAGATGGGTTCCTGTCTGACAGAGAGTGGTGCTGCTGTTTTGCTGATGTCTTGCCTCCGTGTTTGGCAGAGTTGAAGACTGTGCCAGCAGCCATGACAATGGGAGCCCCTGCCATCATACCTGGAGCCTTTGTGCCACAGTGTGACAGTGATGGCTTCTATAAACCTGTCCAGTGTCATGGTAGCACAGGATACTGCTGGTGTGTGGATAGAAATGGTGTCACGCTGGAAGGCACACATACCCGCGGAATGCCAAAGTGTGAAGCTGCAGTGAAGGAAGAGACTGCTTATGACAAAGAACTGCCACAGTTGAAA\n+>Ap200_1/1_1.000_402\n+AGCCCACAAGACTCAACACATTCAGGTGACAATATGTACGGTATGATGAAAGGTCCCGGCATGCCAGGCAACATCCCAGGGCAGCAGCAGTTTCCTATGAGTGGTCCAGAGCCCATGGCACCGATAGGACCTGACATGCCTCCAGTTATGAATGGTGACGGGATCGGTGAAGGGATGAAACACTCACCACACAATGGTCCAGGCACACCACGTGACGACCTGCCACCGGTCAGCGCCGCTGGCGATATAGCCGGTTATAACATGTCCTTCCAGGACAATGTAAACGACCAGAATGAGTCGGCGGAAATCTTAAAGATAAAACGAAGTATGCAGGAAGAGGCAAAACGATTCGAGAAGGACACTTCGACAGATCCGTCACATCCAGACTACAGCTTCATGCAA\n' |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_diamond/PfPfiji_Trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_diamond/PfPfiji_Trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| b'@@ -0,0 +1,550 @@\n+>Pf1_1/1_1.000_160\n+AGCATTGTCCGTGTTGCGCGGGTCGTCGACGTAACCTCGGTACACCTCAGCGTGCCCGGCCATCTGGTGCGTGAGCCGCTTGAAGACGACTCTCGCCGGCGGCTGCTTGCTGTCCAGCGTCATGCTCTCGAACGCCTTGATCCAGGACTCCTTGACACTG\n+>Pf2_1/1_1.000_160\n+ATCACGCCCCCTGTCGTGGACAACAGGCTAGCCCATTGTAATGGGAAATCTACAGTGGTAAACAAACTGATATACAATATAACCAATATGTATATATATATAACAGATATGGAGACTGATCATAAAATCAACGATTCACTTTTAGGATTAGTCATGTTTG\n+>Pf3_1/1_1.000_160\n+TGTGCGTCGGTGCCGGACTGCAGGCTGTTGTTTGTCGGGAGCACCTCCGGAGTCATCAGTGTCATCAACACCAAGTTCAACCAGAGCAAGCAAAGCCACCTGCAGGTGTTCGGCCACAAAACCTGCCTGTACGGCCATTCCGGGGCCGTCACAGCCTTCT\n+>Pf4_1/1_1.000_160\n+GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT\n+>Pf5_1/1_1.000_160\n+ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT\n+>Pf6_1/1_1.000_160\n+GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA\n+>Pf7_1/1_1.000_160\n+GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT\n+>Pf8_1/1_1.000_160\n+ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT\n+>Pf9_1/1_1.000_160\n+GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAGGTAATTTCCCGATTA\n+>Pf10_1/1_1.000_160\n+CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA\n+>Pf11_1/1_1.000_160\n+AGCATTGTCCGTGTTGCGCGGGTCGTCGACGTAACCTCGGTACACCTCAGCGTGCCCGGCCATCTGGTGCGTGAGCCGCTTGAAGACGACTCTCGCCGGCGGCTGCTTGCTGTCCAGCGTCATGCTCTCGAACGCCTTGATCCAGGACTCCTTGACACTG\n+>Pf12_1/1_1.000_160\n+GCCCTCGGCCACCAAGCCCAAGAGTCCCAACGTGATGCCCAACCTGCCCAAGCACGTGCTGCAGGCCATCGAAGAGAACATGATCTACTACAACAAAATGTACAGTCTCCGAGTCAAGCCGGACCTGCTCCAGGTTCACTAGAGGGCGCTGTGGTGTTCG\n+>Pf13_1/1_1.000_160\n+CGCGTCCACGACCGCCACGCGCACCGAGGTCTACGACAAACTCGCGCCGCAGGAGGCTCCTCTCAACCTGCACAAGCCTCGCGCCGACAGCGTCCCGACCGACGGCAACGGCTGACGGCAGACACTCGAGCCTTGACTACGTGTATGCACAAAGCTACCC\n+>Pf14_1/1_1.000_160\n+ATCACGCCCCCTGTCGTGGACAACAGGCTAGCCCATTGTAATGGGAAATCTACAGTGGTAAACAAACTGATATACAATATAACCAATATGTATATATATATAACAGATATGGAGACTGATCATAAAATCAACGATTCACTTTTAGGATTAGTCATGTTTG\n+>Pf15_1/1_1.000_160\n+TCGTCCCAACAGCAGTCCATCAGTACAAGCAGTGTACAGAAGAAATTTGACAAAAATACTATTGATGCAGTCAAGAGATGGAACACAGAAAATCTTGACATTTATGGACCACTTCGGAACCCCAAAACCGATGGAGGTTCCTCTCCAAACCCAACCACTC\n+>Pf16_1/1_1.000_160\n+CACGTCACGGACGTGCTCGTCTCGAAAATCATCGATATGGTCAAAAAGAAGGAAAAGAAAGGAGGGATCACCATCAAGCCATTCCAGGTCAAGAACCATGTCTGGGTGTTCGTCAACTGTCTAATAGAGAACCCGACGTTCGACTCGCAGACGAAGGAGA\n+>Pf17_1/1_1.000_160\n+TGTGCGTCGGTGCCGGACTGCAGGCTGTTGTTTGTCGGGAGCACCTCCGGAGTCATCAGTGTCATCAACACCAAGTTCAACCAGAGCAAGCAAAGCCACCTGCAGGTGTTCGGCCACAAAACCTGCCTGTACGGCCATTCCGGGGCCGTCACAGCCTTCT\n+>Pf18_1/1_1.000_160\n+TTACGACACCTGCCCCAGATCCTGTCCGTGTCACTGCTGAGGTTCAGCTTTGACTTCCAGAAAATGGAAAGATATAAGGAAACTGGCAAGTTTGTGTTTCCGATAGAGTTGGATATGGCACCTTATGTTGATAAGTTATCAACTGCTGGGTGCACAGAAT\n+>Pf19_1/1_1.000_160\n+GATCTGAAAGAATCTTCTCCAGTAGCAGAGATTAATGGTCCAGAACTTATCGATGAAGCACTGCCAATTTCCGTTGATAACAGTCAAGGAACAACGGCAGAAATTAGACTTGAGCGCAGTCAAAGCCATACTGGAAAAAACGAGGCGGATTTATTTGCAC\n+>Pf20_1/1_1.000_160\n+TTGTACATTCAAAAGCTAGGTGGCCAAATTGTGGAATTGAATACATGTAATAATTATATATCTTTCACCATGAAAAGATGTCCATGGACCAAGTCTATGCATTGCCGATTTTCGTCATTAATATATATCAGAGATGTGATAAAAGATATATGTACTCATA\n+>Pf21_1/1_1.000_117\n+TGCATGTGTCTGTCCCATCATTTATCAATCTTTGCCTGTGTATCCATGGCTGAGTGTAGACCAATCTTGCAACTTCTACATCAACATCACCACTTAACTATTACATTGCTTAACTGT\n+>Pf22_1/1_1.000_303\n+GCGCCGTGTTTGTCTGGGAGGGGGGTGTTCCTGCCACTCGGAAGCCACCTCCGTCCCGGAGCCGCCGGATTTACAAAGAAAAGTGTCATAACATTACAACGAGCCGCACCGAGCCGGCGATGGCAGCTAAAGAACCGGTGCCTCTATTGGCCGATGCCGGCAATCGTA'..b'TCTGAACAAAGAATTAGCATGAAGCATCATTGTATATTCATAAACTGTATTTCTGAACTTACCTCCATGGCATCTTCAATGTTAC\n+>Pf261_1/1_1.000_156\n+CTGACTGTACTCTCTGTTAGAGAGAAATACTCAACACAAACATCACAGACGTTTAACTGCATCTGTGGCCATGCTATAATGACACATGTTTTAGCTAAACAATCAACAAATTCTGCTCCTACACCATTTCATACAATACTGTTAAGTCCACAACAC\n+>Pf262_1/1_1.000_306\n+AAAGTCTTTTGTCTGCTCTCGCGTAAACACTACAAAAAGCGGGTTTACCGAGACAAACTAGTCGCGGCTGGAACGGGGGCGTGGGATATCAGTATTCTGGATCCAGGAGGAGGAGGCGGGATATCCAGATGTGGGATCATGGGGGACGCGCGGTTTCTATCCTGTAGAATCCAGGAAGAGGACGGGGAAAACATGAATGTGTTCCAGCGCAGGCTGTGGAATACCGAAATGCGGGATTCAGTTATCCGGAACATCCGTCTGGTCTGTTGTGGTAATGCTGCGTCACATGATCCAGAACACTTGAAC\n+>Pf263_1/1_1.000_426\n+TGTCCGGAAAACAATCAAATCAAGTACTCCTATTATCGCCCAAATAAAAACCAGCCGATTAATTTGCCCAAAAACCGACGACAAGAGCGCTGGTTTTTCGACTCCGTCTGTCCAAGAAAAACGCCCATCGTGACCATGAGGGAGACATGGAAAATGGGACGATTGAATACGGCGGATCTGTGTCAAGTGTCAAGAATTGGCAGGAGTAAACATACTTCCAGCGTGATAAAGACCGTTCGGTGGCAAATCTGCGGCGGAGTATCGTCATTCAGGAGTATAACAGGTCAACGACAGAACGTAAATATCGGTGTCAGGCCATTTTTGTACAGCACCTATGCACGTGATCAGCGACGAGATTTGCGAAGCGACGACGACAGTTCGAGAACGGCTGCGAGATCTGATCAGTCGCTCATCACAGATGGCGCC\n+>Pf264_1/1_1.000_244\n+ACTAGCCACCTCATTTGGTTCCTCTTCACAACACACTTCATTGAATCAATCTCCATTCTCACCCTCAGCTCATCACTTGGTATTCTTTCCCTGACACACAAATTACACATGCATCAGATCATACTTGTCCCTGTTTGCTCAAGCCTTCCTATCTGTTCTGACTTCATAGCCCATGGCTCACAGCCATACATCAGGATACAACAGTTCCCATGGCAGGCTATCTCTGACCTTACTTGTCAATGCA\n+>Pf265_1/1_1.000_204\n+GTACATTCCATTCTTCTTTTACATTTCTTTTCTTCTTCTTCCCTCTTTAACTCACATAATTTGAACCTTTGCGTTAATTGCCATTCTTTTTCTGCTGTAAAAGTTATATCCGATAACCTGCAAAATATTAGAAACAACATTATATCCCATTTTGGCTCTTTTAGGTTACTGATTAGTATTTCTATTTTATTTTCCATTTCTAAT\n+>Pf266_1/1_1.000_426\n+TCTACTGAGCCGAGTATCTCTCAGCTATACAGCTTCATTAAGCTATCTATCATTCTAATCACTACCACAGGAACTATCATTGCTTTCCAGCTCAAAATCGCTTATCATTGCGACGACAAACGTCATGCAGACTCCCTGAATCAGAAACATCCACGTCAAAGGTCAAAGGAAGCCAGCTGCACTTGTCATCGCCCGGTAAAATACACCAGCACTGACAGGTTAACTGGAACTGACGAACGTCAGTCAGTTGACGTCTTCTCTCGGCTGCCCCTCGAATACGCTTATGTCCAGTGTTACTTCAGCAAATTACAGCCGACCCAATTAGTAATGAGCCGTCACTCGGCCAAGCAATACGGACAGACGAAGTCCAACGCAAGACAACTCTCAGTTGCTGTGCCAGGGCCTGCCTACGAGCAGTGTTTGTTA\n+>Pf267_1/1_1.000_168\n+CTCTGTTGCGGCACCAGATTGGAGCTAGCTCCTGTAGCTAATAGGCTATTACGCTTGACGATTTCCGATCAGGCTATGGAGATGATTCAGGTAACAGAAGCTATACAGATAACTGACATAGTTTATGTAATAAAAGACATACAGGTAAATAACACGATACAGATAATG\n+>Pf268_1/1_1.000_192\n+GCTTTTGTCTCGTTTCTTATGAATTTGTGTCCTGTGAGTTTTTTCGGAGGACTTTTTGTCAGGATCAATCATCCAGAAAAATTATTACCTCGATTTGTTGACGTCGACATTTCTCCGCGGACCGTCATTTTGTCAGTTTGTAAGAAACGGTTCGATCGTTTTGCAGGAAGCCGATTCTCTCTTCGACCTTCT\n+>Pf269_1/1_1.000_317\n+TTGAAGAGACGACGGTCGGTCGGCTCGGTCTCGGTGGCGACTGGCCCGTGGAGTGTTCTCCTGTTGGCTTATCGTCTGCTAGCCGGTCTGAGCGGCCGTAGAGTGTTACTGGCCAGGCAAGTGTCGCCGTGCCATCTCGGTCTGATTCCTTCCTCTACCGAGAACGACGACGACCGATCGATGGCAGCCGCAGAACGTTACTACCACAGCCAGCCGACAGTTAGCAGGAGAGGTTACCGATCAGATTCTGCCGTTTTTAAGGAGAATCAATTTTCGCCGTCCTCCTGCGGGGACTTGTTGTTGTTGTTGTTGCTGCG\n+>Pf270_1/1_1.000_114\n+CACACGAGCCTTAACGGAGACATGAAGCTCTTCTTGGTGAAACGTGTAGATATATCACAGCTCCAAAATAAGCACTTCATTATACTGGCAAATACGTCAGGGTCTAGTTTCTGT\n+>Pf271_1/1_1.000_238\n+TATCATTATAAGCTATTAATTATCCAGGTGCTTTCCTACCTCACCAACGACACTGACGTAATTTCCTTAATAAGCTACAGCTGGCTACAGCACAACATTGCTGCCTGGAATATAAGCAACATGTTAACATTCTACGTTTTAATCCAATCAAACAACATACTTCAAACGGAACCCAATCATATTGCTGGTATGCTTAGCACTTCCATCTGTAGTACTCTTCGCTATCACTGGTCTTTCA\n+>Pf272_1/1_1.000_208\n+GTACGCACGCACACGACTGACTGTCTCTGTGGAGGGGAGGTGTTGATTGCCAAAAAATATTCCCATACGCAGGCTCTCGGCACATACAGTCTAACATATAAACATAGACATACAAACATATACTCAAGACTTTTGTTAAATAATCATTGTCTGTGTAAAACTTCGTGTTTTAATGGTGAAAATTATCTTCGAGTTGTGACATACAGGC\n+>Pf273_1/1_1.000_138\n+AATTTGCATTATTGTTATTATTATAAAGGCAGCTGCCCCATGACTTATTTCCACTATGCCTATCACTCTTTGGCAGTGACAGTAATATCTACCATTGTTTTATTTAGGCCACCTTCTTGTCACTGCCTTGATCTACGA\n+>Pf274_1/1_1.000_279\n+TGTGGGGGTAGAGTGTCGTTCCCAAACATAACCGTACAGATAAGTCCACGCACCATCATCAGAGACGGAGTGGCAGAGAGGGCGCCACCAGCGCCACCGATATGGAAAAAGATTCTACGTCATAAAACTATCGCTGGCGGCATTAGCCTGCAAACCGGGCTCTGTCACAAGGCGCTGGTACAGGGTACGGGGCGCTGGTACAGTACGCTGGTATGCGGTACGCTGGTACGGGTCGTGCCACGCCTAATGGTACGGCTATCCGGTTACCGGTCCTCTCAC\n+>Pf275_1/1_1.000_137\n+CTCGGAGCGATCGTCTTCACCCGGGCTGAAATGCGATTGAACCACTTTGCCTACCGTACTGGTCACTACACAGGGACTACATTTCTCAAGGTTCTTAATAGTGATTCAGCACAATTAGATAATAATAATAATAATAA\n' |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_tblastx/AcAcaud_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_tblastx/AcAcaud_trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,38 @@ +>Ac1_1/1_1.000_151 +TCGCTCTCCTCCGCCTTTTCTCTAAGCTTAAAAATTATGAAGAGTCTGCACCAGAGACAACTCCTTAGCACATCGACCGACCAGCTGGCCATAAAATGTCTTATTTATACCTTTGTCATGAGCCTTGATAATCCTTTGTGCCAGTGGTGGC +>Ac2_1/1_1.000_160 +ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTG +>Ac3_1/1_1.000_160 +ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGC +>Ac4_1/1_1.000_160 +AAACAATGCAATCCTCTACCATTGCCAAGATATGAAGAACAAGTAAATGGCACATCAACAACAATGATAATAATAAGTGCTAATAACAATAAGAGTAATACAATTACCACAATATCTGAGAACAAGGGGCTTAAGCATAGCTATCATTATTTGGGAGGGG +>Ac5_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Ac6_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>Ac7_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Ac8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Ac9_1/1_1.000_160 +GCCATTCGTCTTAGGAGAAGTTTGTCGTCAGGAAAGATACATGAGGCCTGGATTCTTTCTGACACCGACTCGACGATGTCATTACCTTGTCCACCTGGAACCAACCCCTCATCGACTTCAGCGGATCCATATCTGGTGATCACCAGAAAAACGAACACTA +>Ac10_1/1_1.000_160 +GCCTGGGTATTATTTACCACAGTAACCTTTCATCAGTTTGTGGTGAAAGTACGTGACGTTATGCATTGGCAAGATTGGACATTTTGGTTCGCCCTGTTTTGTACGCATAATAATGTATGTAGTTGTATTTTCCAAAATAATTGTTATATTAGCTATCCAA +>Ac11_1/1_1.000_160 +ACAATTACACAGGTATCAACAAATGTTCACTGCACCTGTCAGTTCCACAAACATAAAGATTACACACATGTACACATCTTTACAAAATATTTACAATTTTGTATTCTTAATTCTATCCACTTGGCTCTGGAAGGCCTTCAGCCATCAGATGATGTGTTTA +>Ac12_1/1_1.000_160 +CAATCCAGCACTAGCAGGAGTGTTGGCCGGAAGGTTGATGATATTTTTCAGTCAAAGAATCTGCATGCTCCAGATGATCGCCTATCAGACAAGGATAACCGTGACAAGTCCAAGAACCCTTTACTTAACAATGAGATGACTCCTCAGTCATTTTCTCGAG +>Ac13_1/1_1.000_141 +GATTACATGCAAAACATAATAGAAATGTTTGTCCCAAGGTCTTACCAGTTTATAGTTTTACATTCGTGTCTTGAAATAAGAAAATGCCTTTATGAGAGTGTATTATTACTCAGTAGATGGAAATTAGCTTACCGGGGGATA +>Ac14_1/1_1.000_160 +CCTGTTGTGACTCGTTCCCTGACGTCGTGCACGCAAGCGCACGCGCGTGCGCGCCGGGTTAGGCACACATACGCGGCACAGGTGCGCAGTATTAGACAGACGCAGACGCAGGCGTCCAGACACGCCAGCCAGCACGGTTACAATGTCCATATCACAATGA +>Ac15_1/1_1.000_147 +CTGAATGTCAACCAGTCACTGACCATCAGCTACATGTCTCTAATGGTCACTAGCATGAAACATGAAATGCCTGCTTATAGTGGGTCTGTAACTGGTAGGATACTGATTACATGTGGAGGCTTATTAAAGGGGTATCCTATTATTTTT +>Ac16_1/1_1.000_160 +CTATGTTGGCTACTGCTAAGGATGTGCTACTTGCCTGATGTAAACAATTCCCAGAATGAATATAAACCAATCATAAGGAGAACTATGGAACCATCCTTAAATGTATTAATCTTATTTAAAATTATGTGCACATCTTGTTTGGCAGAAGGTACATTAAAGC +>Ac17_1/1_1.000_160 +ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGC +>Ac18_1/1_1.000_160 +ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTG +>Ac19_1/1_1.000_160 +GCCAGTGAACTCATTAGGCTCTGTCTGCGCCGATATGATAAGAACGAGTTTGACAGCGATGGTTATATTATGAACAGCGAGCTCGCCTACGATGATGACTCTGAAATGCCTGATGACCTAATTGACCGTTTAGAAGCTGGAAATATTACAAGCTTTGTGC |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_tblastx/AmAmphi_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_tblastx/AmAmphi_trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,40 @@ +>Am1_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Am2_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>Am3_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Am4_1/1_1.000_147 +ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAAGTT +>Am5_1/1_1.000_160 +TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTG +>Am6_1/1_1.000_160 +ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAAT +>Am7_1/1_1.000_160 +GGGGCCCGGGATGTCGAGGATGTTGTACTCGTAGTTGCTGTGGTTGACGTGGTATTGTTGTTCCTGGCTGTGGCTCCGTTACCACTTGACGTGGCTGTTGTGGTGCTGGTGGAAAAACGACTAGTGGTTGTGTCTGCAACTAATTCCTCGCCTCTAATCA +>Am8_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAAAGAGCTTCTATGGTT +>Am9_1/1_1.000_160 +AGCCATCAAAGGTTGCTAATCATGTTGAGTTGTATTGTCAAGCATTTCTACTCGAGGCAACCATTAATAATTGAAGTTATCAGTTATATTGTCAACTCAATGGAAAATCAAATGGATTTAATTAAGGAAGGAAGATTTTGTACTTGTAAATCTGCATTTT +>Am10_1/1_1.000_160 +AGCAACTTTGCCACCACCACCACCACCAACAATAACAACAACAGCTGCAACACCGCGACCAATAACAACAACAACACTGGTAACACTAACCACGTCACCACCAGAAATAACATCTTCACAACCATCACCAACACTACCATTAACTCAACTTATAACAATA +>Am11_1/1_1.000_160 +ATTTTTTGTAGATATTTTTATCTATTTACATTTCTATCTTTATTTCTCCCTACGACCGAAGGCCTCAAAGAGCATATGATTTATTTCTGTCCATTTATCGACCGTGCGTCTGTCTGTCCATCCGCCTCCCTTCCACAAACAGCTGCCGCTACTGTTATAT +>Am12_1/1_1.000_160 +ATAAAGTGGGCCATACAAAGTGAGACCTTACACATATATGAATGTCTAAATTGTCCTATGTTGTCCCATTTAACATGTTTAGTTTGTGGTATTTTTCAAACAAATATAACATGGGGTTTGAATTGGCCGGAATCTAGCACATTAGTCTCTGAGGAAATTT +>Am13_1/1_1.000_160 +ACAACTCCTCCAATAGTACTACCAGCTTGTCAGGGTGAACCAGATGGTAATGCACCTGATCCTGACTCGTGCTCACGATATGTAGTATGTCTCAATCAGGAACCGGTTAATGACTATCCATGTGATCCAAGTACCTTCTTCAACGACCTACCCGAGTACA +>Am14_1/1_1.000_160 +TACTTTCCTGAAATTAGTTCTAATGGTTTCATTGTGATGACAAAGTTTAATATGTCAAGCATAATAAACTTGATTGTGTTTTTCCACCTCAGCAGTCATTTATACATTTTATTGAATGTAGAGGGTGTTGAGACATTCAGTGTTGTTATACTTGCAACAA +>Am15_1/1_1.000_160 +ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAAT +>Am16_1/1_1.000_160 +TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTG +>Am17_1/1_1.000_160 +ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAAAACCAGTATGGCCAAA +>Am18_1/1_1.000_160 +CGAACATCTCATGAAGTGACTCAGACCTCATTTACCCCTAAGGGCTCTATGTTAGGGGGACATGTCATTCCACAGATATGCATGGATGACTCGCATGCATCCAGGGCATTACGGTACAGTAAACGTCCAACAGATGCCCCTCAGATACGACCCATAGAGC +>Am19_1/1_1.000_160 +TTTAGTGAAGAATTTATAATGACTCATGATGTTTGTGTCAATGTACTAAACTTAATGGCACAAATTGCGAACTCATTTTTTTTCTATTATATGTGGGTCTTTTCATTCAACCAGCATTTAGTATATAGACAATTTCTATCTATTCACTTGGATAAAGCAA +>Am20_1/1_1.000_160 +ACCTGTCCCCAACCCCAATCATTAAATCTTTCCCCTTTCGCATGTTCACAGCCCAGCTGCAGCACAACTAGAAAATCCAGACATGCTGAAAATACATGTTATTTGTGTATCTGGCATGTAATTTGTTTCACTCAAAACAGTAACTCTTCTTCAGGAGGTA |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_tblastx/ApApomp_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_tblastx/ApApomp_trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,40 @@ +>Ap1_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Ap2_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Ap3_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>Ap4_1/1_1.000_135 +CGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCACTCAATAATTATTGACATATTACAATTGATTCGGATTAAAAAAATGGCGCTAGGCTTAAAACACAGACAGTTCGCTAGC +>Ap5_1/1_1.000_160 +AATCTACTGACAGATACCTGGAACGAGATGCAGGTCAAGTGGTCGTGTTGTGGTGTGGATGGCTACTCCGACTGGACGCAAGCTGAAGGTCTGGCCACGGGTCACTACGTGCCGCAGTCCTGCTGTCAGAACACGATGAGTACAAGCTGCACGTCACAGA +>Ap6_1/1_1.000_160 +TGGCGAAATGTAGTGGTCATTGATGGATTTTATTGCAATCAGTGTTACATATTACAAGCATTTCTTAATAAACAAAAAGTTGCACGAGATATTTTTTACTTAAAGGTTTTATGGGATGAACACAGTCAATTATATTCATGTAAAAGGCCTTATCCGAGAA +>Ap7_1/1_1.000_160 +TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCT +>Ap8_1/1_1.000_160 +GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAA +>Ap9_1/1_1.000_160 +TGTCTTTACTTCTATCCTTCTCATCATGTTTTACATCATTTTTATTGCTGCCTCTCTTCTCAGCCCTTTCCACACTTTCATGTTTATCTTTTGATTTTTCAACTTCAACTCCATCTTCATCATCATTCTCATGCATTAATTCTTCTATTTCTTCTTCCAA +>Ap10_1/1_1.000_160 +GCAGTGGTGGGAAGTTGTTCACCCTGGCTTGGTGTCCCATGTTTCTCTGTAATTCCTGTTCCTTTCTCTGTAGTTCCTCAGCCTTCCTCTCCAGTTCTTCCTGACGTCTCTTCAGGTCATCTGTGGCAGCCTGGGCCGTGGTCTTGGCGGCTGAGTATGG +>Ap11_1/1_1.000_160 +ACGACAGAGGTCCTCTGCTTGATGAATATGGTTACACCAGAGGATTTGGAAGATGAAGAGGAATATGAAGAAATTTTGGAGGATGTCAAAGAAGAGTGCAGCAAATATGGTTATGTGAAGAGTATAGAGATCCCACGGCCCATTAAGGGTGTGGAAGTGC +>Ap12_1/1_1.000_160 +TGTCTTTACTTCTATCCTTCTCATCATGTTTTACATCATTTTTATTGCTGCCTCTCTTCTCAGCCCTTTCCACACTTTCATGTTTATCTTTTGATTTTTCAACTTCAACTCCATCTTCATCATCATTCTCATGCATTAATTCTTCTATTTCTTCTTCCAA +>Ap13_1/1_1.000_160 +GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAA +>Ap14_1/1_1.000_160 +TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCT +>Ap15_1/1_1.000_160 +GTTGTCAGTGGATCTCGTGATGCAACACTGAGGCTATGGAATGTCGATACTGGCCAGTGTCTGCATGTTCTGATGGGACATATGGCAGCTGTACGGTGTGTGCAGTATGATGGCAAGCGTGTTGTTAGTGGTGCCTATGATTATACAGTTAGAGTGTGGG +>Ap16_1/1_1.000_160 +AGATTTATATTTGAGAATGTTTTGAGTACGACTTCTGTACAGACACACAGCAGAATGACCCTTGTATTGTTTAACAACGTTCAAAATTTCCTGATTCTTCTACCGAAAAAAATACATAAGAAGAGCCACCAAGACGATCAGATCACGGAGGTACTGGCAT +>Ap17_1/1_1.000_160 +GCAGACTCGGCTGGCACGGCCACCGCCTTCCTCTGTGGAGTGAAGGCTCGCTACGGAACGCTGGGTCTGGGACCGAGAGCCACACGATCTGACTGTAGACAGAGTCACATCAACAAACTGAAGTGTATAGGAGACATGGCACAACAAGCAGGTATGAGGA +>Ap18_1/1_1.000_160 +CCGGCCTGCAAGACGCCATTTTACTTCGTCTGTCAATCGAGGTCAAAGGTCACTACCGTTGTCTCCGAGAAGCACACAGACGCCGAGCTGGTTCACACGCTGTGTATTCGGCACAGATCTACTGTTGCTTGGGATATTTTAGCCGGCGAACGAGCGAAAT +>Ap19_1/1_1.000_160 +CCGGCGATCGTTCAGAGGGCCAGCGGTCTGGCCATGTCAGAGATCTATCACCTGCGCTTCTGCGATGGGGATCGGCTGAACGTCAGCTGCCCGGACAACTGGCAGATCCACATCTCGTCCAGCTACTTCGTCTACGTCAGCGGCGTCGACGGCCGCGGCG +>Ap20_1/1_1.000_160 +CATGAAGGACCTGTGTGGCAGGTGGCTTGGGCACATCCAATGTTTGGTAATCTGATAGCATCATGTAGTTATGACAGAAAGGTGATTATTTGGAAGGAGACTGGAGGGACATGGGCAAAGCTTTATGAATACAACAATCATGATTCCTCAGTTAATTCAG |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/inputs_tblastx/PfPfiji_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/inputs_tblastx/PfPfiji_trinity.fasta Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,40 @@ +>Pf1_1/1_1.000_160 +AGCATTGTCCGTGTTGCGCGGGTCGTCGACGTAACCTCGGTACACCTCAGCGTGCCCGGCCATCTGGTGCGTGAGCCGCTTGAAGACGACTCTCGCCGGCGGCTGCTTGCTGTCCAGCGTCATGCTCTCGAACGCCTTGATCCAGGACTCCTTGACACTG +>Pf2_1/1_1.000_160 +ATCACGCCCCCTGTCGTGGACAACAGGCTAGCCCATTGTAATGGGAAATCTACAGTGGTAAACAAACTGATATACAATATAACCAATATGTATATATATATAACAGATATGGAGACTGATCATAAAATCAACGATTCACTTTTAGGATTAGTCATGTTTG +>Pf3_1/1_1.000_160 +TGTGCGTCGGTGCCGGACTGCAGGCTGTTGTTTGTCGGGAGCACCTCCGGAGTCATCAGTGTCATCAACACCAAGTTCAACCAGAGCAAGCAAAGCCACCTGCAGGTGTTCGGCCACAAAACCTGCCTGTACGGCCATTCCGGGGCCGTCACAGCCTTCT +>Pf4_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Pf5_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Pf6_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>Pf7_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Pf8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Pf9_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAGGTAATTTCCCGATTA +>Pf10_1/1_1.000_160 +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>Pf11_1/1_1.000_160 +AGCATTGTCCGTGTTGCGCGGGTCGTCGACGTAACCTCGGTACACCTCAGCGTGCCCGGCCATCTGGTGCGTGAGCCGCTTGAAGACGACTCTCGCCGGCGGCTGCTTGCTGTCCAGCGTCATGCTCTCGAACGCCTTGATCCAGGACTCCTTGACACTG +>Pf12_1/1_1.000_160 +GCCCTCGGCCACCAAGCCCAAGAGTCCCAACGTGATGCCCAACCTGCCCAAGCACGTGCTGCAGGCCATCGAAGAGAACATGATCTACTACAACAAAATGTACAGTCTCCGAGTCAAGCCGGACCTGCTCCAGGTTCACTAGAGGGCGCTGTGGTGTTCG +>Pf13_1/1_1.000_160 +CGCGTCCACGACCGCCACGCGCACCGAGGTCTACGACAAACTCGCGCCGCAGGAGGCTCCTCTCAACCTGCACAAGCCTCGCGCCGACAGCGTCCCGACCGACGGCAACGGCTGACGGCAGACACTCGAGCCTTGACTACGTGTATGCACAAAGCTACCC +>Pf14_1/1_1.000_160 +ATCACGCCCCCTGTCGTGGACAACAGGCTAGCCCATTGTAATGGGAAATCTACAGTGGTAAACAAACTGATATACAATATAACCAATATGTATATATATATAACAGATATGGAGACTGATCATAAAATCAACGATTCACTTTTAGGATTAGTCATGTTTG +>Pf15_1/1_1.000_160 +TCGTCCCAACAGCAGTCCATCAGTACAAGCAGTGTACAGAAGAAATTTGACAAAAATACTATTGATGCAGTCAAGAGATGGAACACAGAAAATCTTGACATTTATGGACCACTTCGGAACCCCAAAACCGATGGAGGTTCCTCTCCAAACCCAACCACTC +>Pf16_1/1_1.000_160 +CACGTCACGGACGTGCTCGTCTCGAAAATCATCGATATGGTCAAAAAGAAGGAAAAGAAAGGAGGGATCACCATCAAGCCATTCCAGGTCAAGAACCATGTCTGGGTGTTCGTCAACTGTCTAATAGAGAACCCGACGTTCGACTCGCAGACGAAGGAGA +>Pf17_1/1_1.000_160 +TGTGCGTCGGTGCCGGACTGCAGGCTGTTGTTTGTCGGGAGCACCTCCGGAGTCATCAGTGTCATCAACACCAAGTTCAACCAGAGCAAGCAAAGCCACCTGCAGGTGTTCGGCCACAAAACCTGCCTGTACGGCCATTCCGGGGCCGTCACAGCCTTCT +>Pf18_1/1_1.000_160 +TTACGACACCTGCCCCAGATCCTGTCCGTGTCACTGCTGAGGTTCAGCTTTGACTTCCAGAAAATGGAAAGATATAAGGAAACTGGCAAGTTTGTGTTTCCGATAGAGTTGGATATGGCACCTTATGTTGATAAGTTATCAACTGCTGGGTGCACAGAAT +>Pf19_1/1_1.000_160 +GATCTGAAAGAATCTTCTCCAGTAGCAGAGATTAATGGTCCAGAACTTATCGATGAAGCACTGCCAATTTCCGTTGATAACAGTCAAGGAACAACGGCAGAAATTAGACTTGAGCGCAGTCAAAGCCATACTGGAAAAAACGAGGCGGATTTATTTGCAC +>Pf20_1/1_1.000_160 +TTGTACATTCAAAAGCTAGGTGGCCAAATTGTGGAATTGAATACATGTAATAATTATATATCTTTCACCATGAAAAGATGTCCATGGACCAAGTCTATGCATTGCCGATTTTCGTCATTAATATATATCAGAGATGTGATAAAAGATATATGTACTCATA |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_diamond_dna/RBH_AcAcaudAmAmphi --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_diamond_dna/RBH_AcAcaudAmAmphi Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +>Ac5_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Am1_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Ac7_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Am3_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Ac6_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>Am2_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_diamond_dna/RBH_AcAcaudApApomp --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_diamond_dna/RBH_AcAcaudApApomp Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,4 @@ +>Ac23_1/1_1.000_366 +ACTGAGGCTCGAACACAACAAAAAGGTGATGAGCAGTCAGCACTTAATAGAATATTACAGCAAGTAGCCAGTAATGTAGTTGATGTAGCAGCATTAGATAATCAAGGAGTAGACCAAGTTGAATACACAGATAGAGCTAGACAATACAGCCATAACCTGTCATCGTGGTGTGCTAGCACCCAGAAAGTACGAGGACCTCAACGTCTACCTGTTGGCGTAGCCACTCCACACACAGTCCTGTCTGGACAACCTATCACCTTAGCTGATATTGAACTGATAACTCATGCTGCCCAACAAGCGGCACGGTCACTACAAGAGGTCAAAGTTCGCCACAAAGAAGACTTGGTTGTACCTTTTGGCGTGCCA +>Ap46_1/1_1.000_217 +CCACAACCAAGTGGCGGGTATAACAGCACCGAGGCTCGAACACAGCAAAAAGGTGATGAGCAGTCAGCTCTTAATAGAATATTACAGCAAGTAGCCAGTAATGTAGTTGATGTAGCAGCATTAGATAATCAAGGAGTAGATCAAGTTGAGTACACAGATAGAGCTAGACAGTACAGCCATAACCTGTCATCATGGTGTGCTACCACCCAGAAAGTAC |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_diamond_dna/RBH_AcAcaudPfPfiji --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_diamond_dna/RBH_AcAcaudPfPfiji Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>Ac8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Pf8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Ac5_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Pf7_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_diamond_dna/RBH_AmAmphiPfPfiji --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_diamond_dna/RBH_AmAmphiPfPfiji Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>Am8_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAAAGAGCTTCTATGGTT +>Pf9_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAGGTAATTTCCCGATTA +>Am1_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Pf7_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_diamond_dna/RBH_ApApompPfPfiji --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_diamond_dna/RBH_ApApompPfPfiji Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +>Ap2_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Pf5_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Ap1_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Pf4_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Ap4_1/1_1.000_160 +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>Pf10_1/1_1.000_160 +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>Ap3_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>Pf6_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_dna_tblastx/RBH_AcAcaud_AmAmphi_dna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_dna_tblastx/RBH_AcAcaud_AmAmphi_dna Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,12 @@ +>Ac5_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Am1_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Ac7_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Am3_1/1_1.000_160 +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>Ac6_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>Am2_1/1_1.000_160 +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_dna_tblastx/RBH_AcAcaud_PfPfiji_dna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_dna_tblastx/RBH_AcAcaud_PfPfiji_dna Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>Ac8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Pf8_1/1_1.000_160 +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>Ac5_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Pf7_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_dna_tblastx/RBH_AmAmphi_PfPfiji_dna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_dna_tblastx/RBH_AmAmphi_PfPfiji_dna Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,8 @@ +>Am8_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAAAGAGCTTCTATGGTT +>Pf9_1/1_1.000_160 +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAGGTAATTTCCCGATTA +>Am1_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>Pf7_1/1_1.000_160 +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_dna_tblastx/RBH_ApApomp_PfPfiji_dna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_dna_tblastx/RBH_ApApomp_PfPfiji_dna Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,16 @@ +>Ap2_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Pf5_1/1_1.000_160 +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>Ap4_1/1_1.000_135 +CGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCACTCAATAATTATTGACATATTACAATTGATTCGGATTAAAAAAATGGCGCTAGGCTTAAAACACAGACAGTTCGCTAGC +>Pf10_1/1_1.000_160 +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>Ap1_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Pf4_1/1_1.000_160 +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>Ap3_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>Pf6_1/1_1.000_160 +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_prot/ReciprocalBestHits_AmAmphi_AcAcaud.fasta Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,12 @@ +>Ac7_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APRITRSCLAIATPNGRHDICRKKACGTIGNRQAFPQPCGSCPSAPVFDLEHQ +>Am3_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APRITRSCLAIATPNGRHDICRKKACGTIGNRQAFPQPCGSCPSAPVFDLEHQ +>Ac5_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APGCGFADDMAKALSACGTCLCHTTGIFLAVAAFVLTALGIVCVTRSADPSLW +>Am1_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APGCGFADDMAKALSACGTCLCHTTGIFLAVAAFVLTALGIVCVTRSADPSLW +>Ac6_1/1_1.000_160||2...160||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +SL*YVPVESCHHHFDYCHCRCRRHDHVLHYHPLYDHHFYPSKTC*SISSQW*A +>Am2_1/1_1.000_160||2...160||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +SL*YVPVESCHHHFDYCHCRCRRHDHVLHYHPLYDHHFYPSKTC*SISSQW*A |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_prot/ReciprocalBestHits_ApApomp_AcAcaud.fasta Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,4 @@ +>Ac23_1/1_1.000_366||3...188||[[1/1]][[1/6]]||3.22580645161||0||3.22580645161||62.0 +TFWVLAHHDDRLWLYCLALSVYSTWSTP*LSNAATSTTLLATCCNILLSADCSSPFCCVRAS +>Ap46_1/1_1.000_217||30...215||[[1/1]][[1/6]]||3.22580645161||0||3.22580645161||62.0 +TFWVVAHHDDRLWLYCLALSVYST*STP*LSNAATSTTLLATCCNILLRADCSSPFCCVRAS |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_prot/ReciprocalBestHits_PfPfiji_AcAcaud.fasta Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,8 @@ +>Ac8_1/1_1.000_160||3...158||[[1/1]][[1/6]]||0.0||0||0.0||52.0 +QRRATSSYWHWQWNPNYSRNKHWLPVVWVSNW**RCSC*RSWGQSRTDAFG* +>Pf8_1/1_1.000_160||3...158||[[1/1]][[1/6]]||0.0||0||0.0||52.0 +QRRATSSYWHWQWNPNYSRNKHWLPVVWVSNW**RCSC*RSWGQSRTDAFG* +>Ac5_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APGCGFADDMAKALSACGTCLCHTTGIFLAVAAFVLTALGIVCVTRSADPSLW +>Pf7_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APGCGFADDMAKALSACGTCLCHTTGIFLAVAAFVLTALGIVCVTRSADPSLW |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_prot/ReciprocalBestHits_PfPfiji_AmAmphi.fasta Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,8 @@ +>Am1_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APGCGFADDMAKALSACGTCLCHTTGIFLAVAAFVLTALGIVCVTRSADPSLW +>Pf7_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +APGCGFADDMAKALSACGTCLCHTTGIFLAVAAFVLTALGIVCVTRSADPSLW +>Am8_1/1_1.000_160||2...145||[[1/1]][[1/6]]||0.0||0||0.0||48.0 +LFHAEYFYI*WVNTWKTQCDLPCL*YKQPCLLRPDFLVLNNSLVLLLI +>Pf9_1/1_1.000_160||2...145||[[1/1]][[1/6]]||0.0||0||0.0||48.0 +LFHAEYFYI*WVNTWKTQCDLPCL*YKQPCLLRPDFLVLNNSLVLLLI |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/outputs_prot/ReciprocalBestHits_PfPfiji_ApApomp.fasta Fri Feb 01 10:23:16 2019 -0500 |
| [ |
| @@ -0,0 +1,20 @@ +>Ap3_1/1_1.000_160||3...158||[[1/1]][[1/6]]||0.0||0||0.0||52.0 +HAVHWTSVILFVCLDGSQTRGRPSNAHPSPAP*NRRGR*TPRARHWRREVWW +>Pf6_1/1_1.000_160||3...158||[[1/1]][[1/6]]||0.0||0||0.0||52.0 +HAVHWTSVILFVCLDGSQTRGRPSNAHPSPAP*NRRGR*TPRARHWRREVWW +>Ap1_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +IAFWQNL*PRHQSHKCPLYAHPFITDTGRFEVCFWFLARFKGKLFRIGFYKAT +>Pf4_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +IAFWQNL*PRHQSHKCPLYAHPFITDTGRFEVCFWFLARFKGKLFRIGFYKAT +>Ap130_1/1_1.000_300||18...68||[[1/1]][[1/2]]||23.5294117647||0||23.5294117647||17.0 +VWLCVCVRVYLWVFVYL +>Pf172_1/1_1.000_246||137...187||[[1/1]][[1/2]]||23.5294117647||0||23.5294117647||17.0 +LWVCICACVYLRLFAYV +>Ap4_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +RPRRVVLSQADFDLSRPFAYLHDDCSTLYDLVTLPFNQALLPSNLVQSVSTHP +>Pf10_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +RPRRVVLSQADFDLSRPFAYLHDDCSTLYDLVTLPFNQALLPSNLVQSVSTHP +>Ap2_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +ILRHTAFVVLGERERGTTNCNHDYVTFVYKPNVLASKIIKRKLTECDWRWSTG +>Pf5_1/1_1.000_160||1...159||[[1/1]][[1/6]]||0.0||0||0.0||53.0 +ILRHTAFVVLGERERGTTNCNHDYVTFVYKPNVLASKIIKRKLTECDWRWSTG |
| b |
| diff -r 000000000000 -r 90b57ab0bd1d test-data/pairwise.out --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/pairwise.out Fri Feb 01 10:23:16 2019 -0500 |
| b |
| @@ -0,0 +1,120 @@ +Pair of species: +('PfPfiji_Trinity.fasta', 'ApApomp_Trinity.fasta') +Pair of species: +('PfPfiji_Trinity.fasta', 'AmAmphi_Trinity.fasta') +Pair of species: +('PfPfiji_Trinity.fasta', 'AcAcaud_Trinity.fasta') +Pair of species: +('ApApomp_Trinity.fasta', 'AmAmphi_Trinity.fasta') +Pair of species: +('ApApomp_Trinity.fasta', 'AcAcaud_Trinity.fasta') +Pair of species: +('AmAmphi_Trinity.fasta', 'AcAcaud_Trinity.fasta') +-------------------- Pairwise PfPfiji_AmAmphi -------------------- + +database : PfPfiji_Trinity.fasta +query file : AmAmphi_Trinity.fasta + +***** RUN FIRST BLAST ***** + + +database : AmAmphi_Trinity.fasta +query file : only the sequences of PfPfiji_Trinity.fasta which matched during the last BLAST + +***** RUN SECOND BLAST ***** + + +Number of pairwises parsed = 2 + + + +-------------------- Pairwise AmAmphi_AcAcaud -------------------- + +database : AmAmphi_Trinity.fasta +query file : AcAcaud_Trinity.fasta + +***** RUN FIRST BLAST ***** + + +database : AcAcaud_Trinity.fasta +query file : only the sequences of AmAmphi_Trinity.fasta which matched during the last BLAST + +***** RUN SECOND BLAST ***** + + +Number of pairwises parsed = 3 + + + +-------------------- Pairwise ApApomp_AmAmphi -------------------- + +database : ApApomp_Trinity.fasta +query file : AmAmphi_Trinity.fasta + +***** RUN FIRST BLAST ***** + + +database : AmAmphi_Trinity.fasta +query file : only the sequences of ApApomp_Trinity.fasta which matched during the last BLAST + +***** RUN SECOND BLAST ***** + + +Number of pairwises parsed = 0 + + + +-------------------- Pairwise PfPfiji_ApApomp -------------------- + +database : PfPfiji_Trinity.fasta +query file : ApApomp_Trinity.fasta + +***** RUN FIRST BLAST ***** + + +database : ApApomp_Trinity.fasta +query file : only the sequences of PfPfiji_Trinity.fasta which matched during the last BLAST + +***** RUN SECOND BLAST ***** + + +Number of pairwises parsed = 5 + + + +-------------------- Pairwise PfPfiji_AcAcaud -------------------- + +database : PfPfiji_Trinity.fasta +query file : AcAcaud_Trinity.fasta + +***** RUN FIRST BLAST ***** + + +database : AcAcaud_Trinity.fasta +query file : only the sequences of PfPfiji_Trinity.fasta which matched during the last BLAST + +***** RUN SECOND BLAST ***** + + +Number of pairwises parsed = 2 + + + +-------------------- Pairwise ApApomp_AcAcaud -------------------- + +database : ApApomp_Trinity.fasta +query file : AcAcaud_Trinity.fasta + +***** RUN FIRST BLAST ***** + + +database : AcAcaud_Trinity.fasta +query file : only the sequences of ApApomp_Trinity.fasta which matched during the last BLAST + +***** RUN SECOND BLAST ***** + + +Number of pairwises parsed = 1 + + + |
