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planemo upload for repository https://github.com/abims-sbr/adaptsearch commit 3c7982d775b6f3b472f6514d791edcb43cd258a1-dirty |
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README.rst filter_assembly.xml macros.xml scripts/S01_script_to_choose.py scripts/S02a_remove_redondancy_from_velvet_oases.py scripts/S02b_format_fasta_name_trinity.py scripts/S03_choose_one_variants_per_locus_trinity.py scripts/S04_find_orf.py scripts/S05_filter.py static/images/adaptsearch_picture_helps.png test-data/trinity.output test-data/trinity/Acaud_trinity.fasta test-data/trinity/Amphi_trinity.fasta test-data/trinity/Apomp_trinity.fasta test-data/trinity/Pfiji_trinity.fasta test-data/trinity_and_velvet.output test-data/trinity_and_velvet_up.output test-data/trinity_out/AcAcaud_trinity.fasta test-data/trinity_out/AmAmphi_trinity.fasta test-data/trinity_out/ApApomp_trinity.fasta test-data/trinity_out/PfPfiji_trinity.fasta test-data/trinity_up.output test-data/velvet.output test-data/velvet/Ac_transcriptome_25591.fasta test-data/velvet/Ac_transcriptome_25591_oneline.fasta test-data/velvet/Ap_transcriptome_35099.fasta test-data/velvet/Ap_transcriptome_35099_oneline.fasta test-data/velvet/Pg_transcriptome_90109.fasta test-data/velvet/Pg_transcriptome_90109_oneline.fasta test-data/velvet_out/AcAc_transcriptome_25591.fasta test-data/velvet_out/ApAp_transcriptome_35099.fasta test-data/velvet_out/PgPg_transcriptome_90109.fasta test-data/velvet_up.output |
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| diff -r 000000000000 -r 7a813e633d1c README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Feb 01 10:22:32 2019 -0500 |
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| @@ -0,0 +1,14 @@ +Changelog +--------- + +**Version 2.0 - 14/04/2017** + + - 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 cap3, fastaformatter and python + |
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| diff -r 000000000000 -r 7a813e633d1c filter_assembly.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filter_assembly.xml Fri Feb 01 10:22:32 2019 -0500 |
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| b'@@ -0,0 +1,191 @@\n+<tool name="Filter assemblies" id="filter_assemblies" version="2.0.3">\n+\n+ <description>\n+ Filter the outputs of Velvet or Trinity assemblies\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="0.0.14">fastx_toolkit</requirement>\n+ <requirement type="package" version="10.2011">cap3</requirement>\n+ </requirements>\n+\n+ <command>\n+ <![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/S02a_remove_redondancy_from_velvet_oases.py\' . &&\n+ ln -s \'$__tool_directory__/scripts/S02b_format_fasta_name_trinity.py\' . &&\n+ ln -s \'$__tool_directory__/scripts/S03_choose_one_variants_per_locus_trinity.py\' . &&\n+ ln -s \'$__tool_directory__/scripts/S04_find_orf.py\' . &&\n+ ln -s \'$__tool_directory__/scripts/S05_filter.py\' . &&\n+\n+ python \'$__tool_directory__/scripts/S01_script_to_choose.py\'\n+\n+ \'$infiles\'\n+ $length_seq_max\n+ $percent_identity\n+ $overlap_length\n+ > ${log}\n+ ]]>\n+ </command>\n+\n+ <inputs>\n+ <param name="inputs" type="data" format="fasta" multiple="true" label="Input files" />\n+ <param name="percent_identity" type="integer" value="100" label="Overlap percent identity cutoff" help="Cap3 parameter (-p N); minimum percent identity of an overlap. The specified value should be more than 65%." />\n+ <param name="overlap_length" type="integer" value="60" label="Overlap length cutoff" help="Cap3 parameter (-o N); minimum length of an overlap (in base pairs). The specified value should be more than 15 base pairs." />\n+ <param name="length_seq_max" type="integer" value="100" label="Minimum sequence length" help="Keep sequences which length is higher than the minimum sequence length " />\n+ </inputs>\n+\n+ <outputs>\n+ <collection name="output_fasta" type="list" label="Filter Assemblies outputs">\n+ <discover_datasets pattern="__name_and_ext__" directory="outputs" />\n+ </collection>\n+ <data format="txt" name="log" label="Filter Assemblies Summary"/>\n+ </outputs>\n+\n+\t<tests>\n+ <test>\n+ <param name="inputs" ftype="fasta" value="trinity/Pfiji_trinity.fasta,trinity/Apomp_trinity.fasta,trinity/Amphi_trinity.fasta,trinity/Acaud_trinity.fasta,velvet/Pg_transcriptome_90109.fasta,velvet/Ap_transcriptome_35099.fasta,velvet/Ac_transcriptome_25591.fasta" />\n+ <param name="percent_identity" value="100" />\n+ <param name="overlap_length" value="60" />\n+ <param name="length_seq_max" value="100" />\n+ <output name="log" value="trinity_and_velvet_up.output" />\n+ <output_collection name="output_fasta" type="list">\n+ <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />\n+ <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />\n+ <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />\n+ <element name="AcAcaud_trinity" value="trinity_out/AcAcaud_trinity.fasta" />\n+ <element name="AmAmphi_trinity" value="trinity_out/AmAmphi_trinity.fasta" />\n+ <element name="ApApomp_trinity" value="trinity_out/ApApomp_trinity.fasta" />\n+ <element name="PfPfiji_trinity" value="trinity_out/PfPfiji_trinity.fasta" />\n+ </output_collection>\n+ </test> \n+ <test>\n+ <param name="inputs" ftype="fasta" value="trinity/Pfiji_trinity.fasta,trinity/Apomp_trinity.fasta,trinity/Amphi_trinity.fasta,'..b'/>\n+ </output_collection>\n+ </test>\n+ <test>\n+ <param name="inputs" ftype="fasta" value="velvet/Pg_transcriptome_90109.fasta,velvet/Ap_transcriptome_35099.fasta,velvet/Ac_transcriptome_25591.fasta" />\n+ <param name="percent_identity" value="100" />\n+ <param name="overlap_length" value="60" />\n+ <param name="length_seq_max" value="100" />\n+ <output name="log" value="velvet_up.output" />\n+ <output_collection name="output_fasta" type="list">\n+ <element name="AcAc_transcriptome_25591" value="velvet_out/AcAc_transcriptome_25591.fasta" />\n+ <element name="ApAp_transcriptome_35099" value="velvet_out/ApAp_transcriptome_35099.fasta" />\n+ <element name="PgPg_transcriptome_90109" value="velvet_out/PgPg_transcriptome_90109.fasta" />\n+ </output_collection>\n+ </test>\n+ \n+ </tests>\n+\n+\t<help>\n+\n+@HELP_AUTHORS@\n+\n+<![CDATA[\n+\n+**Description**\n+\n+This tool reformats Velvet Oases or Trinity assemblies for the AdaptSearch galaxy suite and selects only one variant per gene according to its length and quality check.\n+\n+---------\n+\n+**Input format**\n+\n+(1) Sequences are in the sequential format:\n+\n+| >seqname1\n+| AAAGAGAGACCACATGTCAGTAGC -on one or several lines -\n+| >seqname2\n+| AAGGCCTGACCACATGAGTTAAGC -on one or several lines -\n+| etc ...\n+|\n+\n+2) The file name should begin with a two letter abbreviation of the species name (for isntance, \'Ap\' if the species is Alvinella pompejana).\n+\n+**For Velvet Oases assemblies input**\n+ \n+ The headers must be as follow : *>Locus_i_Transcript_i/j_Confidence_x.xxx_Length_N* where i is the locus number, j the transcript variant among all versions of the transcript, x.xxx the confidence value and N the length.\n+\n+**For Trinity assemblies inputs** \n+ \n+ The headers must be as follow : *>cj_gj_ij Len=j path=[j:0-j]* where all the j are integers (locus number, transcript variant, length, position...)\n+\n+**The tool handles the case if input files come from both assemblers (there is no need for input files to be exclusively from one or another assembler).**\n+\n+---------\n+\n+**Parameters**\n+\n+ - \'Input files\' : a collection of fasta files (one file per species).\n+ - \'Overlap percent identity cutoff\' : cap3 -p parameter : minimum percent identity of an overlap.\n+ must be > 65 ; default : 100.\n+ - \'Overlap length cutoff\' (integer) : cap3 -o parameter : minimum length of an overlap (in base pairs).\n+ must be > 15 ; default : 60.\n+ - \'Minimum sequence length\' (integer) : only keep sequences which are longer than the specified value.\n+ default : 100.\n+\n+---------\n+\n+**Steps**:\n+ \n+The tool:\n+ 1) Modifies the sequence name to add the species abbreviation using the 2 first letters of the name of the transcriptome file : note that each species abbreviation must be unique\n+ 2) Selects one allelic sequence from each transcript (c or locus) using the length of the sequence and its level of confidence\n+ 3) Selects the best ORF from the sequence between two stop codons\n+ 4) Performs a CAP3 from the full set of ORFs to minimize redundancy\n+ 5) Retrieves the initial transcript sequences from the remaining set of proceeded ORF sequences\n+\n+**Outputs**\n+\n+ - \'Filter Assemblies Summary\' : the log file.\n+ - \'Filter Assemblies outputs\' : the main results.\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 - 15/01/2018**\n+\n+ - Input files can be a mix from files coming either from Trinity or Velvet Oases assemblers\n+\n+**Version 2.0 - 14/04/2017**\n+\n+ - NEW: Replace the zip between tools by Dataset Collection\n+\n+**Version 1.0 - 13/04/2017**\n+\n+ - TEST: Add funtional test with planemo\n+ - IMPROVEMENT: Use conda dependencies for cap3, fastaformatter and python\n+\n+ ]]>\n+\t</help>\n+\n+</tool>\n' |
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| diff -r 000000000000 -r 7a813e633d1c macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 01 10:22:32 2019 -0500 |
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| @@ -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> |
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| diff -r 000000000000 -r 7a813e633d1c scripts/S01_script_to_choose.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S01_script_to_choose.py Fri Feb 01 10:22:32 2019 -0500 |
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| @@ -0,0 +1,54 @@ +#!/usr/bin/env python +#coding: utf-8 + +## AUTHOR: Eric Fontanillas +## LAST VERSION: 10.2017 by Victor Mataigne + +import glob, sys, string, os + +def nameFormatting(name, script_path, prefix): + f = open(name, "r") + f1 = f.readline() # Only need to check first line to know the assembler which has been used + f.close() + name_find_orf_input = "" + + if f1.startswith(">Locus"): + name_remove_redondancy = "02_%s" %name + os.system("python S02a_remove_redondancy_from_velvet_oases.py %s %s" %(name, name_remove_redondancy)) + name_find_orf_input = "%s%s" %(prefix, name) + os.system("sed -e 's/Locus_/%s/g' -e 's/_Confidence_/_/g' -e 's/_Transcript_/_/g' -e 's/_Length_/_/g' %s > %s" % (prefix, name_remove_redondancy, name_find_orf_input)) + elif f1.startswith(">c"): + #Format the name of the sequences with good name + name_format_fasta = "03%s" %name + os.system("python S02b_format_fasta_name_trinity.py %s %s %s" %(name, name_format_fasta, prefix)) + #Apply first script to avoid reductant sequences + name_find_orf_input = "04%s" %name + os.system("python S03_choose_one_variants_per_locus_trinity.py %s %s" %(name_format_fasta, name_find_orf_input)) + + return name_find_orf_input + +def main(): + os.mkdir("outputs") + script_path = os.path.dirname(sys.argv[0]) + length_seq_max = sys.argv[2] + percent_identity = sys.argv[3] + overlap_length = sys.argv[4] + + for name in str.split(sys.argv[1], ","): + prefix=name[0:2] + name_fasta_formatter = "01%s" %name + os.system("cat '%s' | fasta_formatter -w 0 -o '%s'" % (name, name_fasta_formatter)) + name_find_orf_input = nameFormatting(name_fasta_formatter, script_path, prefix) + #Pierre guillaume find_orf script for keeping the longuest ORF + name_find_orf = "05%s"% name + os.system("python S04_find_orf.py %s %s" %(name_find_orf_input, name_find_orf)) + #Apply cap3 + os.system("cap3 %s -p %s -o %s"%(name_find_orf, percent_identity, overlap_length)) + #Il faudrait faire un merge des singlets et contigs! TODO + os.system("zcat -f < '%s.cap.singlets' | fasta_formatter -w 0 -o '%s'" % (name_find_orf, prefix)) + #Apply pgbrun script filter script TODO length parameter + name_filter = "%s%s"%(prefix, name) + os.system("python S05_filter.py %s %s outputs/%s" %(prefix, length_seq_max, name_filter)) + +if __name__ == "__main__": + main() |
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| diff -r 000000000000 -r 7a813e633d1c scripts/S02a_remove_redondancy_from_velvet_oases.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S02a_remove_redondancy_from_velvet_oases.py Fri Feb 01 10:22:32 2019 -0500 |
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| @@ -0,0 +1,122 @@ +#!/usr/bin/env python +## AUTHOR: Eric Fontanillas +## LAST VERSION: 06.12.2011 + +## DESCRIPTION: Remove redondant transcripts (i.e. transcript from the same locus) from Oases output on the basis of two recursive criterias (see in DEF1): + ## 1. [CRITERIA 1] Keep in priority seq with BEST "confidence_oases_criteria" present in the fasta name + ## 2. [CRITERIA 2] Second choice (if same coverage) : choose the longuest sequence (once any "N" have been removed => effective_length = length - N number +## => criticize of this approach: the transcripts may come from a same locus but may be not redundant (non-overlapping) ==> SEE "DEF2" for an alternative + +################### +###### DEF 1 ###### +################### +def dico_filtering_redundancy(path_in): + f_in = open(path_in, "r") + bash = {} + bash_unredundant = {} + file_read = f_in.read() + S1 = file_read.split(">") + k = 0 + + ## 1 ## Extract each transcript and group them in same locus if they share the same "short_fasta_name" + for element in S1: + if element != "": + S2 = element.split("\n") + fasta_name = S2[0] + fasta_seq = S2[1:-1] # that line was unindented + fasta_seq = "".join(fasta_seq) # that line was unindented + L = fasta_name.split("_") + short_fasta_name = L[0] + L[1] + + ## Used later for [CRITERIA 1] (see below) + confidence_oases_criteria = L[-3] + countN = fasta_seq.count("N") + length = len(fasta_seq) + effective_length = length - countN + + if short_fasta_name not in list(bash.keys()): + bash[short_fasta_name] = [[fasta_name, fasta_seq, confidence_oases_criteria, effective_length]] + else: + bash[short_fasta_name].append([fasta_name, fasta_seq, confidence_oases_criteria, effective_length]) + k = k+1 + f_in.close() + + for key in list(bash.keys()): + ## 2 ## IF ONE TRANSCRIPT PER LOCUS: + ## In this case => we record directly + if len(bash[key]) == 1: + entry = bash[key][0] + name = entry[0] + seq = entry[1] + bash_unredundant[name] = seq + + ## 3 ## IF MORE THAN ONE TRANSCRIPTS PER LOCUS: + ## In this case: + ## 1. [CRITERIA 1] Keep in priority seq with BEST "confidence_oases_criteria" present in the fasta name + ## 2. [CRITERIA 2] Second choice (if same coverage) : choose the longuest sequence (once any "N" have been removed => effective_length = length - N numb + elif len(bash[key]) > 1: ### means there are more than 1 seq + MAX_CONFIDENCE = {} + MAX_LENGTH = {} + for entry in bash[key]: ## KEY = short fasta name || VALUE = list of list, e.g. : [[fasta_name1, fasta_seq1],[fasta_name2, fasta_seq2][fasta_name3, fasta_seq3]] + name = entry[0] + seq = entry[1] + effective_length = entry[3] + confidence_oases_criteria = entry[2] + + ## Bash for [CRITERIA 2] + MAX_LENGTH[effective_length] = entry + + ## Bash for [CRITERIA 1] + # confidence_oases_criteria = string.atof(confidence_oases_criteria) + confidence_oases_criteria = float(confidence_oases_criteria) + if confidence_oases_criteria not in list(MAX_CONFIDENCE.keys()): + MAX_CONFIDENCE[confidence_oases_criteria] = entry + else: ## IF SEVERAL SEQUENCES WITH THE SAME CONFIDENCE INTERVAL => RECORD ONLY THE LONGUEST ONE [CRITERIA 2] + current_seq_length = effective_length + yet_recorded_seq_length = MAX_CONFIDENCE[confidence_oases_criteria][3] + if current_seq_length > yet_recorded_seq_length: + MAX_CONFIDENCE[confidence_oases_criteria] = entry ## Replace the previous recorded entry with the same confidence interval but lower length + + ## Sort keys() for MAX_CONFIDENCE bash + KC = list(MAX_CONFIDENCE.keys()) + KC.sort() + + ## Select the best entry + MAX_CONFIDENCE_KEY = KC[-1] ## [CRITERIA 1] + BEST_ENTRY = MAX_CONFIDENCE[MAX_CONFIDENCE_KEY] + + BEST_fasta_name = BEST_ENTRY[0] + BEST_seq = BEST_ENTRY[1] + bash_unredundant[BEST_fasta_name] = BEST_seq + + return bash_unredundant +#~#~#~#~#~#~#~#~#~# + +################### +### RUN RUN RUN ### +################### +import string, os, sys, re + +path_IN = sys.argv[1] +path_OUT = sys.argv[2] +file_OUT = open(path_OUT, "w") +dico = dico_filtering_redundancy(path_IN) ### DEF1 ### +KB = list(dico.keys()) + +## Sort the fasta_name depending their number XX : ApXX +BASH_KB = {} +for name in KB: + L = name.split("_") + nb = int(L[1]) + BASH_KB[nb] = name +NEW_KB = [] +KKB = list(BASH_KB.keys()) +KKB.sort() + +for nb in KKB: + fasta_name = BASH_KB[nb] + seq = dico[fasta_name] + file_OUT.write(">%s\n" %fasta_name) + file_OUT.write("%s\n" %seq) + +file_OUT.close() \ No newline at end of file |
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| diff -r 000000000000 -r 7a813e633d1c scripts/S02b_format_fasta_name_trinity.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S02b_format_fasta_name_trinity.py Fri Feb 01 10:22:32 2019 -0500 |
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| @@ -0,0 +1,66 @@ +#!/usr/bin/env python +## AUTHOR: Eric Fontanillas +## LAST VERSION: 06.12.2011 +## DESCRIPTION: format fasta name in TRINITY output + +from os import listdir +import re + +################### +###### DEF 1 ###### +################### +def dico_format_fasta_name(path_in, SUFFIX): + f_in = open(path_in, "r") + bash = {} + file_read = f_in.read() + S1 = file_read.split(">") + k = 0 + + for element in S1: + if element != "": + S2 = element.split("\n") + fasta_name = S2[0] + fasta_seq = S2[1] + L = fasta_name.split("_") + match=re.search('(\D+)(\d+)', L[0]) + short_fasta_name= SUFFIX + match.group(2) + "_" + L[1] + "_" + L[2] + bash[short_fasta_name] = fasta_seq + + return bash +#~#~#~#~#~#~#~#~#~# + +################### +### RUN RUN RUN ### +################### +import string, os, sys, re + +path_IN = sys.argv[1] +path_OUT = sys.argv[2] +suffix= sys.argv[3] +file_OUT = open(path_OUT, "w") +#Extract suffix info + +dico = dico_format_fasta_name(path_IN, suffix) ### DEF1 ### + +print((len(list(dico.keys())))) + +KB = list(dico.keys()) + +## Sort the fasta_name depending their number XX : ApXX +BASH_KB = {} +for name in KB: + L = name.split("_") + nb = L[0][2:] + nb = int(nb) + BASH_KB[nb] = name + +KKB = list(BASH_KB.keys()) +KKB.sort() + +for nb in KKB: + fasta_name = BASH_KB[nb] + seq = dico[fasta_name] + file_OUT.write(">%s\n" %fasta_name) + file_OUT.write("%s\n" %seq) + +file_OUT.close() |
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| diff -r 000000000000 -r 7a813e633d1c scripts/S03_choose_one_variants_per_locus_trinity.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S03_choose_one_variants_per_locus_trinity.py Fri Feb 01 10:22:32 2019 -0500 |
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| @@ -0,0 +1,111 @@ +#!/usr/bin/env python +## AUTHOR: Eric Fontanillas +## LAST VERSION: 06.12.2011 + +## DESCRIPTION: Remove redondant transcripts (i.e. transcript from the same locus) from TRINITY on the basis of 1 criteria: + ## 1. [CRITERIA 1] choose the longuest sequence (once any "N" have been removed => effective_length = length - N number + + + +################### +###### DEF 1 ###### +################### +def dico_filtering_redundancy(path_in): + f_in = open(path_in, "r") + bash = {} + bash_unredundant = {} + file_read = f_in.read() + S1 = file_read.split(">") + k = 0 + + ## 1 ## Extract each transcript and group them in same locus if they share the same "short_fasta_name" + for element in S1: + if element != "": + S2 = element.split("\n") + fasta_name = S2[0] + fasta_seq = S2[1] + + L = fasta_name.split("_") + short_fasta_name = L[0] + L[1] ## 1.1. ## Extract short fasta name + + ## Used later for [CRITERIA 1] (see below) + + countN = fasta_seq.count("N") + length = len(fasta_seq) + effective_length = length - countN + + if short_fasta_name not in list(bash.keys()): + bash[short_fasta_name] = [[fasta_name, fasta_seq, effective_length]] + else: + bash[short_fasta_name].append([fasta_name, fasta_seq, effective_length]) + k = k+1 + if k%1000 == 0: + print (k) + f_in.close() + + for key in list(bash.keys()): + ## 2 ## IF ONE TRANSCRIPT PER LOCUS: + ## In this case => we record directly + if len(bash[key]) == 1: + entry = bash[key][0] + name = entry[0] + seq = entry[1] + bash_unredundant[name] = seq + + ## 3 ## IF MORE THAN ONE TRANSCRIPTS PER LOCUS: + ## In this case: + ## [CRITERIA 1]: Choose the longuest sequence (once any "N" have been removed => effective_length = length - N numb + elif len(bash[key]) > 1: ### means there are more than 1 seq + MAX_LENGTH = {} + for entry in bash[key]: ## KEY = short fasta name || VALUE = list of list, e.g. : [[fasta_name1, fasta_seq1],[fasta_name2, fasta_seq2][fasta_name3, fasta_seq3]] + name = entry[0] + seq = entry[1] + effective_length = entry[2] + + ## Bash for [CRITERIA 1] + MAX_LENGTH[effective_length] = entry + + ## Sort keys() for MAX_LENGTH bash + KC = list(MAX_LENGTH.keys()) + KC.sort() + + ## Select the best entry + MAX_LENGTH_KEY = KC[-1] ## [CRITERIA 1] + BEST_ENTRY = MAX_LENGTH[MAX_LENGTH_KEY] + + BEST_fasta_name = BEST_ENTRY[0] + BEST_seq = BEST_ENTRY[1] + bash_unredundant[BEST_fasta_name] = BEST_seq + + return bash_unredundant +#~#~#~#~#~#~#~#~#~# + +################### +### RUN RUN RUN ### +################### +import string, os, sys, re + +path_IN = sys.argv[1] +path_OUT = sys.argv[2] +file_OUT = open(path_OUT, "w") +dico = dico_filtering_redundancy(path_IN) ### DEF1 ### +KB = list(dico.keys()) + +## Sort the fasta_name depending their number XX : ApXX +BASH_KB = {} +for name in KB: + L = name.split("_") + nb = L[0][2:] + nb = int(nb) + BASH_KB[nb] = name + +KKB = list(BASH_KB.keys()) +KKB.sort() + +for nb in KKB: + fasta_name = BASH_KB[nb] + seq = dico[fasta_name] + file_OUT.write(">%s\n" %fasta_name) + file_OUT.write("%s\n" %seq) + +file_OUT.close() \ No newline at end of file |
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| diff -r 000000000000 -r 7a813e633d1c scripts/S04_find_orf.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S04_find_orf.py Fri Feb 01 10:22:32 2019 -0500 |
| [ |
| @@ -0,0 +1,64 @@ +#!/usr/bin/env python +#keeps the longest ORF found in the 6 possible ORF alltogether +#python find_ORF.py file output + +def find_orf(entry): + orf={} + orf_length={} + stop=['TAA','TAG','TGA'] + for i in range(0,3): + pos=i + orf[i]=[0] + while pos<len(entry): + if entry[pos:pos+3] in stop: + orf[i].append(pos-1) + orf[i].append(pos+3) + pos+=3 + orf[i].append(len(entry)-1) + orf_length[i]=[] + for u in range(1,len(orf[i])): + orf_length[i].append(orf[i][u]-orf[i][u-1]+1) + orf[i]=[orf[i][orf_length[i].index(max(orf_length[i]))],orf[i][orf_length[i].index(max(orf_length[i]))+1]] + orf_max={0:max(orf_length[0]),1:max(orf_length[1]),2:max(orf_length[2])} + orf=orf[max(list(orf_max.keys()), key=(lambda k: orf_max[k]))] + if orf[0]==0: + orf[0]=orf[0]+max(list(orf_max.keys()), key=(lambda k: orf_max[k])) + return orf + + +def reverse_seq(entry): + nt={'A':'T','T':'A','G':'C','C':'G', 'N':'N'} + seqlist=[] + for i in range(len(entry)-1,-1,-1): + seqlist.append(nt[entry[i]]) + seq=''.join(seqlist) + return seq + +# RUN + +import string, os, sys, re, itertools + +path_IN = sys.argv[1] +file_OUT = open(sys.argv[2], "w") +inc=1 +threshold=0 #minimal length of the ORF + +with open (path_IN, "r") as f_in: + for ignored, line in itertools.izip_longest(*[f_in]*2): + name=">"+path_IN[:2]+str(inc)+"_1/1_1.000_" + high_plus=find_orf(line[:-1]) + reverse=reverse_seq(line[:-1]) + high_minus=find_orf(reverse) + if high_plus[1]-high_plus[0]>threshold or high_minus[1]-high_minus[0]>threshold: + inc+=1 + if high_plus[1]-high_plus[0]>high_minus[1]-high_minus[0]: + file_OUT.write("%s" %name) + file_OUT.write(str(high_plus[1]-high_plus[0]+1)+"\n") + file_OUT.write("%s" %line[high_plus[0]:high_plus[1]+1]) + file_OUT.write("\n") + else: + file_OUT.write("%s" %name) + file_OUT.write(str(high_minus[1]-high_minus[0]+1)+"\n") + file_OUT.write("%s" %reverse[high_minus[0]:high_minus[1]+1]) + file_OUT.write("\n") +file_OUT.close() |
| b |
| diff -r 000000000000 -r 7a813e633d1c scripts/S05_filter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/S05_filter.py Fri Feb 01 10:22:32 2019 -0500 |
| [ |
| @@ -0,0 +1,21 @@ +#!/usr/bin/env python +#filters the sequences depending on their length after cap3, makes the sequences names compatible with the phylogeny workflow +#python filter.py file length_threshold_nucleotides output + +import string, os, sys, re, itertools + +path_IN = sys.argv[1] +threshold = int(sys.argv[2]) #minimum number of nucleotides for one sequence +file_OUT = open(sys.argv[3], "w") +inc = 1 +with open(path_IN, "r") as f_in: + for ignored, sequence in itertools.izip_longest(*[f_in]*2): + name=">"+path_IN[:2]+str(inc)+"_1/1_1.000_" + if len(sequence)-1>threshold-1: + inc+=1 + file_OUT.write("%s" %name) + file_OUT.write(str(len(sequence)-1)+"\n") + file_OUT.write("%s" %sequence) +file_OUT.close() + +#filtre eventuel sur les petits transcrits \ No newline at end of file |
| b |
| diff -r 000000000000 -r 7a813e633d1c static/images/adaptsearch_picture_helps.png |
| b |
| Binary file static/images/adaptsearch_picture_helps.png has changed |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity.output Fri Feb 01 10:22:32 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +22 +Number of segment pairs = 342; number of pairwise comparisons = 2 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +21 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity/Acaud_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity/Acaud_trinity.fasta Fri Feb 01 10:22:32 2019 -0500 |
| [ |
| @@ -0,0 +1,44 @@ +>c0_g1_i1_len:160 path=[1:0-159] +GCCAGTGAACTCATTAGGCTCTGTCTGCGCCGATATGATAAGAACGAGTTTGACAGCGATGATGACAGCATGAACAGCGAGCTCGCCTACGATGATGACTCTGAAATGCCTGATGACCTAATTGACCGTTTGGAGATGTGCGACTTTTATGAAATGGAAG +>c0_g2_i1_len:160 path=[1484:0-159] +GCCACCACTGGCACAAAGGATTATCAAGGCTCATGACAAAGGTATAAATAAGACATTTTATGGCCAGCTGGTCGGTCGATGTGCTAAGGAGTTGTCTCTGGTGCAGACTCTTCATAATTTTTAAGCTTAGAGAAAAGGCGGAGGAGAGCGATTATAGCGA +>c2_g1_i1_len:160 path=[1:0-159] +ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTG +>c3_g1_i1_len:160 path=[175:0-159] +ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGC +>c4_g1_i1_len:160 path=[526:0-159] +AAACAATGCAATCCTCTACCATTGCCAAGATATGAAGAACAAGTAAATGGCACATCAACAACAATGATAATAATAAGTGCTAATAACAATAAGAGTAATACAATTACCACAATATCTGAGAACAAGGGGCTTAAGCATAGCTATCATTATTTGGGAGGGG +>c7_g1_i1_len:160 path=[355:0-99 737:100-159] +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>c8_g1_i1_len:160 path=[795:0-129 18:130-159] +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>c9_g1_i1_len:160 path=[209:0-159] +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>c12_g1_i1_len:160 path=[1:0-159] +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>c13_g1_i1_len:160 path=[307:0-159] +GCCATTCGTCTTAGGAGAAGTTTGTCGTCAGGAAAGATACATGAGGCCTGGATTCTTTCTGACACCGACTCGACGATGTCATTACCTTGTCCACCTGGAACCAACCCCTCATCGACTTCAGCGGATCCATATCTGGTGATCACCAGAAAAACGAACACTA +>c14_g1_i1_len:160 path=[1:0-159] +GCCTGGGTATTATTTACCACAGTAACCTTTCATCAGTTTGTGGTGAAAGTACGTGACGTTATGCATTGGCAAGATTGGACATTTTGGTTCGCCCTGTTTTGTACGCATAATAATGTATGTAGTTGTATTTTCCAAAATAATTGTTATATTAGCTATCCAA +>c15_g1_i1_len:160 path=[817:0-159] +CTGGGCATGGTGGCTACCAAAACGGAGTATAGAACACTGTGTGACTTTTATGTTGATAATAGAAAATATATTCTCTATATAGACGAAGACTGCAGGGTGTCTAGAATATCGCCTAATAAAATTAGAATAGGGAGTCTGCAGTTGATCCGGAAACTACCAG +>c15_g2_i1_len:160 path=[319:0-159] +ACAATTACACAGGTATCAACAAATGTTCACTGCACCTGTCAGTTCCACAAACATAAAGATTACACACATGTACACATCTTTACAAAATATTTACAATTTTGTATTCTTAATTCTATCCACTTGGCTCTGGAAGGCCTTCAGCCATCAGATGATGTGTTTA +>c16_g1_i1_len:160 path=[506:0-159] +CAATCCAGCACTAGCAGGAGTGTTGGCCGGAAGGTTGATGATATTTTTCAGTCAAAGAATCTGCATGCTCCAGATGATCGCCTATCAGACAAGGATAACCGTGACAAGTCCAAGAACCCTTTACTTAACAATGAGATGACTCCTCAGTCATTTTCTCGAG +>c17_g1_i1_len:160 path=[1462:0-159] +GATTACATGCAAAACATAATAGAAATGTTTGTCCCAAGGTCTTACCAGTTTATAGTTTTACATTCGTGTCTTGAAATAAGAAAATGCCTTTATGAGAGTGTATTATTACTCAGTAGATGGAAATTAGCTTACCGGGGGATATAATTTAGGCCGGAAACCC +>c17_g2_i1_len:160 path=[587:0-159] +TGTTTGTCCCAAGGTCTTACCAGTTTATAGTTTTACATTCGTGTCTTGAAATTCAGTAGATGGAAATTAGTGCTTATAGTGGGTTTGGGCAATCGATTTTTTTTTTTTTTTTTTTAAAAAAAAAGGCGAGGCCGAGAGAAGATTCCTAGCGAACAGCCTA +>c19_g1_i1_len:160 path=[147:0-159] +CCTGTTGTGACTCGTTCCCTGACGTCGTGCACGCAAGCGCACGCGCGTGCGCGCCGGGTTAGGCACACATACGCGGCACAGGTGCGCAGTATTAGACAGACGCAGACGCAGGCGTCCAGACACGCCAGCCAGCACGGTTACAATGTCCATATCACAATGA +>c21_g1_i1_len:160 path=[476:0-159] +CTGAATGTCAACCAGTCACTGACCATCAGCTACATGTCTCTAATGGTCACTAGCATGAAACATGAAATGCCTGCTTATAGTGGGTCTGTAACTGGTAGGATACTGATTACATGTGGAGGCTTATTAAAGGGGTATCCTATTATTTTTTAAAACCCCCCCC +>c22_g1_i1_len:160 path=[185:0-159] +CTATGTTGGCTACTGCTAAGGATGTGCTACTTGCCTGATGTAAACAATTCCCAGAATGAATATAAACCAATCATAAGGAGAACTATGGAACCATCCTTAAATGTATTAATCTTATTTAAAATTATGTGCACATCTTGTTTGGCAGAAGGTACATTAAAGC +>c24_g1_i1_len:160 path=[1:0-159] +ATCTGTAATGTCGTTTACCACACACTGGACACTGATATTTCCGCTCGCCAGTGTGTGGTAAACGATATTACAGATCAGATGTGCTGGCAATCCATATCAGTACACACAGCAGTGAAAAAAATCATAAATGTGACATCTGTGGCAAGGCTTTCTCAAATGC +>c25_g1_i1_len:160 path=[475:0-159] +ATGTTAGTAAAAGAGATTAAAGAGTACCGAGAGATAAAAGAGAAGGCTAGAACCTATCTATGTTATATTATAAGTAGTAACCTATCTTATGGTTCAAGCATAAATGAGGAGACTCTTCAAGAGAGTATGGAGATGTTAAAGAGGGCAATCCCAAAGAGTG +>c27_g1_i1_len:160 path=[720:0-159] +GCCAGTGAACTCATTAGGCTCTGTCTGCGCCGATATGATAAGAACGAGTTTGACAGCGATGGTTATATTATGAACAGCGAGCTCGCCTACGATGATGACTCTGAAATGCCTGATGACCTAATTGACCGTTTAGAAGCTGGAAATATTACAAGCTTTGTGC |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity/Amphi_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity/Amphi_trinity.fasta Fri Feb 01 10:22:32 2019 -0500 |
| [ |
| @@ -0,0 +1,40 @@ +>c3_g1_i1 len=160 path=[242:0-159] +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>c6_g1_i1 len=160 path=[1:0-64 583:65-88 90:89-159] +CAGCCTACCACTGAGAAGAGATACTTCAACATGTCTTACTGGGGTAGAAGTGGTGGTCGTACAGCGGGTGGTAATGCAGGACGTGGTCGTGGCGGCGGCAGCGGCAGTGGCAGTAGTCAAAGTGGTGGTGGCAGCTTTCTACAGGAACGTATCAAAGAGA +>c10_g1_i1 len=160 path=[878:0-159] +GCACCTAGAATTACCCGAAGTTGCTTGGCAATAGCGACACCTAACGGTCGCCATGATATTTGCAGGAAGAAGGCATGTGGTACCATTGGGAACCGTCAAGCGTTTCCTCAGCCCTGTGGCAGCTGCCCGTCTGCGCCCGTGTTTGACCTTGAGCACCAAG +>c13_g1_i1 len=160 path=[426:0-159] +ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAAGTTTAGCACACAAGGA +>c21_g1_i1 len=160 path=[1:0-159] +TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTG +>c24_g1_i1 len=160 path=[1:0-159] +ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAAT +>c29_g1_i1 len=160 path=[1:0-159] +GGGGCCCGGGATGTCGAGGATGTTGTACTCGTAGTTGCTGTGGTTGACGTGGTATTGTTGTTCCTGGCTGTGGCTCCGTTACCACTTGACGTGGCTGTTGTGGTGCTGGTGGAAAAACGACTAGTGGTTGTGTCTGCAACTAATTCCTCGCCTCTAATCA +>c30_g1_i1 len=160 path=[175:0-159] +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAAAGAGCTTCTATGGTT +>c38_g1_i1 len=160 path=[1249:0-159] +AGCCATCAAAGGTTGCTAATCATGTTGAGTTGTATTGTCAAGCATTTCTACTCGAGGCAACCATTAATAATTGAAGTTATCAGTTATATTGTCAACTCAATGGAAAATCAAATGGATTTAATTAAGGAAGGAAGATTTTGTACTTGTAAATCTGCATTTT +>c43_g1_i1 len=160 path=[1:0-159] +AGCAACTTTGCCACCACCACCACCACCAACAATAACAACAACAGCTGCAACACCGCGACCAATAACAACAACAACACTGGTAACACTAACCACGTCACCACCAGAAATAACATCTTCACAACCATCACCAACACTACCATTAACTCAACTTATAACAATA +>c45_g1_i1 len=160 path=[1:0-67 69:68-72 74:73-159] +ATTTTTTGTAGATATTTTTATCTATTTACATTTCTATCTTTATTTCTCCCTACGACCGAAGGCCTCAAAGAGCATATGATTTATTTCTGTCCATTTATCGACCGTGCGTCTGTCTGTCCATCCGCCTCCCTTCCACAAACAGCTGCCGCTACTGTTATAT +>c48_g1_i1 len=160 path=[1:0-159] +ATAAAGTGGGCCATACAAAGTGAGACCTTACACATATATGAATGTCTAAATTGTCCTATGTTGTCCCATTTAACATGTTTAGTTTGTGGTATTTTTCAAACAAATATAACATGGGGTTTGAATTGGCCGGAATCTAGCACATTAGTCTCTGAGGAAATTT +>c52_g1_i1 len=160 path=[680:0-159] +ACAACTCCTCCAATAGTACTACCAGCTTGTCAGGGTGAACCAGATGGTAATGCACCTGATCCTGACTCGTGCTCACGATATGTAGTATGTCTCAATCAGGAACCGGTTAATGACTATCCATGTGATCCAAGTACCTTCTTCAACGACCTACCCGAGTACA +>c53_g1_i1 len=160 path=[202:0-159] +TACTTTCCTGAAATTAGTTCTAATGGTTTCATTGTGATGACAAAGTTTAATATGTCAAGCATAATAAACTTGATTGTGTTTTTCCACCTCAGCAGTCATTTATACATTTTATTGAATGTAGAGGGTGTTGAGACATTCAGTGTTGTTATACTTGCAACAA +>c57_g1_i1 len=160 path=[1:0-159] +ACCACACAATCATCTAGTGAAACATTTACCAAAACACCCTCTGAAACTGTTCGGTCAGAAGAAGACAGTGCTAAAAAGCAGAAAACTTTCATCAAAAGCCCACAGGCAGTTGCTGTATCTGAAGAATCTACAAAAACAAATTTAACTTTTGTTGCTAAAT +>c58_g1_i1 len=160 path=[1:0-159] +TACTGCTGTCGAAGTGATGGCGCTTGGAACAGTGTGATAACCTTGCCTACAAATAGGCCATTCTATTTGCTCAGATACACAAGTCAATGTCAGCTGGTGAAAGGAATGAAAGTCAGAAGGGAAGTATTCTACTGGGATAATGAAGATATTAACAATATTG +>c59_g1_i1 len=160 path=[1:0-86 88:87-159] +ACAGTTCTAAATAGCATTCGCCAAATGATATTGAAAGCATATTTTATGAATAGTGGTTCACAGATGAAAGATCATTATTGGGAACCCGTTCCAGCTTTTGTAGATCATTTTGTTCTTGCTATAGATCATCGACCCAGAATACAAAACCAGTATGGCCAAA +>c60_g1_i1 len=160 path=[203:0-159] +CGAACATCTCATGAAGTGACTCAGACCTCATTTACCCCTAAGGGCTCTATGTTAGGGGGACATGTCATTCCACAGATATGCATGGATGACTCGCATGCATCCAGGGCATTACGGTACAGTAAACGTCCAACAGATGCCCCTCAGATACGACCCATAGAGC +>c65_g1_i1 len=160 path=[661:0-159] +TTTAGTGAAGAATTTATAATGACTCATGATGTTTGTGTCAATGTACTAAACTTAATGGCACAAATTGCGAACTCATTTTTTTTCTATTATATGTGGGTCTTTTCATTCAACCAGCATTTAGTATATAGACAATTTCTATCTATTCACTTGGATAAAGCAA +>c72_g1_i1 len=160 path=[463:0-159] +ACCTGTCCCCAACCCCAATCATTAAATCTTTCCCCTTTCGCATGTTCACAGCCCAGCTGCAGCACAACTAGAAAATCCAGACATGCTGAAAATACATGTTATTTGTGTATCTGGCATGTAATTTGTTTCACTCAAAACAGTAACTCTTCTTCAGGAGGTA |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity/Apomp_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity/Apomp_trinity.fasta Fri Feb 01 10:22:32 2019 -0500 |
| [ |
| @@ -0,0 +1,42 @@ +>c2_g1_i1 len=160 path=[1:0-159] +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>c4_g1_i1 len=160 path=[1:0-159] +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>c5_g1_i1 len=160 path=[726:0-159] +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>c8_g1_i1 len=160 path=[1:0-159] +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>c8_g2_i1 len=160 path=[873:0-159] +CCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCACTCAATAATTATTGACATATTACAATTGATTCGGATTAAAAAAATGGCGCTAGGCTTAAAACACAGACAGTTCGCTAGCTGATTAGGCTCTTTTTAAGGCGAA +>c10_g1_i1 len=160 path=[221:0-159] +AATCTACTGACAGATACCTGGAACGAGATGCAGGTCAAGTGGTCGTGTTGTGGTGTGGATGGCTACTCCGACTGGACGCAAGCTGAAGGTCTGGCCACGGGTCACTACGTGCCGCAGTCCTGCTGTCAGAACACGATGAGTACAAGCTGCACGTCACAGA +>c11_g1_i1 len=160 path=[1:0-159] +TGGCGAAATGTAGTGGTCATTGATGGATTTTATTGCAATCAGTGTTACATATTACAAGCATTTCTTAATAAACAAAAAGTTGCACGAGATATTTTTTACTTAAAGGTTTTATGGGATGAACACAGTCAATTATATTCATGTAAAAGGCCTTATCCGAGAA +>c12_g1_i1 len=160 path=[1:0-159] +TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCT +>c13_g1_i1 len=160 path=[303:0-159] +GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAA +>c14_g1_i1 len=160 path=[201:0-159] +TTGGAAGAAGAAATAGAAGAATTAATGCATGAGAATGATGATGAAGATGGAGTTGAAGTTGAAAAATCAAAAGATAAACATGAAAGTGTGGAAAGGGCTGAGAAGAGAGGCAGCAATAAAAATGATGTAAAACATGATGAGAAGGATAGAAGTAAAGACA +>c16_g1_i1 len=160 path=[761:0-159] +CCATACTCAGCCGCCAAGACCACGGCCCAGGCTGCCACAGATGACCTGAAGAGACGTCAGGAAGAACTGGAGAGGAAGGCTGAGGAACTACAGAGAAAGGAACAGGAATTACAGAGAAACATGGGACACCAAGCCAGGGTGAACAACTTCCCACCACTGC +>c17_g1_i1 len=160 path=[1:0-159] +ACGACAGAGGTCCTCTGCTTGATGAATATGGTTACACCAGAGGATTTGGAAGATGAAGAGGAATATGAAGAAATTTTGGAGGATGTCAAAGAAGAGTGCAGCAAATATGGTTATGTGAAGAGTATAGAGATCCCACGGCCCATTAAGGGTGTGGAAGTGC +>c18_g1_i1 len=160 path=[407:0-115 522:116-159] +TTGGAAGAAGAAATAGAAGAATTAATGCATGAGAATGATGATGAAGATGGAGTTGAAGTTGAAAAATCAAAAGATAAACATGAAAGTGTGGAAAGGGCTGAGAAGAGAGGCAGCAATAAAAATGATGTAAAACATGATGAGAAGGATAGAAGTAAAGACA +>c19_g1_i1 len=160 path=[459:0-159] +GCGAAAACTGGTTTTAACACAAATAATTGTTACAGTACCAGGTTTCGGAACACGTTTGCATATAACCAGCGAGAGTGGTGCTCAGTTCTGTTATGTATGACAGTCCTTCTCCTCAACATGCAACGGAAGCGAGCACTTCCATCATCACATTTGTCAATAA +>c20_g1_i1 len=160 path=[1:0-159] +TTCGTAATGAATCTTTTTGACTGGTATTCCGCAGGATACTCAATAATTATTGTCGCATTCTTCGAAGTTATCGCCATTTCTTGGATATACGGTCTCCAACGGTTCAAGAAGGACATTCAGATGATGGTTGGCAAGGGGCGATGGATCAATGCTAGTTTCT +>c21_g1_i1 len=160 path=[500:0-159] +GTTGTCAGTGGATCTCGTGATGCAACACTGAGGCTATGGAATGTCGATACTGGCCAGTGTCTGCATGTTCTGATGGGACATATGGCAGCTGTACGGTGTGTGCAGTATGATGGCAAGCGTGTTGTTAGTGGTGCCTATGATTATACAGTTAGAGTGTGGG +>c22_g1_i1 len=160 path=[884:0-159] +AGATTTATATTTGAGAATGTTTTGAGTACGACTTCTGTACAGACACACAGCAGAATGACCCTTGTATTGTTTAACAACGTTCAAAATTTCCTGATTCTTCTACCGAAAAAAATACATAAGAAGAGCCACCAAGACGATCAGATCACGGAGGTACTGGCAT +>c23_g1_i1 len=160 path=[203:0-159] +GCAGACTCGGCTGGCACGGCCACCGCCTTCCTCTGTGGAGTGAAGGCTCGCTACGGAACGCTGGGTCTGGGACCGAGAGCCACACGATCTGACTGTAGACAGAGTCACATCAACAAACTGAAGTGTATAGGAGACATGGCACAACAAGCAGGTATGAGGA +>c25_g1_i1 len=160 path=[1:0-159] +CCGGCCTGCAAGACGCCATTTTACTTCGTCTGTCAATCGAGGTCAAAGGTCACTACCGTTGTCTCCGAGAAGCACACAGACGCCGAGCTGGTTCACACGCTGTGTATTCGGCACAGATCTACTGTTGCTTGGGATATTTTAGCCGGCGAACGAGCGAAAT +>c26_g1_i1 len=160 path=[195:0-159] +CCGGCGATCGTTCAGAGGGCCAGCGGTCTGGCCATGTCAGAGATCTATCACCTGCGCTTCTGCGATGGGGATCGGCTGAACGTCAGCTGCCCGGACAACTGGCAGATCCACATCTCGTCCAGCTACTTCGTCTACGTCAGCGGCGTCGACGGCCGCGGCG +>c27_g1_i1 len=160 path=[1887:0-159] +CATGAAGGACCTGTGTGGCAGGTGGCTTGGGCACATCCAATGTTTGGTAATCTGATAGCATCATGTAGTTATGACAGAAAGGTGATTATTTGGAAGGAGACTGGAGGGACATGGGCAAAGCTTTATGAATACAACAATCATGATTCCTCAGTTAATTCAG |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity/Pfiji_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity/Pfiji_trinity.fasta Fri Feb 01 10:22:32 2019 -0500 |
| [ |
| @@ -0,0 +1,40 @@ +>c7_g1_i1 len=160 path=[411:0-159] +AGCATTGTCCGTGTTGCGCGGGTCGTCGACGTAACCTCGGTACACCTCAGCGTGCCCGGCCATCTGGTGCGTGAGCCGCTTGAAGACGACTCTCGCCGGCGGCTGCTTGCTGTCCAGCGTCATGCTCTCGAACGCCTTGATCCAGGACTCCTTGACACTG +>c9_g1_i1 len=160 path=[187:0-159] +ATCACGCCCCCTGTCGTGGACAACAGGCTAGCCCATTGTAATGGGAAATCTACAGTGGTAAACAAACTGATATACAATATAACCAATATGTATATATATATAACAGATATGGAGACTGATCATAAAATCAACGATTCACTTTTAGGATTAGTCATGTTTG +>c24_g1_i1 len=160 path=[1:0-159] +TGTGCGTCGGTGCCGGACTGCAGGCTGTTGTTTGTCGGGAGCACCTCCGGAGTCATCAGTGTCATCAACACCAAGTTCAACCAGAGCAAGCAAAGCCACCTGCAGGTGTTCGGCCACAAAACCTGCCTGTACGGCCATTCCGGGGCCGTCACAGCCTTCT +>c26_g1_i1 len=160 path=[501:0-91 19:92-159] +GGTCGCCTTATAAAAACCAATCCGAAACAGTTTTCCTTTGAAACGTGCCAAAAACCAAAAACATACTTCAAATCTTCCAGTGTCTGTTATAAAGGGGTGAGCGTAGAGAGGGCACTTGTGAGATTGGTGTCTGGGTTAAAGATTTTGCCAAAAAGCGATT +>c27_g1_i1 len=160 path=[58:0-159] +ATACTCAGGCACACAGCATTTGTCGTACTAGGCGAGAGAGAGAGAGGAACGACTAATTGCAACCACGATTACGTTACATTTGTTTACAAACCAAACGTACTGGCGTCGAAGATAATTAAGAGGAAGCTGACTGAATGCGATTGGCGTTGGTCTACGGGTT +>c32_g1_i1 len=160 path=[628:0-159] +GCCATGCAGTACACTGGACTTCTGTTATTCTGTTTGTTTGCCTTGACGGCAGCCAAACCCGCGGAAGACCTTCAAATGCTCATCCGAGCCCTGCTCCATGAAATAGAAGAGGAAGGTGAACTCCAAGAGCGAGGCATTGGCGCCGTGAAGTATGGTGGAA +>c33_g1_i1 len=160 path=[256:0-159] +GCACCGGGATGCGGATTTGCTGACGATATGGCAAAAGCATTGTCAGCGTGCGGAACCTGTTTATGTCACACCACTGGCATCTTCCTGGCCGTCGCAGCCTTCGTTCTGACGGCACTCGGTATTGTCTGCGTCACGCGATCAGCTGACCCGAGCCTTTGGT +>c35_g1_i1 len=160 path=[301:0-159] +ATCAAAGAAGAGCAACATCGAGCTACTGGCACTGGCAATGGAATCCTAATTATAGCAGAAACAAGCACTGGTTGCCTGTTGTCTGGGTCAGCAATTGGTAGTAGAGGTGTTCCTGCTGAAGAAGTTGGGGTCAAAGCAGGACAGATGCTTTTGGATAACT +>c36_g1_i1 len=160 path=[470:0-136 190:137-159] +GTATTAATAAAAGGACAAGACTATTATTTAATACCAAGAAATCTGGCCTTAATAAGCATGGTTGCTTATATCATAAGCATGGTAAATCACATTGTGTTTTCCATGTGTTTACCCATCAGATGTAAAAATATTCTGCATGAAATAGGTAATTTCCCGATTA +>c37_g1_i1 len=160 path=[281:0-159] +CGGCCGCGGCGCGTCGTTCTCAGCCAAGCTGACTTCGACTTGAGCCGTCCATTCGCTTATTTACACGACGACTGCTCGACCCTTTACGACTTAGTCACACTTCCGTTTAACCAGGCCCTGCTACCCTCCAATCTCGTCCAATCGGTCTCTACGCATCCGA +>c39_g1_i1 len=160 path=[303:0-159] +AGCATTGTCCGTGTTGCGCGGGTCGTCGACGTAACCTCGGTACACCTCAGCGTGCCCGGCCATCTGGTGCGTGAGCCGCTTGAAGACGACTCTCGCCGGCGGCTGCTTGCTGTCCAGCGTCATGCTCTCGAACGCCTTGATCCAGGACTCCTTGACACTG +>c40_g1_i1 len=160 path=[412:0-159] +CGAACACCACAGCGCCCTCTAGTGAACCTGGAGCAGGTCCGGCTTGACTCGGAGACTGTACATTTTGTTGTAGTAGATCATGTTCTCTTCGATGGCCTGCAGCACGTGCTTGGGCAGGTTGGGCATCACGTTGGGACTCTTGGGCTTGGTGGCCGAGGGC +>c41_g1_i1 len=160 path=[33:0-25 346:26-159] +CGCGTCCACGACCGCCACGCGCACCGAGGTCTACGACAAACTCGCGCCGCAGGAGGCTCCTCTCAACCTGCACAAGCCTCGCGCCGACAGCGTCCCGACCGACGGCAACGGCTGACGGCAGACACTCGAGCCTTGACTACGTGTATGCACAAAGCTACCC +>c42_g1_i1 len=160 path=[173:0-159] +ATCACGCCCCCTGTCGTGGACAACAGGCTAGCCCATTGTAATGGGAAATCTACAGTGGTAAACAAACTGATATACAATATAACCAATATGTATATATATATAACAGATATGGAGACTGATCATAAAATCAACGATTCACTTTTAGGATTAGTCATGTTTG +>c43_g1_i1 len=160 path=[1:0-113 115:114-159] +TCGTCCCAACAGCAGTCCATCAGTACAAGCAGTGTACAGAAGAAATTTGACAAAAATACTATTGATGCAGTCAAGAGATGGAACACAGAAAATCTTGACATTTATGGACCACTTCGGAACCCCAAAACCGATGGAGGTTCCTCTCCAAACCCAACCACTC +>c44_g1_i1 len=160 path=[53:0-159] +CACGTCACGGACGTGCTCGTCTCGAAAATCATCGATATGGTCAAAAAGAAGGAAAAGAAAGGAGGGATCACCATCAAGCCATTCCAGGTCAAGAACCATGTCTGGGTGTTCGTCAACTGTCTAATAGAGAACCCGACGTTCGACTCGCAGACGAAGGAGA +>c45_g1_i1 len=160 path=[333:0-159] +TGTGCGTCGGTGCCGGACTGCAGGCTGTTGTTTGTCGGGAGCACCTCCGGAGTCATCAGTGTCATCAACACCAAGTTCAACCAGAGCAAGCAAAGCCACCTGCAGGTGTTCGGCCACAAAACCTGCCTGTACGGCCATTCCGGGGCCGTCACAGCCTTCT +>c50_g1_i1 len=160 path=[53:0-159] +TTACGACACCTGCCCCAGATCCTGTCCGTGTCACTGCTGAGGTTCAGCTTTGACTTCCAGAAAATGGAAAGATATAAGGAAACTGGCAAGTTTGTGTTTCCGATAGAGTTGGATATGGCACCTTATGTTGATAAGTTATCAACTGCTGGGTGCACAGAAT +>c52_g1_i1 len=160 path=[53:0-159] +GATCTGAAAGAATCTTCTCCAGTAGCAGAGATTAATGGTCCAGAACTTATCGATGAAGCACTGCCAATTTCCGTTGATAACAGTCAAGGAACAACGGCAGAAATTAGACTTGAGCGCAGTCAAAGCCATACTGGAAAAAACGAGGCGGATTTATTTGCAC +>c53_g1_i1 len=160 path=[1:0-159] +TTGTACATTCAAAAGCTAGGTGGCCAAATTGTGGAATTGAATACATGTAATAATTATATATCTTTCACCATGAAAAGATGTCCATGGACCAAGTCTATGCATTGCCGATTTTCGTCATTAATATATATCAGAGATGTGATAAAAGATATATGTACTCATA |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity_and_velvet.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_and_velvet.output Fri Feb 01 10:22:32 2019 -0500 |
| b |
| @@ -0,0 +1,53 @@ +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +22 +Number of segment pairs = 342; number of pairwise comparisons = 2 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4422; number of pairwise comparisons = 1 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +21 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4160; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4032; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity_and_velvet_up.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_and_velvet_up.output Fri Feb 01 10:22:32 2019 -0500 |
| b |
| @@ -0,0 +1,53 @@ +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +21 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +22 +Number of segment pairs = 342; number of pairwise comparisons = 2 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4032; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4160; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4422; number of pairwise comparisons = 1 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/trinity_out/AcAcaud_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_out/AcAcaud_trinity.fasta Fri Feb 01 10:22:32 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 7a813e633d1c test-data/trinity_out/AmAmphi_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_out/AmAmphi_trinity.fasta Fri Feb 01 10:22:32 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 7a813e633d1c test-data/trinity_out/ApApomp_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_out/ApApomp_trinity.fasta Fri Feb 01 10:22:32 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 7a813e633d1c test-data/trinity_out/PfPfiji_trinity.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_out/PfPfiji_trinity.fasta Fri Feb 01 10:22:32 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 7a813e633d1c test-data/trinity_up.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trinity_up.output Fri Feb 01 10:22:32 2019 -0500 |
| b |
| @@ -0,0 +1,32 @@ +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +21 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +20 +Number of segment pairs = 380; number of pairwise comparisons = 3 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +22 +Number of segment pairs = 342; number of pairwise comparisons = 2 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet.output Fri Feb 01 10:22:32 2019 -0500 |
| b |
| @@ -0,0 +1,21 @@ +Number of segment pairs = 4422; number of pairwise comparisons = 1 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4032; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4160; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet/Ac_transcriptome_25591.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet/Ac_transcriptome_25591.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,6436 @@\n+>Locus_1_Transcript_1/2_Confidence_1.000_Length_6683\n+TAAACTGCAACGCCAATATGTGATGTTCAATTCTGAACGTTGTTCAGTTTTATTTTGTTT\n+ACTGGATTGTTTACCAATAAAATATTGTGTACAAAGTGCCCAACTTGACATGGTTTGGCT\n+GTAGTAATGTTCTGCAACGAGTTATTCATTTCGGAATTGTGGAAAAATAAGACAGGCTGG\n+TACTGCATTTAGTGGATTAGCCATGGTAAATGTTTCAAACATGAAGTCATACATCTGCCT\n+TACACACAAATGTGCTGTGCCTTATACAAAACACTGGTTCTGCACTTCTGCAATAATTTA\n+TTGACTGCTGACTTCTTGGACATGCAAGTCCAAGCACACAAGATGTACAAGGTTTTAAAA\n+GGATGCAGCAGCAGTAGCAAGGACAAACACCATTCACTGGCCTCTGTGCCATAACCAGAT\n+GTGTTAACAACAGGCATATTAAAGACTCCCACATCCAATAACCTGATCACTATAGCTGTT\n+TACACACGAATGAGAAGTGAAGACACCGATAACAGGCTGCTTGTACTACTTGTGTTATGA\n+GAGTAGTGGTAGAATAATAAAATAATACATTGAACTAGTTCTTTGCCTTCCGATAGAATG\n+CTTGACAAAACGAACTCAAATTTTGTGCTCTTACAATTTGTCGAATAATCACATACGGGC\n+AAAGCCTACAAAAAGAACCAGCTATTTAATTAAGAAATTTTGCACTCTGCCAACACAACC\n+ATTGACAGATGTAGATTCGAAATATCAAGTCAGTTTGCCATGTGTATACAGGTGTGTATA\n+TACAGAACATGGTCACTGAATGCTGTGTACACAATATACCTAAGGGCAAGGAATTAAACA\n+TTAACTAGCTTCAGTCAGATTACAACTTGTCCAGGAAGTTGTCCAGTGGAGGAACGCCCT\n+CCTTCAGCCCTTTGCGTTTTCTCGTCTCTTGGACGATTATGTTAGGCTTGGAGTTGTCCA\n+CAAACGGATCGCCTGGGAGGATCTGCCAGTGATCAAACACACACTGTGGGAATGCCTGGC\n+CACCAGTGTTGGACCTCAGGTCGGCAGTGAAACCAAATGATTCGTTTACAGGAAGGTATG\n+CCTTGACCTGGAACATCGGGGTTCCCACCACTTGGTTCTCCTCAATGACAACACCTCGTC\n+TTCTGTTCAGCACACCATAAATGCCACCAACAGCTTGCTCAGGGCACTGGATCTCAACCA\n+GGTATATTGGTTCCATCAACCTTGGTTCAGCTGTCAGCACACATGCATAGAGACATCTTC\n+TTGTTGTTGGGATGATCTGGCCACCACCACGGTGAATAGCATCAGCATGCAGTGTGACAT\n+CAAGAATGTTGAAGCGGATTCCTCTCATGTTCTCTTCACAGAGTACACCCTCCTTGCTAG\n+CCCACTGGAAGCCAGCCACAACACTGTCTTTGATTTCATTCAGGTACTGGACACCCTTTG\n+TGCAGTCAATGACCAGGTTTGGTCCTGTGCCATCAGGTCCAAAGCACCAGATCTTACGAG\n+CCTCAGTAACATCAAACTCGTATGTGTCGGCCAGGTATCTAGCTCTCTCCTTCTGATCCT\n+GACGAGCACTGACCTTCTCTCCCCTATCAATCTCTTCAGGTAAGCCATCTGGCAGTGGTG\n+CAGCAACCATGAAGAGACGATTGTGCTTGTTTGGTGATTTTGACAAGCAGGTTCTGTCAG\n+ATGTGTTACTGACAGTCTCTCTATATGAGACAACAGGGTCAGATTTCTTGATTGGGATGC\n+AGGCATGATCTTCTTCCAAGTCCTTGAGGCAGATTTCCAGATGAAGTTCACCAGCTCCAG\n+CAACAATGTGCTCTCAAGATTCCTCAATGGAACACTGCACCAGGGGATCAGATTTTGACA\n+GACGTTTCAATCCTTCAACAAGCTTGGGCAGATCAGCTGGGTTTTTACACTCAACAGCCA\n+CACGCACAACTGGACTGACACTGAACTTCATCACTTTCAAGTTGTGGGCATGCTCGTACG\n+TGCTGATGGTTCCAGTCTTCAGAATGTACTGGTCAACACCAACCAGACCACAAACATTAC\n+CACAGGGCACATCTTCAATTGGCTCTATGTAACGACCCATCATAAGGATTGTTCTCTGGA\n+TGGCCTTCACATAGAGATCTTCCTTCTTCCCAGGGATAAAGTTGGGACCCATGATCCTAG\n+CCTTCATACCTGTTGACACAACACCAGAGAACACACGACCAAATGCATAGAATCTACCCT\n+TGTCTGATGTTGGTACCATCTTGGAGATGTACATCATCAGTGGTCCATTGGGGTCACAGT\n+TCTTGATTCCCAGAGCAGCCTCATCGTCATGTGGCCCCTCATACAGCATCTCCATACGGT\n+ACCTCTGAGCCGCTACTGGTGACGGCAGATGGATGGTTATCATCTGAAGCAAAGCATCAC\n+CAGCTGGCAGCCATTTACGCATGACAACCTTCAACAGTTGTTTGTCTATGAGGTCCTTGT\n+CATCACTTGTCAGTTTGATGCCAAGTTTCTCAACCAGCTTCAGTGTCTCTTCCTTTGGCT\n+TCTTCATGCAGAACTCAAACATCTTGTAAATGGGGTCAAGGATGTATTGTGTGAAACCAC\n+GACAATAGCCCTTCTGCATTTCTTTGCCCCATCTCTTCTCCTTTGGGTTGTAGAACTGGT\n+CTCCCCACAGCCTCTTCATCAGTTTTGGTTCCTCAATCTTGAACTTGTCTGCATACATCT\n+CGGCAAACTGCTTCAGTGTGAATGCCCAGCCATGGAGTCCAGATCCAAAGCCAACTGTAC\n+CCTTGGATGGATCAACATGGATGTTACCCATCGGTCCCTCGTCGTCAGCATAAGTGGCAA\n+TGATTACATTGATGCTTTCAATGATACGGGAGAAGGTCTGGTAGAGGTCCTCAGCACCAA\n+GCTGTAGGGTCAGCAGAGCCAAGTCCATCTTGTTCATGAACAGTACTGGCTTGATACGCT\n+CAGCAATGGCCTGACGCAGCACAGTCTCTGTTTGTACACACACGCCCGACACACAGTCGA\n+CAACAACCAGAGCACCATCTGTAACACGAAGGGCAGCAGTCACCTCCGAGGAGAAATCCA\n+CGTGACCAGGTGAGTCAATCAAGTTGATCAGGAAAGCAGTCTCTCCCTCCTCTCTTGGCT\n+GCTCGATCAACTTCAAATCTTTTTCTGGCAGCTGGTAAAAGAGTGAAATTGCTGTTGATT\n+TGATGGTAATACATCTTTCCTGCTCATCCTTCCTTGTGCCTTTTTCTCGGGTCCGCCATA\n+AAAGACAACTGCTCTTGATAGTTGTCTCGGAAGAGACTTGAAAACATCCAAGATGGTGAA\n+CTTTACGGTAGACGAGATCCGTGCGATCATGGACAAGAAGAAGAACATACGTAACATGTC\n+CGTGATTGCTCATGTGGATCATGGCAAGTCGACGCTGACTGATTCGTTGGTGAGCAAGGC\n+TGGCATTATTGCTGGCTCCAAGGCTGGCGAGACCCGCTTCACAGACACAAGGAAGGATGA\n+GCAGGAAAGATGTATTACCATCAAATCAACAGCAATTTCACTCTTTTACCAGCTGCCAGA\n+AAAAGATTTGAAGTTGATCGAGCAGCCAAGAGAGGAGGGAGAGACTGCTTTCCTGATCAA\n+CTTGATTGACTCACCTGGTCACGTGGATTTCTCCTCGGAGGTGACTGCTGCCCTTCGTGT\n+TACAGATGGTGCTCTGGTTGTTGTCGACTGTGTGTCGGGCGTGTGTGTACAAACAGAGAC\n+TGTGCTGCGTCAGGCCATTGCTGAGCGTATCAAGCCAGTACTGTTCATGAACAAGATGGA\n+CTTGGCTCTGCTGACCCTA'..b'CCAGCTCTCCCTCCCTGGAGGGCTTGTTCGGCGGCGACTG\n+CGGTCGGCATATGAGTGCCGTTCCGTTGATGACGACGGCTATGTCGTCGACGAACAAGCC\n+GTCCGGATGCTTCTCATCGCACGGCAGTTCTATCACGTCGAGGCTGATGCGTCTCAGGGC\n+GTCGACCAGCTGCTCGTGCTCGGCGCGGGCCTTCTCGATGTTGATCGGCGACGCGCCCGG\n+CTTCAGATCGAAGCTCGACGTCTCGGCGAACGAGTTCGCGATCCGGCTGACCAGAGCGAA\n+GTTGTACTTGAAACAATTAGATCCAGCCATTTTCTCCGGCATGATGAATCCTTCTCCGAC\n+CGAGCTACTCTGCGCCGAGACGACAACGAGGCTCGCCGTGACCGCTAC\n+>Locus_68_Transcript_1/4_Confidence_0.300_Length_794\n+TCCGATCTTGTCTCGTGTTTATTTCTTGTTACACATCACACAGAATGATGCTAGCAGGTC\n+ACTTTCTATTGTAATCCATGGTTTACTGGGATTTTGCCGCGATCCTCTTGTCACGTTCCT\n+CTGCTATCGTCAACCTCAGTCCCTTGCCAGCTGGTAATGACACCCACGGCTTGTTACCTT\n+TACCAATAATGAACACGTTGTTCAAACGTGTGGCAAATGAGTGGCCCATGCTGTCCTTGA\n+TGTGAACAATATCAAAGCCACCAGGATGACGTTCTCTGTGTGTCACAAGGCCAACACGAC\n+CCAAGTTGTGCCCACCAGTGATCATGCACAAATTTCCTGATTCAAACTTGATGAAATCCT\n+TTATCTTGCCTGTGGCAATGTCAACCTGAACTGTGTCATTGACCTTGATCATTGGATCTG\n+GATAGCGAATGGTACGAGCATCATGAGTGACCAGATGTGGAACTCCCTTCAGTCCAATGA\n+TTATCTTCTTTACCTTACACAGTTTGTACTTGGCTTCTTGGGAAGTGATACGGTGAATGG\n+TGAAACGACCTTTGACATCATAGATGAGACGGAAGTTTTCAGCCGTCTTCTCTATTGTGA\n+TCACATCCATAAAGCCAGCAGGGTATGTCTTGTCAGTTCTCACTTTGCCATCAACCTTGA\n+TCAGACGTTGGTTTACAATCTTCTTCACCTCATCATATGTCAAGGCATACTTCAGGCGAT\n+TTCTCAAGAACACCACCGGACGAGATGGGTGTTCGTGGTCCAAGGAAGCATTTGAAGAGG\n+CTTCATGCCCCTAA\n+>Locus_68_Transcript_2/4_Confidence_0.500_Length_1615\n+TCCGATCTTGTCTCGTGTTTATTTCTTGTTACACATCACACAGAATGATGCTAGCAGGTC\n+ACTTTCTATTGTAATCCATGGTTTACTGGGATTTTGCCGCGATCCTCTTGTCACGTTCCT\n+CTGCTATCGTCAACCTCAGTCCCTTGCCAGCTGGTAATGACACCCACGGCTTGTTACCTT\n+TACCAATAATGAACACGTTGTTCAAACGTGTGGCAAATGAGTGGCCCATGCTGTCCTTGA\n+TGTGAACAATATCAAAGCCACCAGGATGACGTTCTCTGTGTGTCACAAGGCCAACACGAC\n+CCAAGTTGTGCCCACCAGTGATCATGCACAAATTTCCTGATTCAAACTTGATGAAATCCT\n+TTATCTTGCCTGTGGCAATGTCAACCTGAACTGTGTCATTGACCTTGATCATTGGATCTG\n+GATAGCGAATGGTACGAGCATCATGAGTGACCAGATGTGGAACTCCCTTCAGTCCAATGA\n+TTATCTTCTTTACCTTACACAGTTTGTACTTGGCTTCTTGGGAAGTGATACGGTGAATGG\n+TGAAACGACCTTTGACATCATAGATGAGACGGAAGTTTTCAGCCGTCTTCTCTATTGTGA\n+TCACATCCATAAAGCCAGCAGGGTATGTCTTGTCAGTTCTCACTTTGCCATCAACCTTGA\n+TCAGACGTTGGTTTACAATCTTCTTCACCTCATCATATGTCAAGGCATACTTCAGGCGAT\n+TTCTCAAGAACACCACCGGAGGGAGACACTCTCGCATCTTGTGTGGACCAGTGCTTGGGC\n+GTGGGGCAAAAACACCCCCAAGCTTGTCCAACATCCAGTGTTTAGGGGCATGAAGCCTCT\n+TCAAATGCTTCCTTGGACCACGAACACCCATCTCGTCCGGTGGTGTTCTTGAGAAATCGC\n+CTGAAGTATGCCTTGACATATGATGAGGTGAAGAAGATTGTAAACCAACGTCTGATCAAG\n+GTTGATGGCAAAGTGAGAACTGACAAGACATACCCTGCTGGCTTTATGGATGTGATCACA\n+ATAGAGAAGACGGCTGAAAACTTCCGTCTCATCTATGATGTCAAAGGTCGTTTCACCATT\n+CACCGTATCACTTCCCAAGAAGCCAAGTACAAACTGTGTAAGGTAAAGAAGATAATCATT\n+GGACTGAAGGGAGTTCCACATCTGGTCACTCATGATGCTCGTACCATTCGCTATCCAGAT\n+CCAATGATCAAGGTCAATGACACAGTTCAGGTTGACATTGCCACAGGCAAGATAAAGGAT\n+TTCATCAAGTTTGAATCAGGAAATTTGTGCATGATCACTGGTGGGCACAACTTGGGTCGT\n+GTTGGCCTTGTGACACACAGAGAACGTCATCCTGGTGGCTTTGATATTGTTCACATCAAG\n+GACAGCATGGGCCACTCATTTGCCACACGTTTGAACAACGTGTTCATTATTGGTAAAGGT\n+AACAAGCCGTGGGTGTCATTACCAGCTGGCAAGGGACTGAGGTTGACGATAGCAGAGGAA\n+CGTGACAAGAGGATCGCGGCAAAATCCCAGTAAACCATGGATTACAATAGAAAGTGACCT\n+GCTAGCATCATTCTGTGTGATGTGTAACAAGAAATAAACACGAGACAAGATCGGA\n+>Locus_68_Transcript_3/4_Confidence_0.400_Length_912\n+TTAGGGGCATGAAGCCTCTTTTTCCCGTACCACCGGACGAGATGGGTGTTCGTGGTCCAA\n+GGAAGCATTTGAAGAGGCTTCATGCCCCTAAACACTGGATGTTGGACAAGCTTGGGGGTG\n+TTTTTGCCCCACGCCCAAGCACTGGTCCACACAAGATGCGAGAGTGTCTCCCTCTGGTGG\n+TGTTCTTGAGAAATCGCCTGAAGTATGCCTTGACATATGATGAGGTGAAGAAGATTGTAA\n+ACCAACGTCTGATCAAGGTTGATGGCAAAGTGAGAACTGACAAGACATACCCTGCTGGCT\n+TTATGGATGTGATCACAATAGAGAAGACGGCTGAAAACTTCCGTCTCATCTATGATGTCA\n+AAGGTCGTTTCACCATTCACCGTATCACTTCCCAAGAAGCCAAGTACAAACTGTGTAAGG\n+TAAAGAAGATAATCATTGGACTGAAGGGAGTTCCACATCTGGTCACTCATGATGCTCGTA\n+CCATTCGCTATCCAGATCCAATGATCAAGGTCAATGACACAGTTCAGGTTGACATTGCCA\n+CAGGCAAGATAAAGGATTTCATCAAGTTTGAATCAGGAAATTTGTGCATGATCACTGGTG\n+GGCACAACTTGGGTCGTGTTGGCCTTGTGACACACAGAGAACGTCATCCTGGTGGCTTTG\n+ATATTGTTCACATCAAGGACAGCATGGGCCACTCATTTGCCACACGTTTGAACAACGTGT\n+TCATTATTGGTAAAGGTAACAAGCCGTGGGTGTCATTACCAGCTGGCAAGGGACTGAGGT\n+TGACGATAGCAGAGGAACGTGACAAGAGGATCGCGGCAAAATCCCAGTAAACCATGGATT\n+ACAATAGAAAGTGACCTGCTAGCATCATTCTGTGTGATGTGTAACAAGAAATAAACACGA\n+GACAAGATCGGA\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet/Ac_transcriptome_25591_oneline.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet/Ac_transcriptome_25591_oneline.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,398 @@\n+Locus_1_Transcript_1/2_Confidence_1.000_Length_6683\n+TAAACTGCAACGCCAATATGTGATGTTCAATTCTGAACGTTGTTCAGTTTTATTTTGTTTACTGGATTGTTTACCAATAAAATATTGTGTACAAAGTGCCCAACTTGACATGGTTTGGCTGTAGTAATGTTCTGCAACGAGTTATTCATTTCGGAATTGTGGAAAAATAAGACAGGCTGGTACTGCATTTAGTGGATTAGCCATGGTAAATGTTTCAAACATGAAGTCATACATCTGCCTTACACACAAATGTGCTGTGCCTTATACAAAACACTGGTTCTGCACTTCTGCAATAATTTATTGACTGCTGACTTCTTGGACATGCAAGTCCAAGCACACAAGATGTACAAGGTTTTAAAAGGATGCAGCAGCAGTAGCAAGGACAAACACCATTCACTGGCCTCTGTGCCATAACCAGATGTGTTAACAACAGGCATATTAAAGACTCCCACATCCAATAACCTGATCACTATAGCTGTTTACACACGAATGAGAAGTGAAGACACCGATAACAGGCTGCTTGTACTACTTGTGTTATGAGAGTAGTGGTAGAATAATAAAATAATACATTGAACTAGTTCTTTGCCTTCCGATAGAATGCTTGACAAAACGAACTCAAATTTTGTGCTCTTACAATTTGTCGAATAATCACATACGGGCAAAGCCTACAAAAAGAACCAGCTATTTAATTAAGAAATTTTGCACTCTGCCAACACAACCATTGACAGATGTAGATTCGAAATATCAAGTCAGTTTGCCATGTGTATACAGGTGTGTATATACAGAACATGGTCACTGAATGCTGTGTACACAATATACCTAAGGGCAAGGAATTAAACATTAACTAGCTTCAGTCAGATTACAACTTGTCCAGGAAGTTGTCCAGTGGAGGAACGCCCTCCTTCAGCCCTTTGCGTTTTCTCGTCTCTTGGACGATTATGTTAGGCTTGGAGTTGTCCACAAACGGATCGCCTGGGAGGATCTGCCAGTGATCAAACACACACTGTGGGAATGCCTGGCCACCAGTGTTGGACCTCAGGTCGGCAGTGAAACCAAATGATTCGTTTACAGGAAGGTATGCCTTGACCTGGAACATCGGGGTTCCCACCACTTGGTTCTCCTCAATGACAACACCTCGTCTTCTGTTCAGCACACCATAAATGCCACCAACAGCTTGCTCAGGGCACTGGATCTCAACCAGGTATATTGGTTCCATCAACCTTGGTTCAGCTGTCAGCACACATGCATAGAGACATCTTCTTGTTGTTGGGATGATCTGGCCACCACCACGGTGAATAGCATCAGCATGCAGTGTGACATCAAGAATGTTGAAGCGGATTCCTCTCATGTTCTCTTCACAGAGTACACCCTCCTTGCTAGCCCACTGGAAGCCAGCCACAACACTGTCTTTGATTTCATTCAGGTACTGGACACCCTTTGTGCAGTCAATGACCAGGTTTGGTCCTGTGCCATCAGGTCCAAAGCACCAGATCTTACGAGCCTCAGTAACATCAAACTCGTATGTGTCGGCCAGGTATCTAGCTCTCTCCTTCTGATCCTGACGAGCACTGACCTTCTCTCCCCTATCAATCTCTTCAGGTAAGCCATCTGGCAGTGGTGCAGCAACCATGAAGAGACGATTGTGCTTGTTTGGTGATTTTGACAAGCAGGTTCTGTCAGATGTGTTACTGACAGTCTCTCTATATGAGACAACAGGGTCAGATTTCTTGATTGGGATGCAGGCATGATCTTCTTCCAAGTCCTTGAGGCAGATTTCCAGATGAAGTTCACCAGCTCCAGCAACAATGTGCTCTCAAGATTCCTCAATGGAACACTGCACCAGGGGATCAGATTTTGACAGACGTTTCAATCCTTCAACAAGCTTGGGCAGATCAGCTGGGTTTTTACACTCAACAGCCACACGCACAACTGGACTGACACTGAACTTCATCACTTTCAAGTTGTGGGCATGCTCGTACGTGCTGATGGTTCCAGTCTTCAGAATGTACTGGTCAACACCAACCAGACCACAAACATTACCACAGGGCACATCTTCAATTGGCTCTATGTAACGACCCATCATAAGGATTGTTCTCTGGATGGCCTTCACATAGAGATCTTCCTTCTTCCCAGGGATAAAGTTGGGACCCATGATCCTAGCCTTCATACCTGTTGACACAACACCAGAGAACACACGACCAAATGCATAGAATCTACCCTTGTCTGATGTTGGTACCATCTTGGAGATGTACATCATCAGTGGTCCATTGGGGTCACAGTTCTTGATTCCCAGAGCAGCCTCATCGTCATGTGGCCCCTCATACAGCATCTCCATACGGTACCTCTGAGCCGCTACTGGTGACGGCAGATGGATGGTTATCATCTGAAGCAAAGCATCACCAGCTGGCAGCCATTTACGCATGACAACCTTCAACAGTTGTTTGTCTATGAGGTCCTTGTCATCACTTGTCAGTTTGATGCCAAGTTTCTCAACCAGCTTCAGTGTCTCTTCCTTTGGCTTCTTCATGCAGAACTCAAACATCTTGTAAATGGGGTCAAGGATGTATTGTGTGAAACCACGACAATAGCCCTTCTGCATTTCTTTGCCCCATCTCTTCTCCTTTGGGTTGTAGAACTGGTCTCCCCACAGCCTCTTCATCAGTTTTGGTTCCTCAATCTTGAACTTGTCTGCATACATCTCGGCAAACTGCTTCAGTGTGAATGCCCAGCCATGGAGTCCAGATCCAAAGCCAACTGTACCCTTGGATGGATCAACATGGATGTTACCCATCGGTCCCTCGTCGTCAGCATAAGTGGCAATGATTACATTGATGCTTTCAATGATACGGGAGAAGGTCTGGTAGAGGTCCTCAGCACCAAGCTGTAGGGTCAGCAGAGCCAAGTCCATCTTGTTCATGAACAGTACTGGCTTGATACGCTCAGCAATGGCCTGACGCAGCACAGTCTCTGTTTGTACACACACGCCCGACACACAGTCGACAACAACCAGAGCACCATCTGTAACACGAAGGGCAGCAGTCACCTCCGAGGAGAAATCCACGTGACCAGGTGAGTCAATCAAGTTGATCAGGAAAGCAGTCTCTCCCTCCTCTCTTGGCTGCTCGATCAACTTCAAATCTTTTTCTGGCAGCTGGTAAAAGAGTGAAATTGCTGTTGATTTGATGGTAATACATCTTTCCTGCTCATCCTTCCTTGTGCCTTTTTCTCGGGTCCGCCATAAAAGACAACTGCTCTTGATAGTTGTCTCGGAAGAGACTTGAAAACATCCAAGATGGTGAACTTTACGGTAGACGAGATCCGTGCGATCATGGACAAGAAGAAGAACATACGTAACATGTCCGTGATTGCTCATGTGGATCATGGCAAGTCGACGCTGACTGATTCGTTGGTGAGCAAGGCTGGCATTATTGCTGGCTCCAAGGCTGGCGAGACCCGCTTCACAGACACAAGGAAGGATGAGCAGGAAAGATGTATTACCATCAAATCAACAGCAATTTCACTCTTTTACCAGCTGCCAGAAAAAGATTTGAAGTTGATCGAGCAGCCAAGAGAGGAGGGAGAGACTGCTTTCCTGATCAACTTGATTGACTCACCTGGTCACGTGGATTTCTCCTCGGAGGTGACTGCTGCCCTTCGTGTTACAGATGGTGCTCTGGTTGTTGTCGACTGTGTGTCGGGCGTGTGTGTACAAACAGAGACTGTGCTGCGTCAGGCCATTGCTGAGCGTATCAAGCCAGTACTGTTCATGAACAAGATGGACTTGGCTCTGCTGACCCTACAGCTTGGTGCTGAGGACCTCTACCAGACCTTCTCCCGTATCATTGAAAGCATCAATGTAATCATTGCCACTTATGCTGACGACGAGGGACCGATGGGTAACATCCATGTTGATCCATCCAAGGGTAC'..b'CAAAGATTTCTCTACCTGTCCAAAGGACATCGCCACCTTCCAGCTTCGTTTCCTCATCTCCTTTGTTCTCCACTTCAACAACTTTAAGTCCGAGTTCCTTTCTTAGCACCTGTCGGACGACAGCCAGCTCTCCCTCCCTGGAGGGCTTGTTCGGCGGCGACTGCGGTCGGCATATGAGTGCCGTTCCGTTGATGACGACGGCTATGTCGTCGACGAACAAGCCGTCCGGATGCTTCTCATCGCACGGCAGTTCTATCACGTCGAGGCTGATGCGTCTCAGGGCGTCGACCAGCTGCTCGTGCTCGGCGCGGGCCTTCTCGATGTTGATCGGCGACGCGCCCGGCTTCAGATCGAAGCTCGACGTCTCGGCGAACGAGTTCGCGATCCGGCTGACCAGAGCGAAGTTGTACTTGAAACAATTAGATCCAGCCATTTTCTCCGGCATGATGAATCCTTCTCCGACCGAGCTACTCTGCGCCGAGACGACAACGAGGCTCGCCGTGACCGCTAC\n+Locus_68_Transcript_1/4_Confidence_0.300_Length_794\n+TCCGATCTTGTCTCGTGTTTATTTCTTGTTACACATCACACAGAATGATGCTAGCAGGTCACTTTCTATTGTAATCCATGGTTTACTGGGATTTTGCCGCGATCCTCTTGTCACGTTCCTCTGCTATCGTCAACCTCAGTCCCTTGCCAGCTGGTAATGACACCCACGGCTTGTTACCTTTACCAATAATGAACACGTTGTTCAAACGTGTGGCAAATGAGTGGCCCATGCTGTCCTTGATGTGAACAATATCAAAGCCACCAGGATGACGTTCTCTGTGTGTCACAAGGCCAACACGACCCAAGTTGTGCCCACCAGTGATCATGCACAAATTTCCTGATTCAAACTTGATGAAATCCTTTATCTTGCCTGTGGCAATGTCAACCTGAACTGTGTCATTGACCTTGATCATTGGATCTGGATAGCGAATGGTACGAGCATCATGAGTGACCAGATGTGGAACTCCCTTCAGTCCAATGATTATCTTCTTTACCTTACACAGTTTGTACTTGGCTTCTTGGGAAGTGATACGGTGAATGGTGAAACGACCTTTGACATCATAGATGAGACGGAAGTTTTCAGCCGTCTTCTCTATTGTGATCACATCCATAAAGCCAGCAGGGTATGTCTTGTCAGTTCTCACTTTGCCATCAACCTTGATCAGACGTTGGTTTACAATCTTCTTCACCTCATCATATGTCAAGGCATACTTCAGGCGATTTCTCAAGAACACCACCGGACGAGATGGGTGTTCGTGGTCCAAGGAAGCATTTGAAGAGGCTTCATGCCCCTAA\n+Locus_68_Transcript_2/4_Confidence_0.500_Length_1615\n+TCCGATCTTGTCTCGTGTTTATTTCTTGTTACACATCACACAGAATGATGCTAGCAGGTCACTTTCTATTGTAATCCATGGTTTACTGGGATTTTGCCGCGATCCTCTTGTCACGTTCCTCTGCTATCGTCAACCTCAGTCCCTTGCCAGCTGGTAATGACACCCACGGCTTGTTACCTTTACCAATAATGAACACGTTGTTCAAACGTGTGGCAAATGAGTGGCCCATGCTGTCCTTGATGTGAACAATATCAAAGCCACCAGGATGACGTTCTCTGTGTGTCACAAGGCCAACACGACCCAAGTTGTGCCCACCAGTGATCATGCACAAATTTCCTGATTCAAACTTGATGAAATCCTTTATCTTGCCTGTGGCAATGTCAACCTGAACTGTGTCATTGACCTTGATCATTGGATCTGGATAGCGAATGGTACGAGCATCATGAGTGACCAGATGTGGAACTCCCTTCAGTCCAATGATTATCTTCTTTACCTTACACAGTTTGTACTTGGCTTCTTGGGAAGTGATACGGTGAATGGTGAAACGACCTTTGACATCATAGATGAGACGGAAGTTTTCAGCCGTCTTCTCTATTGTGATCACATCCATAAAGCCAGCAGGGTATGTCTTGTCAGTTCTCACTTTGCCATCAACCTTGATCAGACGTTGGTTTACAATCTTCTTCACCTCATCATATGTCAAGGCATACTTCAGGCGATTTCTCAAGAACACCACCGGAGGGAGACACTCTCGCATCTTGTGTGGACCAGTGCTTGGGCGTGGGGCAAAAACACCCCCAAGCTTGTCCAACATCCAGTGTTTAGGGGCATGAAGCCTCTTCAAATGCTTCCTTGGACCACGAACACCCATCTCGTCCGGTGGTGTTCTTGAGAAATCGCCTGAAGTATGCCTTGACATATGATGAGGTGAAGAAGATTGTAAACCAACGTCTGATCAAGGTTGATGGCAAAGTGAGAACTGACAAGACATACCCTGCTGGCTTTATGGATGTGATCACAATAGAGAAGACGGCTGAAAACTTCCGTCTCATCTATGATGTCAAAGGTCGTTTCACCATTCACCGTATCACTTCCCAAGAAGCCAAGTACAAACTGTGTAAGGTAAAGAAGATAATCATTGGACTGAAGGGAGTTCCACATCTGGTCACTCATGATGCTCGTACCATTCGCTATCCAGATCCAATGATCAAGGTCAATGACACAGTTCAGGTTGACATTGCCACAGGCAAGATAAAGGATTTCATCAAGTTTGAATCAGGAAATTTGTGCATGATCACTGGTGGGCACAACTTGGGTCGTGTTGGCCTTGTGACACACAGAGAACGTCATCCTGGTGGCTTTGATATTGTTCACATCAAGGACAGCATGGGCCACTCATTTGCCACACGTTTGAACAACGTGTTCATTATTGGTAAAGGTAACAAGCCGTGGGTGTCATTACCAGCTGGCAAGGGACTGAGGTTGACGATAGCAGAGGAACGTGACAAGAGGATCGCGGCAAAATCCCAGTAAACCATGGATTACAATAGAAAGTGACCTGCTAGCATCATTCTGTGTGATGTGTAACAAGAAATAAACACGAGACAAGATCGGA\n+Locus_68_Transcript_3/4_Confidence_0.400_Length_912\n+TTAGGGGCATGAAGCCTCTTTTTCCCGTACCACCGGACGAGATGGGTGTTCGTGGTCCAAGGAAGCATTTGAAGAGGCTTCATGCCCCTAAACACTGGATGTTGGACAAGCTTGGGGGTGTTTTTGCCCCACGCCCAAGCACTGGTCCACACAAGATGCGAGAGTGTCTCCCTCTGGTGGTGTTCTTGAGAAATCGCCTGAAGTATGCCTTGACATATGATGAGGTGAAGAAGATTGTAAACCAACGTCTGATCAAGGTTGATGGCAAAGTGAGAACTGACAAGACATACCCTGCTGGCTTTATGGATGTGATCACAATAGAGAAGACGGCTGAAAACTTCCGTCTCATCTATGATGTCAAAGGTCGTTTCACCATTCACCGTATCACTTCCCAAGAAGCCAAGTACAAACTGTGTAAGGTAAAGAAGATAATCATTGGACTGAAGGGAGTTCCACATCTGGTCACTCATGATGCTCGTACCATTCGCTATCCAGATCCAATGATCAAGGTCAATGACACAGTTCAGGTTGACATTGCCACAGGCAAGATAAAGGATTTCATCAAGTTTGAATCAGGAAATTTGTGCATGATCACTGGTGGGCACAACTTGGGTCGTGTTGGCCTTGTGACACACAGAGAACGTCATCCTGGTGGCTTTGATATTGTTCACATCAAGGACAGCATGGGCCACTCATTTGCCACACGTTTGAACAACGTGTTCATTATTGGTAAAGGTAACAAGCCGTGGGTGTCATTACCAGCTGGCAAGGGACTGAGGTTGACGATAGCAGAGGAACGTGACAAGAGGATCGCGGCAAAATCCCAGTAAACCATGGATTACAATAGAAAGTGACCTGCTAGCATCATTCTGTGTGATGTGTAACAAGAAATAAACACGAGACAAGATCGGA\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet/Ap_transcriptome_35099.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet/Ap_transcriptome_35099.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,6714 @@\n+>Locus_1_Transcript_1/1_Confidence_1.000_Length_257\n+TCAAGGAGCCCGGCTCGGACATTTGGACGTTGGTCAAGTCCCAGACTTTGATGGCCGTGT\n+GGATGTTTGAGCCGGTGGCTATGTAGTTACTGTCTGAGCAGACGGCCATTGGGAAGTGGT\n+CGTTGGTGTGCAGTCTGATTGTTGTGACCAGCTTGCAGTTCTCCGTGCTCCACAGGTGCA\n+GGTTTTCGTGTGAGCCGGCCACGATATATCTGCCATCCATTGAGAAGTTAGCACCAAAAA\n+GGAATGTCTTGTTGCTG\n+>Locus_2_Transcript_1/2_Confidence_1.000_Length_264\n+TTGTTTCGGACTTGGTATCTGTGAGCATCAAGGGTTTTAGTATTTTGATTCTCTAGAAGT\n+TGCACGTAGAAACACAGCATGGGAGCAGAAAAGAAACACATCAACATCGTGGTTATTGGC\n+CACGTAGACTCCGGGAAGTCTACCACCACTGGCCATCTGATCTACAAGTGTGGTGGCATC\n+GACAAGAGAACCATTGAAAAGTTCGAGAAGGAGGCCCAGGAGATGGGTAAAGGCTCCTTC\n+AAGTATGCCTGGGTGTTGGACAAA\n+>Locus_2_Transcript_2/2_Confidence_1.000_Length_242\n+CTTTTCATCCGGCTTCTCTAGGCGAAAGCTCTAGAAGTTGCACGTAGAAACACAGCATGG\n+GAGCAGAAAAGAAACACATCAACATCGTGGTTATTGGCCACGTAGACTCCGGGAAGTCTA\n+CCACCACTGGCCATCTGATCTACAAGTGTGGTGGCATCGACAAGAGAACCATTGAAAAGT\n+TCGAGAAGGAGGCCCAGGAGATGGGTAAAGGCTCCTTCAAGTATGCCTGGGTGTTGGACA\n+AA\n+>Locus_3_Transcript_1/1_Confidence_1.000_Length_558\n+GCGGATCAAAATGAAAACAGACGACGGTGTAAAATATGATCATGACACCGTGCGTTTGCA\n+ATCAAGGAATATTAATACTATGAATTTAGGCACTGATTTCTTAACATCACGATTTTCACC\n+TCGGTTGCAATTAAGTAGAACGATTCTGGTTAGAACATGGTACAGTCTAGTTTTTCTCTC\n+AAACACTTAGCTATGTTTCCACACAGTATGTGATGTACTGGATATTTCCTATTGATCCAG\n+CATTCAAACAGTTTTTAACTTGCTCCGGCACTAGGCACTGGCAAGAGGGGTTATAAGGAG\n+AAGACGGTCTAGGCAATAAAACAGTGCTGACACCTAGGGAGTTCAATGGAACCAGCCATA\n+TTATTACATTAAGCAAAAGCAACTAACTACTGAATGGTGAGCAAGAGGATTTCATGTCTT\n+GCGCACTCTGTGATTGAAAACAAGAAACAAAAAGGAAAAAATAACTGACACCCGCATAAC\n+ACACTTGATAAATGGTATACTTCTTTGAGCAAATGCTTGTCTAACAGCAATGTCAAAGAT\n+ATAAAACAGACAGACAGA\n+>Locus_4_Transcript_1/2_Confidence_1.000_Length_299\n+CAAACTTCTGACGGTGGAATCAGCACTTTCTTTAGACTTTGTCATGACGAGTCTGGCCCC\n+TCCATCGTTCACAGGAAGTGCTTCTAAAGATAGTTGTGACCATCCCAACTGCCGTGACCA\n+CTCACAACAACAAACAACATTCTGTCTGCTCAGTGGCCCGTGGGCGACCTTTGTTCAGTG\n+CCAGGGAACTCGTCATGACAAAGTCTAAAGAAAGTGCTGATTCCACCGTCAGAAGTTTGC\n+TATACGAAATCCAGTCACACCATTCTGCTCTTCAAACATTACACAAACCAATCTTTTCC\n+>Locus_4_Transcript_2/2_Confidence_1.000_Length_331\n+ACTCCGTATGGATTGGTGGATCGATCCTCGCCTCCCTGTCCACCTTCCAGCAGATGAGGA\n+TCAGCAAGCAGGAGTACGACGAGTCTGGACCATCCATCGTTCACAGGAAGTGCTTCTAAA\n+GATAGTTGTGACCATCCCAACTGCCGTGACCACTCACAACAACAAACAACATTCTGTCTG\n+CTCAGTGGCCCGTGGGCGACCTTTGTTCAGTGCCAGGGAACTCGTCATGACAAAGTCTAA\n+AGAAAGTGCTGATTCCACCGTCAGAAGTTTGCTATACGAAATCCAGTCACACCATTCTGC\n+TCTTCAAACATTACACAAACCAATCTTTTCC\n+>Locus_5_Transcript_1/1_Confidence_1.000_Length_505\n+TAACAGTCCATCTCATGTTGGCGTGGATGAAACAGTAGACGTTCAGAAGCCTGCTACTTT\n+GTTTACATGACAGCAAATCCCTCGATTGCTCTTCAAAGAATTCACAGTCCATGCATGTTG\n+ATGTAAACTGGTGTGGTCTGGTGACCAGCAAGCTTGGTTTGGTGCTTGTTTCACTGTGTG\n+TCCTTTGAACAGTAATGTGTAACATTAATCCCTTTGTGAAGATCATTCTTCATTTCAATG\n+CATCACTCTTCTCTCTAGGAAATTCTTCCAAGCTGTTTGGTTTTAATGTTGAATTCGATC\n+AGGAGGCTGCCTTGCAATCTAGGAAATTGTCGCTTTTAACTATTTATTCCTTAGTGTAAA\n+TTGTTTCTTTGTTAGCACAATTGGTTGAACTCTATTCAAGTGCATGCCAGTGAAGGAAGC\n+ATTATTGAAATTTGCAATGTATTTATTTTAAGATGTCATTTTCTTCAATAAACAAGTATG\n+CTGCAGTTTGTTCTGCCAAAAAAAA\n+>Locus_6_Transcript_1/1_Confidence_1.000_Length_375\n+AAAATATACAGATTTAATAACAGCAATTGATAAACACTTTGAAAGCAAATTGTCATCTGT\n+TGAGAAAGATGACATATTATTATCAGAATCTCACTTTGCACAATGTGGTTCTTTGTCTGA\n+CACAGTTAGCAGCTATCTTCACACTGTGATGACAGTCTCCAAGTGGAAGAAGAAAGTCAA\n+AGCAATGCAGCAGACACCAGGACAACCACTACTTCTAATTATTTGTAGTGCTGCAAGTCG\n+AGCAGTAGACTTGATAAGAGATTTGAGGTCCTTTTCTCAAGATAATTGTAAAGTTGCAAA\n+GCTATTTGCAAAACACATGAAGCTGGAAGAACAAGTAAAATTCTTGAAGAAAAATGTAAT\n+ACAGGCAGGAGTTGG\n+>Locus_7_Transcript_1/2_Confidence_1.000_Length_290\n+GCAGAAGGAAAGGCCCAAAGGGTTGTCCCGATGTCCGTCCCGCGGGCCAGACTCGACCCT\n+CTCCGGCAGATCGGCAGCCCCAGTACCACCCTGCCAGATCGTGTTCGGGTGGGTTTTTTA\n+TCGACCTGCCGGGGACTGGCCGAGTAGTGACCGATCACGGGCGAACCGGAAACCGACACG\n+ACAACCCCGGACATCAGAAGACGGGACGACACACACACGCAAACGGAGAGATAGACGCAA\n+GACGACTACATCAGCACAGACGTCCGCCGCACACGGACTCGGACGCGGAC\n+>Locus_7_Transcript_2/2_Confidence_1.000_Length_292\n+GCAGAAGGAAAGGCCCAAAGGGTTGTCCCGATGTCCGTCCCGCGGGCCAGACTCGACCCT\n+CTCCGGCAGATCGGCAGCCCCAGTACCACCCTGCCAGATCGTGTTCGGGTGGGTTTTTTA\n+TCGACCTGCCGGGGACTGGCCGAGTAGTGACCGATCACGGGCGAACCGGAAACCGACACG\n+ACAACCCCGGACATCAGAAGACGGGACG'..b'0.278_Length_914\n+CAGATAGTAGTGCGGAGATAAATAAAATGTTGGTTGGTGTTGCTTTGACTAGGGTGTTGT\n+AGCATATCATAGAGATAGGGAAGGTGTTTAAGCTTCCTGGTTTTAGGCTTAGAACGCCCT\n+ACCTTAACAATTACTATCTCCGCACTACTATCTGGAGTGGCAATAGCTCTATCGGCCCAC\n+TCCATGCTATCGATATGAATGGGCCTTGAACTCAACCTATTCGGCTTCATTCCCCTTATT\n+ATAGCAACAAGATCTAATCAAGAAAAAGAGGCAGCCTGTAAATACTTTCTAGCCCAAGCC\n+ATCCCATCCGCTATCTTTCTACTAGCCCTAGTATTAATACCAGACATCCCTACAACCTCT\n+GCCGTAATTCTCGTCGCACTATTTATAAAAATAGGAATCGCCCCATGTCACCAATGATTT\n+CCTTCTGTTATAAACGCACTAGCTTGGCCGCAAGCATGGACCCTCATTACTGTACAAAAA\n+ATTGCACCATTCTTCATAATTCTCCACATAGTTGGTAACACGACCATTCTCACTTTCCAT\n+AGCAGCCGCTATTTCATCTATTATTGGCGGACTAGGCGGCATAAATCAAACACAACTACG\n+CCCACTATTGGCCTACTCATCTATCGGGCACATAGGCTGAATACTAGGAGCAGTTTTAGT\n+TTCAAATAGCGCTGCCACGCTCTATTTCTCTTCTTATCTCTTTATTGTATCAACAACAAT\n+TCTAAGCGCCGTTCTATTAAAAACTAACTCCTTGTTTTCCCTACCACTATTTAAATCATC\n+AACAACTCTATCAACCATTCTATTCCTCTCCTTCATAAACATAGGGGGCCTTCCTCCATT\n+CTTCGGTTTCTTTATTAAAGCTTTCGTAATACTTAACTTACTTTCCAGCAATCTGGCCCC\n+CCTCACCTTCTTCT\n+>Locus_65_Transcript_4/7_Confidence_0.111_Length_302\n+CAGATAGTAGTGCGGAGATAAATAAAATGTTGGTTGGTGTTGCTTTGACTAGGGTGTTGT\n+AGCATATCATAGAGATAGGGAAGGTGTTTAAGCTTCCTGGTTTTAGGCTTAGAACGCCCT\n+ACCTTAACAATTACTATCTCACATGGTTTTATTTTATGGGGTTCAATTTAGAGACCCCTC\n+TCGTCACTCATGAAAAATACCGAGAAGAAGAATTAGTACAAATAAAAAAGCTGGAAGAAT\n+GGCCTGAGAAATAATAGTTGAGGATGGGAGGAGTGGGATCGGTATTAGTAGGGCAATTTC\n+TA\n+>Locus_65_Transcript_5/7_Confidence_0.185_Length_374\n+CACTCGGCCCGAACCCCATTTTCTTTACGATTTTTTTTACTTGCAGTAATATTTCTAATC\n+TTCGACGTAGAAATTGCCCTACTAATACCGATCCCACTCCTCCCATCCTCAACTATTATT\n+TCTCAGGCCATTCTTCCAGCTTTTTTATTTGTACTAATTCTTCTTCTCGGTATTTTTCAT\n+GAGTGACGAGAGGGGTCTCTAAATTGAACCCCATAAAATAAAACCATGTGAGATAGTAAT\n+TGTTAAGGTAGGGCGTTCTAAGCCTAAAACCAGGAAGCTTAAACACCTTCCCTATCTCTA\n+TGATAAGCTACAACACCCTAGTCAAAGCAACACCAACCAACATTTTATTTATCTCCGCAC\n+TACTATCTGGAGTG\n+>Locus_65_Transcript_6/7_Confidence_0.222_Length_821\n+CAGATAGTAGTGCGGAGATAAATAAAATGTTGGTTGGTGTTGCTTTGACTAGGGTGTTGT\n+AGCATATCATAGAGATAGGGAAGGTGTTTAAGCTTCCTGGTTTTAGGCTTAGAACGCCCT\n+ACCTTAACAATTACTATCTCCGCACTACTATCTGGAGTGGCAATAGCTCTATCGGCCCAC\n+TCCATGCTATCGATATGAATGGGCCTTGAACTCAACCTATTCGGCTTCATTCCCCTTATT\n+ATAGCAACAAGATCTAATCAAGAAAAAGAGGCAGCCTGTAAATACTTTCTAGCCCAAGCC\n+ATCCCATCCGCTATCTTTCTACTAGCCCTAGTATTAATACCAGACATCCCTACAACCTCT\n+GCCGTAATTCTCGTCGCACTATTTATAAAAATAGGAATCGCCCCATGTCACCAATGATTT\n+CCTTCTGTTATAAACGCACTAGCTTGGCCGCAAGCATGGACCCTCATTACTGTACAAAAA\n+ATTGCACCATTCTTCATAATTCTCCACATAGTTGGTAACACGACCATTCTCACTTTCCAT\n+AGCAGCCGCTATTTCATCTATTATTGGCGGACTAGGCGGCATAAATCAAACACAACTACG\n+CCCACTATTGGCCTACTCATCTATCGGGCACATAGGCTGAATACTAGGAGCAGTTTTAGT\n+TTCAAATAGCGCTGCCACGCTCTATTTCTCTTCTTATCTCTTTATTGTATCAACAACAAT\n+TCTAAGCGCCGTTCTATTAAAAACTAACTCCTTGTTTTCCCTACCACTATTTAAATCATC\n+AACAACTCTATCAACCATTCTATTCCTCTCCTTCATAAACA\n+>Locus_65_Transcript_7/7_Confidence_0.204_Length_775\n+AGAAGAAGGTGAGGGGGGCCAGATTGCTGGAAAGTAAGTTAAGTATTACGAAAGCTTTAA\n+TAAAGAAACCGAAGAATGGAGGAAGGCCCCCTATGTTTATGAAGGAGAGGAATAGAATGG\n+TTGATAGAGTTGTTGATGATTTAAATAGTGGTAGGGAAAACAAGGAGTTAGTTTTTAATA\n+GAACGGCGCTTAGAATTGTTGTTGATACAATAAAGAGATAAGAAGAGAAATAGAGCGTGG\n+CAGCGCTATTTGAAACTAAAACTGCTCCTAGTATTCAGCCTATGTGCCCGATAGATGAGT\n+AGGCCAATAGTGGGCGTAGTTGTGTTTGATTTATGCCGCCTAGTCCGCCAATAATAGATG\n+AAATAGCGGCTGCTATGGAAGTGAGAATGGTCGTGTTAACCAACTATGTGGAGAATTATG\n+AAGAATGGTGCAATTTTTTGTACAGTAATGAGGGTCCATGCTTGCGGCCAAGCTAGTGCG\n+TTTATAACAGAAGGAAATCATTGGTGACATGGGGCGATTCCTATTTTTATAAATAGTGCG\n+ACGAGAATTACGGCAGAGGTTGTAGGGATGTCTGGTATTAATACTAGGGCTAGTAGAAAG\n+ATAGCGGATGGGATGGCTTGGGCTAGAAAGTATTTACAGGCTGCCTCTTTTTCTTGATTA\n+GATCTTGTTGCTATAATAAGGGGAATGAAGCCGAATAGGTTGAGTTCAAGGCCCATTCAT\n+ATCGATAGCATGGAGTGGGCCGATAGAGCTATTGCCACTCCAGATAGTAGTGCGG\n+>Locus_66_Transcript_1/1_Confidence_1.000_Length_400\n+TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTAT\n+TAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAA\n+CGGATAGCTCTGATGCTGCTAATTACGGGACCTAATAATCCCCAATACTTTATCCTTAGA\n+GAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAG\n+GAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCGCCATTCTATTTT\n+TACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACG\n+AGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet/Ap_transcriptome_35099_oneline.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet/Ap_transcriptome_35099_oneline.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,398 @@\n+Locus_1_Transcript_1/1_Confidence_1.000_Length_257\n+TCAAGGAGCCCGGCTCGGACATTTGGACGTTGGTCAAGTCCCAGACTTTGATGGCCGTGTGGATGTTTGAGCCGGTGGCTATGTAGTTACTGTCTGAGCAGACGGCCATTGGGAAGTGGTCGTTGGTGTGCAGTCTGATTGTTGTGACCAGCTTGCAGTTCTCCGTGCTCCACAGGTGCAGGTTTTCGTGTGAGCCGGCCACGATATATCTGCCATCCATTGAGAAGTTAGCACCAAAAAGGAATGTCTTGTTGCTG\n+Locus_2_Transcript_1/2_Confidence_1.000_Length_264\n+TTGTTTCGGACTTGGTATCTGTGAGCATCAAGGGTTTTAGTATTTTGATTCTCTAGAAGTTGCACGTAGAAACACAGCATGGGAGCAGAAAAGAAACACATCAACATCGTGGTTATTGGCCACGTAGACTCCGGGAAGTCTACCACCACTGGCCATCTGATCTACAAGTGTGGTGGCATCGACAAGAGAACCATTGAAAAGTTCGAGAAGGAGGCCCAGGAGATGGGTAAAGGCTCCTTCAAGTATGCCTGGGTGTTGGACAAA\n+Locus_2_Transcript_2/2_Confidence_1.000_Length_242\n+CTTTTCATCCGGCTTCTCTAGGCGAAAGCTCTAGAAGTTGCACGTAGAAACACAGCATGGGAGCAGAAAAGAAACACATCAACATCGTGGTTATTGGCCACGTAGACTCCGGGAAGTCTACCACCACTGGCCATCTGATCTACAAGTGTGGTGGCATCGACAAGAGAACCATTGAAAAGTTCGAGAAGGAGGCCCAGGAGATGGGTAAAGGCTCCTTCAAGTATGCCTGGGTGTTGGACAAA\n+Locus_3_Transcript_1/1_Confidence_1.000_Length_558\n+GCGGATCAAAATGAAAACAGACGACGGTGTAAAATATGATCATGACACCGTGCGTTTGCAATCAAGGAATATTAATACTATGAATTTAGGCACTGATTTCTTAACATCACGATTTTCACCTCGGTTGCAATTAAGTAGAACGATTCTGGTTAGAACATGGTACAGTCTAGTTTTTCTCTCAAACACTTAGCTATGTTTCCACACAGTATGTGATGTACTGGATATTTCCTATTGATCCAGCATTCAAACAGTTTTTAACTTGCTCCGGCACTAGGCACTGGCAAGAGGGGTTATAAGGAGAAGACGGTCTAGGCAATAAAACAGTGCTGACACCTAGGGAGTTCAATGGAACCAGCCATATTATTACATTAAGCAAAAGCAACTAACTACTGAATGGTGAGCAAGAGGATTTCATGTCTTGCGCACTCTGTGATTGAAAACAAGAAACAAAAAGGAAAAAATAACTGACACCCGCATAACACACTTGATAAATGGTATACTTCTTTGAGCAAATGCTTGTCTAACAGCAATGTCAAAGATATAAAACAGACAGACAGA\n+Locus_4_Transcript_1/2_Confidence_1.000_Length_299\n+CAAACTTCTGACGGTGGAATCAGCACTTTCTTTAGACTTTGTCATGACGAGTCTGGCCCCTCCATCGTTCACAGGAAGTGCTTCTAAAGATAGTTGTGACCATCCCAACTGCCGTGACCACTCACAACAACAAACAACATTCTGTCTGCTCAGTGGCCCGTGGGCGACCTTTGTTCAGTGCCAGGGAACTCGTCATGACAAAGTCTAAAGAAAGTGCTGATTCCACCGTCAGAAGTTTGCTATACGAAATCCAGTCACACCATTCTGCTCTTCAAACATTACACAAACCAATCTTTTCC\n+Locus_4_Transcript_2/2_Confidence_1.000_Length_331\n+ACTCCGTATGGATTGGTGGATCGATCCTCGCCTCCCTGTCCACCTTCCAGCAGATGAGGATCAGCAAGCAGGAGTACGACGAGTCTGGACCATCCATCGTTCACAGGAAGTGCTTCTAAAGATAGTTGTGACCATCCCAACTGCCGTGACCACTCACAACAACAAACAACATTCTGTCTGCTCAGTGGCCCGTGGGCGACCTTTGTTCAGTGCCAGGGAACTCGTCATGACAAAGTCTAAAGAAAGTGCTGATTCCACCGTCAGAAGTTTGCTATACGAAATCCAGTCACACCATTCTGCTCTTCAAACATTACACAAACCAATCTTTTCC\n+Locus_5_Transcript_1/1_Confidence_1.000_Length_505\n+TAACAGTCCATCTCATGTTGGCGTGGATGAAACAGTAGACGTTCAGAAGCCTGCTACTTTGTTTACATGACAGCAAATCCCTCGATTGCTCTTCAAAGAATTCACAGTCCATGCATGTTGATGTAAACTGGTGTGGTCTGGTGACCAGCAAGCTTGGTTTGGTGCTTGTTTCACTGTGTGTCCTTTGAACAGTAATGTGTAACATTAATCCCTTTGTGAAGATCATTCTTCATTTCAATGCATCACTCTTCTCTCTAGGAAATTCTTCCAAGCTGTTTGGTTTTAATGTTGAATTCGATCAGGAGGCTGCCTTGCAATCTAGGAAATTGTCGCTTTTAACTATTTATTCCTTAGTGTAAATTGTTTCTTTGTTAGCACAATTGGTTGAACTCTATTCAAGTGCATGCCAGTGAAGGAAGCATTATTGAAATTTGCAATGTATTTATTTTAAGATGTCATTTTCTTCAATAAACAAGTATGCTGCAGTTTGTTCTGCCAAAAAAAA\n+Locus_6_Transcript_1/1_Confidence_1.000_Length_375\n+AAAATATACAGATTTAATAACAGCAATTGATAAACACTTTGAAAGCAAATTGTCATCTGTTGAGAAAGATGACATATTATTATCAGAATCTCACTTTGCACAATGTGGTTCTTTGTCTGACACAGTTAGCAGCTATCTTCACACTGTGATGACAGTCTCCAAGTGGAAGAAGAAAGTCAAAGCAATGCAGCAGACACCAGGACAACCACTACTTCTAATTATTTGTAGTGCTGCAAGTCGAGCAGTAGACTTGATAAGAGATTTGAGGTCCTTTTCTCAAGATAATTGTAAAGTTGCAAAGCTATTTGCAAAACACATGAAGCTGGAAGAACAAGTAAAATTCTTGAAGAAAAATGTAATACAGGCAGGAGTTGG\n+Locus_7_Transcript_1/2_Confidence_1.000_Length_290\n+GCAGAAGGAAAGGCCCAAAGGGTTGTCCCGATGTCCGTCCCGCGGGCCAGACTCGACCCTCTCCGGCAGATCGGCAGCCCCAGTACCACCCTGCCAGATCGTGTTCGGGTGGGTTTTTTATCGACCTGCCGGGGACTGGCCGAGTAGTGACCGATCACGGGCGAACCGGAAACCGACACGACAACCCCGGACATCAGAAGACGGGACGACACACACACGCAAACGGAGAGATAGACGCAAGACGACTACATCAGCACAGACGTCCGCCGCACACGGACTCGGACGCGGAC\n+Locus_7_Transcript_2/2_Confidence_1.000_Length_292\n+GCAGAAGGAAAGGCCCAAAGGGTTGTCCCGATGTCCGTCCCGCGGGCCAGACTCGACCCTCTCCGGCAGATCGGCAGCCCCAGTACCACCCTGCCAGATCGTGTTCGGGTGGGTTTTTTATCGACCTGCCGGGGACTGGCCGAGTAGTGACCGATCACGGGCGAACCGGAAACCGACACGACAACCCCGGACATCAGAAGACGGGACGACACACACACGCACGAACGGAGAGATAGACGCAAGACGACTACATCAGCACAGACGTCCGCCGCACACGGACTCGGACGCGGAC\n+Locus_8_Transcript_1/1_Conf'..b'GTAGGGCAATTTCTACGTCGAAGATTAGAAAGATTACTGCAAGTAAAAAAAATCGTAAAGAAAATGGGGTTCGGGCCGAGTG\n+Locus_65_Transcript_3/7_Confidence_0.278_Length_914\n+CAGATAGTAGTGCGGAGATAAATAAAATGTTGGTTGGTGTTGCTTTGACTAGGGTGTTGTAGCATATCATAGAGATAGGGAAGGTGTTTAAGCTTCCTGGTTTTAGGCTTAGAACGCCCTACCTTAACAATTACTATCTCCGCACTACTATCTGGAGTGGCAATAGCTCTATCGGCCCACTCCATGCTATCGATATGAATGGGCCTTGAACTCAACCTATTCGGCTTCATTCCCCTTATTATAGCAACAAGATCTAATCAAGAAAAAGAGGCAGCCTGTAAATACTTTCTAGCCCAAGCCATCCCATCCGCTATCTTTCTACTAGCCCTAGTATTAATACCAGACATCCCTACAACCTCTGCCGTAATTCTCGTCGCACTATTTATAAAAATAGGAATCGCCCCATGTCACCAATGATTTCCTTCTGTTATAAACGCACTAGCTTGGCCGCAAGCATGGACCCTCATTACTGTACAAAAAATTGCACCATTCTTCATAATTCTCCACATAGTTGGTAACACGACCATTCTCACTTTCCATAGCAGCCGCTATTTCATCTATTATTGGCGGACTAGGCGGCATAAATCAAACACAACTACGCCCACTATTGGCCTACTCATCTATCGGGCACATAGGCTGAATACTAGGAGCAGTTTTAGTTTCAAATAGCGCTGCCACGCTCTATTTCTCTTCTTATCTCTTTATTGTATCAACAACAATTCTAAGCGCCGTTCTATTAAAAACTAACTCCTTGTTTTCCCTACCACTATTTAAATCATCAACAACTCTATCAACCATTCTATTCCTCTCCTTCATAAACATAGGGGGCCTTCCTCCATTCTTCGGTTTCTTTATTAAAGCTTTCGTAATACTTAACTTACTTTCCAGCAATCTGGCCCCCCTCACCTTCTTCT\n+Locus_65_Transcript_4/7_Confidence_0.111_Length_302\n+CAGATAGTAGTGCGGAGATAAATAAAATGTTGGTTGGTGTTGCTTTGACTAGGGTGTTGTAGCATATCATAGAGATAGGGAAGGTGTTTAAGCTTCCTGGTTTTAGGCTTAGAACGCCCTACCTTAACAATTACTATCTCACATGGTTTTATTTTATGGGGTTCAATTTAGAGACCCCTCTCGTCACTCATGAAAAATACCGAGAAGAAGAATTAGTACAAATAAAAAAGCTGGAAGAATGGCCTGAGAAATAATAGTTGAGGATGGGAGGAGTGGGATCGGTATTAGTAGGGCAATTTCTA\n+Locus_65_Transcript_5/7_Confidence_0.185_Length_374\n+CACTCGGCCCGAACCCCATTTTCTTTACGATTTTTTTTACTTGCAGTAATATTTCTAATCTTCGACGTAGAAATTGCCCTACTAATACCGATCCCACTCCTCCCATCCTCAACTATTATTTCTCAGGCCATTCTTCCAGCTTTTTTATTTGTACTAATTCTTCTTCTCGGTATTTTTCATGAGTGACGAGAGGGGTCTCTAAATTGAACCCCATAAAATAAAACCATGTGAGATAGTAATTGTTAAGGTAGGGCGTTCTAAGCCTAAAACCAGGAAGCTTAAACACCTTCCCTATCTCTATGATAAGCTACAACACCCTAGTCAAAGCAACACCAACCAACATTTTATTTATCTCCGCACTACTATCTGGAGTG\n+Locus_65_Transcript_6/7_Confidence_0.222_Length_821\n+CAGATAGTAGTGCGGAGATAAATAAAATGTTGGTTGGTGTTGCTTTGACTAGGGTGTTGTAGCATATCATAGAGATAGGGAAGGTGTTTAAGCTTCCTGGTTTTAGGCTTAGAACGCCCTACCTTAACAATTACTATCTCCGCACTACTATCTGGAGTGGCAATAGCTCTATCGGCCCACTCCATGCTATCGATATGAATGGGCCTTGAACTCAACCTATTCGGCTTCATTCCCCTTATTATAGCAACAAGATCTAATCAAGAAAAAGAGGCAGCCTGTAAATACTTTCTAGCCCAAGCCATCCCATCCGCTATCTTTCTACTAGCCCTAGTATTAATACCAGACATCCCTACAACCTCTGCCGTAATTCTCGTCGCACTATTTATAAAAATAGGAATCGCCCCATGTCACCAATGATTTCCTTCTGTTATAAACGCACTAGCTTGGCCGCAAGCATGGACCCTCATTACTGTACAAAAAATTGCACCATTCTTCATAATTCTCCACATAGTTGGTAACACGACCATTCTCACTTTCCATAGCAGCCGCTATTTCATCTATTATTGGCGGACTAGGCGGCATAAATCAAACACAACTACGCCCACTATTGGCCTACTCATCTATCGGGCACATAGGCTGAATACTAGGAGCAGTTTTAGTTTCAAATAGCGCTGCCACGCTCTATTTCTCTTCTTATCTCTTTATTGTATCAACAACAATTCTAAGCGCCGTTCTATTAAAAACTAACTCCTTGTTTTCCCTACCACTATTTAAATCATCAACAACTCTATCAACCATTCTATTCCTCTCCTTCATAAACA\n+Locus_65_Transcript_7/7_Confidence_0.204_Length_775\n+AGAAGAAGGTGAGGGGGGCCAGATTGCTGGAAAGTAAGTTAAGTATTACGAAAGCTTTAATAAAGAAACCGAAGAATGGAGGAAGGCCCCCTATGTTTATGAAGGAGAGGAATAGAATGGTTGATAGAGTTGTTGATGATTTAAATAGTGGTAGGGAAAACAAGGAGTTAGTTTTTAATAGAACGGCGCTTAGAATTGTTGTTGATACAATAAAGAGATAAGAAGAGAAATAGAGCGTGGCAGCGCTATTTGAAACTAAAACTGCTCCTAGTATTCAGCCTATGTGCCCGATAGATGAGTAGGCCAATAGTGGGCGTAGTTGTGTTTGATTTATGCCGCCTAGTCCGCCAATAATAGATGAAATAGCGGCTGCTATGGAAGTGAGAATGGTCGTGTTAACCAACTATGTGGAGAATTATGAAGAATGGTGCAATTTTTTGTACAGTAATGAGGGTCCATGCTTGCGGCCAAGCTAGTGCGTTTATAACAGAAGGAAATCATTGGTGACATGGGGCGATTCCTATTTTTATAAATAGTGCGACGAGAATTACGGCAGAGGTTGTAGGGATGTCTGGTATTAATACTAGGGCTAGTAGAAAGATAGCGGATGGGATGGCTTGGGCTAGAAAGTATTTACAGGCTGCCTCTTTTTCTTGATTAGATCTTGTTGCTATAATAAGGGGAATGAAGCCGAATAGGTTGAGTTCAAGGCCCATTCATATCGATAGCATGGAGTGGGCCGATAGAGCTATTGCCACTCCAGATAGTAGTGCGG\n+Locus_66_Transcript_1/1_Confidence_1.000_Length_400\n+TGATCGTCTTATAAACCTAACTTGAAAAACCTTCCTACCATTTAGGGCTAGCAGCCCTATTAATTATCACACCTATCGCAGCGCTCTCACTATAATTATAAGTATTGCGCCGGGTTTGAACGGATAGCTCTGATGCTGCTAATTACGGGACCTAATAATCCCCAATACTTTATCCTTAGAGAGCTGTACCTCTTAGCACCAGTCTTTTAAACTGGCGAAAGCACACTTTATGCTTCTAAGGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCGCCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet/Pg_transcriptome_90109.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet/Pg_transcriptome_90109.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,6995 @@\n+>Locus_11_Transcript_1/7_Confidence_0.136_Length_182\n+TCGGACACTTTATTCAGTTGTATCTTTATATACATCAAGCTTGGAACAGGATGTCCGATG\n+TTGGTACCTCTAATGTCCAGGCATCTCTTATTCTCTGTCACTCTTCCCTGTAACTTGCTT\n+GGTACCGCGTAGTCGACCCGTACGACGGGCAGCAATGAGACCAACCTTTCAGTCGAGATC\n+GG\n+>Locus_11_Transcript_2/7_Confidence_0.136_Length_162\n+GGTCTCATTGCTGCCCGTCGTACGGGTCGACTACGCGGTACCAAGCAAGTTACAGGGAAG\n+AGTGACAGAGAATAAGAGATGCCTGGACATTAGAGGTACCAACATCGGACATCCTGTTCC\n+AAGCTTGATGTATATAAAGATACAACTGAATAAAGTGTCCGA\n+>Locus_11_Transcript_3/7_Confidence_0.273_Length_685\n+ACCACCATGGGGATGCTCGAATTCATGGCAACACCACGAACTTTAGGCCAGCAGTTCCTC\n+TTGGCCTTGTACTTGTGATAGGCACGTCCAGCCTTCAGCATTGGCTTGTCGATACGTCCT\n+CCTCCAGCCACTACCCCAATACATGCTCGGTTAGTCGAGGGGATGACCTTCTTTGTTCCG\n+GATGGAAGCTTCACCCTAGTCCTTTTTGTTTCCGGATTGTGGGAGATGACAGTGGCATAG\n+TTACCAAGCACTTGGCCAGTCGTCCACGATCTCCAGTCTTCTCTTCCAGTGAGCACACGA\n+CTGTACCCTCAGGCATCACACCGACGGGAAGGATGTTTCCTATCTGGAGTGTGGCCTTTT\n+TGCCGCAGTAAATGAACTGTCCGGTGTACATGCCCTCGCAGGCGATGAAGTTCTCATGTC\n+TCAGCTTGTACCTATATGGATCACGGAAAACGACACGTGCCAATGGAGCGCCACGTCCTG\n+GATCATGAATGATGTCCCTTATAACACCTTTGATATAGCCATGTCTTTCAGAAAAATCAA\n+ATGCTCGAAGTCTTGCAGCACCTTTCCTGTGTTTCGTGTGTGCCTTGAATACACTGCCAG\n+CACCCTTACGCTGACTCCTGATTACTCGACCCATTGTCGGACCACACCTATAACCCGAAC\n+ATACCTCCTAAACAAACACAACAAC\n+>Locus_11_Transcript_4/7_Confidence_0.273_Length_685\n+GTTGTTGTGTTTGTTTAGGAGGTATGTTCGGGTTATAGGTGTGGTCCGACAATGGGTCGA\n+GTAATCAGGAGTCAGCGTAAGGGTGCTGGCAGTGTATTCAAGGCACACACGAAACACAGG\n+AAAGGTGCTGCAAGACTTCGAGCATTTGATTTTTCTGAAAGACATGGCTATATCAAAGGT\n+GTTATAAGGGACATCATTCATGATCCAGGACGTGGCGCTCCATTGGCACGTGTCGTTTTC\n+CGTGATCCATATAGGTACAAGCTGAGACATGAGAACTTCATCGCCTGCGAGGGCATGTAC\n+ACCGGACAGTTCATTTACTGCGGCAAAAAGGCCACACTCCAGATAGGAAACATCCTTCCC\n+GTCGGTGTGATGCCTGAGGGTACAGTCGTGTGCTCACTGGAAGAGAAGACTGGAGATCGT\n+GGACGACTGGCCAAGTGCTCTGGTAACTATGCCACTGTCTCTCCCACAATCCGGAAACAA\n+AAAGGACTAGGGTGAAGCTTCCATCCGGAACAAAGAAGGTCATCCCCTCGACTAACCGAG\n+CATGTATTGGGGTAGTGGCTGGAGGAGGACGTATCGACAAGCCAATGCTGAAGGCTGGAC\n+GTGCCTATCACAAGTACAAGGCCAAGAGGAACTGCTGGCCTAAAGTTCGTGGTGTTGCCA\n+TGAATTCGAGCATCCCCATGGTGGT\n+>Locus_11_Transcript_5/7_Confidence_0.409_Length_917\n+TCGGACACTTTATTCAGTTGTATCTTTATATACATCAAGCTTGGAACAGGATGTCCGATG\n+TTGGTACCTCTAATGTCCAGGCATCTCTTATTCTCTGTCACTCTTCCCTGTAACTTGCTT\n+GGTACCGCGTAGTCGACCCGTACGACGGGCAGCAATGAGACCAACCTTTCTACCGGCGGA\n+TGTGTCTCTTCTGACAGTTGAAGCCTTACCAATATGTTGATGGTTACCACCACCATGGGG\n+ATGCTCGACTGGATTCATGGCAACACCACGAACTTTAGGCCAGCAGTTCCTCTTGGCCTT\n+GTACTTGTGATAGGCACGTCCAGCCTTCAGCATTGGCTTGTCGATACGTCCTCCTCCAGC\n+CACTACCCCAATACATGCTCGGTTAGTCGAGGGGATGACCTTCTTTGTTCCGGATGGAAG\n+CTTCACCCTAGTCCTTTTTGTTTCCGGATTGTGGGAGATGACAGTGGCATAGTTACCAAG\n+CACTTGGCCAGTCGTCCACGATCTCCAGTCTTCTCTTCCAGTGAGCACACGACTGTACCC\n+TCAGGCATCACACCGACGGGAAGGATGTTTCCTATCTGGAGTGTGGCCTTTTTGCCGCAG\n+TAAATGAACTGTCCGGTGTACATGCCCTCGCAGGCGATGAAGTTCTCATGTCTCAGCTTG\n+TACCTATATGGATCACGGAAAACGACACGTGCCAATGGAGCGCCACGTCCTGGATCATGA\n+ATGATGTCCCTTATAACACCTTTGATATAGCCATGTCTTTCAGAAAAATCAAATGCTCGA\n+AGTCTTGCAGCACCTTTCCTGTGTTTCGTGTGTGCCTTGAATACACTGCCAGCACCCTTA\n+CGCTGACTCCTGATTACTCGACCCATTGTCGGACCACACCTATAACCCGAACATACCTCC\n+TAAACAAACACAACAAC\n+>Locus_11_Transcript_6/7_Confidence_0.409_Length_917\n+GTTGTTGTGTTTGTTTAGGAGGTATGTTCGGGTTATAGGTGTGGTCCGACAATGGGTCGA\n+GTAATCAGGAGTCAGCGTAAGGGTGCTGGCAGTGTATTCAAGGCACACACGAAACACAGG\n+AAAGGTGCTGCAAGACTTCGAGCATTTGATTTTTCTGAAAGACATGGCTATATCAAAGGT\n+GTTATAAGGGACATCATTCATGATCCAGGACGTGGCGCTCCATTGGCACGTGTCGTTTTC\n+CGTGATCCATATAGGTACAAGCTGAGACATGAGAACTTCATCGCCTGCGAGGGCATGTAC\n+ACCGGACAGTTCATTTACTGCGGCAAAAAGGCCACACTCCAGATAGGAAACATCCTTCCC\n+GTCGGTGTGATGCCTGAGGGTACAGTCGTGTGCTCACTGGAAGAGAAGACTGGAGATCGT\n+GGACGACTGGCCAAGTGCTCTGGTAACTATGCCACTGTCTCTCCCACAATCCGGAAACAA\n+AAAGGACTAGGGTGAAGCTTCCATCCGGAACAAAGAAGGTCATCCCCTCGACTAACCGAG\n+CATGTATTGGGGTAGTGGCTGGAGGAGGACGTATCGACAAGCCAATGCTGAAGGCTGGAC\n+GTGCCTATCACAAGTACAAGGCCAAGAGGAACTGCTGGCCTAAAGTTCGTGGTGTTGCCA\n+TGAATCCAGTCGAGCATCCCCATGGTGGTGGTAACCATCAACATATTGGTAAGGCTTCAA\n+CTGTCAGAAGAGACACATCCGCCGGTAGAAAGGTTGGTCTCATTGCTGCCCGTCGTACGG\n+GTCGACTACGCGGTACCAAGCAAGTTACAGGGAAGAGTGACAGAGAATAAGAGATGCCTG\n+GACATTAGAGGTACCAACATCGGACATCCTGTTCCAAGCTTGATGTATATAAAGATACAA\n+'..b'TGTCCTTGTC\n+AGTTATAGGTTTTTTGTTCTTTGACCATGTGACCTCCGGCTCTGGATAACCTGTTGTTTT\n+ACAGGTGAGCTTGAAGCCTTCACCTGCCTCAACATTAACTGGCTGTAACTTGCCCTTAAT\n+ATGTGGTGCAACCTTCTTCTTCTCGACACTAACAGTAACCTTCACGATGGTGGTACCTTT\n+GCCAGACTTGGCACTGACTCTGTACTCACCAGCATCATCAGCCGTAGCATCGACGACCTG\n+TAAGTAATACACATCACTGTCCATATCCCAGTCAACTTTGTACTTCTTGTCACCCTTTTT\n+CTTCGGCTTAATCTTATTCGTGTCCTTGAACCAGGTAACCTCTGCCTCCTCTTCAATTTG\n+ACAAGTTAACTTAAATGTTTCTCCTTCTGTCACAACCAATGGCTGAGGTTCTTTTGTAAA\n+CTTTGGACCTTCTGGCTTCTCCTTTGACTTCTTATCCTTTTCAACTTTTTCTTGTTTTTC\n+TTCTTCTTTCGGTGGTTCCTCTTCCTTTAGCTTTTCTTCTTCCTTAGGTTTTTCTGCTTC\n+TTTTACTTTTTCATCTTCTTTGGGTTTTTCCTCTACGGGTTTTTTTTCTGCCTCCTGCTC\n+TACAGCCTTTTCGGCTGCTTCCTTTGTTACTTCCTTTGTTATCTTCTCTTCCTTTTCAGT\n+CTCTTTCTTCTTTTTTTCCTTTTTCTCTTTCGGTTTTTCTTCTTTTGGCTCTTCCTTTTT\n+TTCCTTCTTCTTTTTCTTCTCTTCCTTTGGCTTATCTTCTGGTTTCTGCTCTTCTTCCTT\n+ATCAATTTTGTCCTCCACCACTTCCTTCTTTTTCTTCTTCTCCTTTGGTTTCTTTTCCTT\n+TGGACTTTCTTCCACCTTTTCCACGGCTTCTTCAACAACCTCTTGTGGCTTTTCTTCCTC\n+TCTTATTTCTTCTTTCTGTTTGTCTTCCTTGGGCTTCTCTTCCTTTGACCTTTCCTCTTC\n+AACCCTTTCTTCTTCCATCTTCTCTTCTATCGGCCCTTCCTCTTTAGACTTTTCTCCCTC\n+GGATCTTGGTTCTTTAGGTTTTTCTTTGTTGAGGATTTCTTCAGATGTTTCAATTATTTC\n+TTCCTCTATTACCTTCACTTCTTCAGGAACAGAGACAGCAACATTAACAGTTGCTGAGAC\n+GGTTCCGCCGTCATTGCTGGCGACAATGGTGTACTGGCCGGCATCATCTGGCGTGGTATC\n+GCTGATGAGCAACAGATGGACATCATCATTTGAGTCGAAGTCAAGTTTGACACGGTCAGT\n+TGACTTTTCAAACTGCTTACTCCCTTTGAACCAGGTGACCTCAGGCTTTGGTTGTCCTAA\n+GACGCGTGCACCGAGCGTAATGGTCTTTCCCGACTTCACGACGACGGGTTCGGGGAAGAG\n+ATCGAACCGAGGCAAAGAGACCGTTTTGTCGGTCACGACTTCCTCCAGTGTGATGTCGCC\n+GAATGCTTCGCTGTCGACGTCCACTGTGGAGTATATTGTCTCCTCAATGATGACGGTCTC\n+TTTCTTTACCACCGTCTCATTTGTCAGCTCCTCATTCTCCTCAAGTGACGTTTTTCCCTC\n+ATCCGTCTTATTTTCTTTAATTAATTTGGCTTCCTCTTTCATGGCTTCATCCACCGCAGA\n+CGGATTATTCACAGCTAATTTGGTTGCCATTTTGTCATCTTCTTCATCAGCTGCATTGCC\n+TCTTTCTTCTTCATCACCAGTAATGGGTGCCGCCATTTCTTTGACATCCGGCACGTCTTT\n+CTTGCTTTCTTTCATTGCCTCTGATATTTCCGAACTATTTTCTGCAGATGTACCATCCAC\n+CAGCGGGTTTGATTTCTCCTCAGCCGTTTCTTTTCTCGATTTCATCAGGATCAGCTGTGG\n+CTTACTGTCCGCCTCTTTTGACTCGATTTCTTCCAACAGCTCCTTGGTGTCTGCGATGTC\n+TATTTCTATGTTCAGATCCTGATCTGCGGAGATCTTCAGTGCCCTAGCAGCTTCTTCCTG\n+TACTATGGCCACTTCCGTTAGACCACCATCCCTGCCATCGGCACCCTGGCGCAGCCTGTT\n+CTCACCGGTATAGGAAATCGTGATGATGTCTTGTTTATCTTTATCTTTGTCCTCGACGAT\n+CACCGTCACGGTGACGGTCATCGAGACCTCGCCGTGAATGTTCGACGCTTTGACGGTGTA\n+ATCATCGGCATCATCAATGGTGCACTCTTTGATGATGAGCGTATACAAATCGGATGCAAC\n+ATCCCAGTGGATCTCTATGTGCTGATCCTGTTTCTTGGGCTTTAGCTCTTTATCGCCCTT\n+ATACCAAGTGACCTGAGGTTGAGGGTCACCTGCTACTTTGCAGCTAAGTTTTACGGTTTC\n+TCCTTCTTTCACAGTGACAGGCTCGGGGATGACTTCGAATCTTGGTCTTGGCAAATCTTC\n+TACTCTCTCTTCTTGCTCTGCGGCCAGCACTTCTTCCACGGATTCTTTTGGCTTCTGGTC\n+CATTTCCACTTCCTTTGGGGCGGTTTCTTTTATTGGTGGTTTTTCCTTCTTTTCAATTGC\n+TTCTTCTCCATCTTCAGATTCTTCATTTACTTCTATCCCTTTCACTTTCTGTTTTTTAAC\n+CTTCTTAATTTTCTTTCCTGATATGTCCACTTCTTCTTTCATCTTAATAATAATCTTTTT\n+CTTCTTCTTCTTTTTCACATCTTTCCCCTCAGATTCTCCTTCACTTGATTCTGACTCACT\n+CGATGTTACTTCAGAGTCAACAAGCTCAGACTCAATTTCTGTTGTCTCTTCTTCAGTAGT\n+AGTAAACTCAACCTCAACTTTATCAATCTTTTCGGATGTCTCCATCACATCAACTTCTGC\n+CTTTTCTATTCTTATAGATTCACTCAATGAACTAATATTCACTGACACTGTACAAGATTC\n+GGAGCCACAATCATTTGTAGCTTTCACTATGTAGTCACCAGAATCTTCAACTGTTGCATT\n+TTTAATTATCAACATGTTTAGGTCATTAGAAGTATCCCAGTCAACCTTCACACGACCTTC\n+TTTCTTTGGTTTGATTTTCTTCTCATCTTTATACCAAGTAATTGATGGATCTGGATTTCC\n+TGTGACCCGACACGTTAAACGGATTGTCTCTCCTTCGTTTACAGTGACTGGCTGCGGTTC\n+TGCGGTGATGACAGGGGCACTAGAGGCACGTGTCGCATCCAGCTGGTCATCAACTGGCTC\n+TTGCTTCACTCTTTCCGTTGGCTCCTTGGCTGGGTATCTTCACAGCGTCGTCCAGCTCAG\n+CCATGTCTTCACTGATGCCGACCTTGTTTTCCGCATAAACCCGAAAGAAATACTGATGGC\n+CTTCCTTAACTTTGGTCACAGTCAAAGTTAAGGTTGTGCCATTTGTCTGTCCGACCTTCT\n+TAAATTTATTTTTCTCGGCTTCTCTCATCACGATCAAGTAAGATGTTAGGTCCGTGTTGC\n+CGGCATCAATCGGTGCATCCCAGCTCAGCGTCACCGAACTACTGTTTACTTCCTTAACAA\n+TTAGATTTGTGGGAGCCGATGGCACGGTCTGAGGTTTCTCAGCAGATGGCTGTTGATGCT\n+TTTCAGAAGTGATTTCTTCTTCAGATGTCTGTTCGGGTTTGGGGGCTGTCTGCGCCTCGG\n+TTGTGATTTTGGCTTCAGACTGAGGCTCGGCTTCTGTGACTTTGCTCTCCGTGACCTCTA\n+CTTGCTCTTCTACTATTTCCACTTCTTCATCCTTCTTGATCACTTTTGATGTTATTTTTA\n+CCGCAGAATCTATCTCAGCAGCTGATTCACTGATGCCAGCACTGTTCTCGGCATAAACCC\n+TGATAAAGTATTCTTTGGCTGGCTCGATGTTAGAAGTAATGGAATATTTCAACGTACCGC\n+CAGACACTTTACCAACTT\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet/Pg_transcriptome_90109_oneline.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet/Pg_transcriptome_90109_oneline.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,398 @@\n+Locus_11_Transcript_1/7_Confidence_0.136_Length_182\n+TCGGACACTTTATTCAGTTGTATCTTTATATACATCAAGCTTGGAACAGGATGTCCGATGTTGGTACCTCTAATGTCCAGGCATCTCTTATTCTCTGTCACTCTTCCCTGTAACTTGCTTGGTACCGCGTAGTCGACCCGTACGACGGGCAGCAATGAGACCAACCTTTCAGTCGAGATCGG\n+Locus_11_Transcript_2/7_Confidence_0.136_Length_162\n+GGTCTCATTGCTGCCCGTCGTACGGGTCGACTACGCGGTACCAAGCAAGTTACAGGGAAGAGTGACAGAGAATAAGAGATGCCTGGACATTAGAGGTACCAACATCGGACATCCTGTTCCAAGCTTGATGTATATAAAGATACAACTGAATAAAGTGTCCGA\n+Locus_11_Transcript_3/7_Confidence_0.273_Length_685\n+ACCACCATGGGGATGCTCGAATTCATGGCAACACCACGAACTTTAGGCCAGCAGTTCCTCTTGGCCTTGTACTTGTGATAGGCACGTCCAGCCTTCAGCATTGGCTTGTCGATACGTCCTCCTCCAGCCACTACCCCAATACATGCTCGGTTAGTCGAGGGGATGACCTTCTTTGTTCCGGATGGAAGCTTCACCCTAGTCCTTTTTGTTTCCGGATTGTGGGAGATGACAGTGGCATAGTTACCAAGCACTTGGCCAGTCGTCCACGATCTCCAGTCTTCTCTTCCAGTGAGCACACGACTGTACCCTCAGGCATCACACCGACGGGAAGGATGTTTCCTATCTGGAGTGTGGCCTTTTTGCCGCAGTAAATGAACTGTCCGGTGTACATGCCCTCGCAGGCGATGAAGTTCTCATGTCTCAGCTTGTACCTATATGGATCACGGAAAACGACACGTGCCAATGGAGCGCCACGTCCTGGATCATGAATGATGTCCCTTATAACACCTTTGATATAGCCATGTCTTTCAGAAAAATCAAATGCTCGAAGTCTTGCAGCACCTTTCCTGTGTTTCGTGTGTGCCTTGAATACACTGCCAGCACCCTTACGCTGACTCCTGATTACTCGACCCATTGTCGGACCACACCTATAACCCGAACATACCTCCTAAACAAACACAACAAC\n+Locus_11_Transcript_4/7_Confidence_0.273_Length_685\n+GTTGTTGTGTTTGTTTAGGAGGTATGTTCGGGTTATAGGTGTGGTCCGACAATGGGTCGAGTAATCAGGAGTCAGCGTAAGGGTGCTGGCAGTGTATTCAAGGCACACACGAAACACAGGAAAGGTGCTGCAAGACTTCGAGCATTTGATTTTTCTGAAAGACATGGCTATATCAAAGGTGTTATAAGGGACATCATTCATGATCCAGGACGTGGCGCTCCATTGGCACGTGTCGTTTTCCGTGATCCATATAGGTACAAGCTGAGACATGAGAACTTCATCGCCTGCGAGGGCATGTACACCGGACAGTTCATTTACTGCGGCAAAAAGGCCACACTCCAGATAGGAAACATCCTTCCCGTCGGTGTGATGCCTGAGGGTACAGTCGTGTGCTCACTGGAAGAGAAGACTGGAGATCGTGGACGACTGGCCAAGTGCTCTGGTAACTATGCCACTGTCTCTCCCACAATCCGGAAACAAAAAGGACTAGGGTGAAGCTTCCATCCGGAACAAAGAAGGTCATCCCCTCGACTAACCGAGCATGTATTGGGGTAGTGGCTGGAGGAGGACGTATCGACAAGCCAATGCTGAAGGCTGGACGTGCCTATCACAAGTACAAGGCCAAGAGGAACTGCTGGCCTAAAGTTCGTGGTGTTGCCATGAATTCGAGCATCCCCATGGTGGT\n+Locus_11_Transcript_5/7_Confidence_0.409_Length_917\n+TCGGACACTTTATTCAGTTGTATCTTTATATACATCAAGCTTGGAACAGGATGTCCGATGTTGGTACCTCTAATGTCCAGGCATCTCTTATTCTCTGTCACTCTTCCCTGTAACTTGCTTGGTACCGCGTAGTCGACCCGTACGACGGGCAGCAATGAGACCAACCTTTCTACCGGCGGATGTGTCTCTTCTGACAGTTGAAGCCTTACCAATATGTTGATGGTTACCACCACCATGGGGATGCTCGACTGGATTCATGGCAACACCACGAACTTTAGGCCAGCAGTTCCTCTTGGCCTTGTACTTGTGATAGGCACGTCCAGCCTTCAGCATTGGCTTGTCGATACGTCCTCCTCCAGCCACTACCCCAATACATGCTCGGTTAGTCGAGGGGATGACCTTCTTTGTTCCGGATGGAAGCTTCACCCTAGTCCTTTTTGTTTCCGGATTGTGGGAGATGACAGTGGCATAGTTACCAAGCACTTGGCCAGTCGTCCACGATCTCCAGTCTTCTCTTCCAGTGAGCACACGACTGTACCCTCAGGCATCACACCGACGGGAAGGATGTTTCCTATCTGGAGTGTGGCCTTTTTGCCGCAGTAAATGAACTGTCCGGTGTACATGCCCTCGCAGGCGATGAAGTTCTCATGTCTCAGCTTGTACCTATATGGATCACGGAAAACGACACGTGCCAATGGAGCGCCACGTCCTGGATCATGAATGATGTCCCTTATAACACCTTTGATATAGCCATGTCTTTCAGAAAAATCAAATGCTCGAAGTCTTGCAGCACCTTTCCTGTGTTTCGTGTGTGCCTTGAATACACTGCCAGCACCCTTACGCTGACTCCTGATTACTCGACCCATTGTCGGACCACACCTATAACCCGAACATACCTCCTAAACAAACACAACAAC\n+Locus_11_Transcript_6/7_Confidence_0.409_Length_917\n+GTTGTTGTGTTTGTTTAGGAGGTATGTTCGGGTTATAGGTGTGGTCCGACAATGGGTCGAGTAATCAGGAGTCAGCGTAAGGGTGCTGGCAGTGTATTCAAGGCACACACGAAACACAGGAAAGGTGCTGCAAGACTTCGAGCATTTGATTTTTCTGAAAGACATGGCTATATCAAAGGTGTTATAAGGGACATCATTCATGATCCAGGACGTGGCGCTCCATTGGCACGTGTCGTTTTCCGTGATCCATATAGGTACAAGCTGAGACATGAGAACTTCATCGCCTGCGAGGGCATGTACACCGGACAGTTCATTTACTGCGGCAAAAAGGCCACACTCCAGATAGGAAACATCCTTCCCGTCGGTGTGATGCCTGAGGGTACAGTCGTGTGCTCACTGGAAGAGAAGACTGGAGATCGTGGACGACTGGCCAAGTGCTCTGGTAACTATGCCACTGTCTCTCCCACAATCCGGAAACAAAAAGGACTAGGGTGAAGCTTCCATCCGGAACAAAGAAGGTCATCCCCTCGACTAACCGAGCATGTATTGGGGTAGTGGCTGGAGGAGGACGTATCGACAAGCCAATGCTGAAGGCTGGACGTGCCTATCACAAGTACAAGGCCAAGAGGAACTGCTGGCCTAAAGTTCGTGGTGTTGCCATGAATCCAGTCGAGCATCCCCATGGTGGTGGTAACCATCAACATATTGGTAAGGCTTCAACTGTCAGAAGAGACACATCCGCCGGTAGAAAGGTTGGTCTCATTGCTGCCCGTCGTACGGGTCGACTACGCGGTACCAAGCAAGTTACAGGGAAGAGTGACAGAGAATAAGAGATGCCTGGACATTAGAGGTACCAACATCGGACATCCTGTTCCAAGCTTGATGTATATAAAGATACAACTGAATAAAGTGTCCGA\n+Locus_11_Transcript_7/7_Confidence_0.409_Length_917\n+TCGGACACTTTATTCAGTTGTATCTTTATATACATCAAGCTTGGAACAG'..b'ACATTAACACTTTGTGATGTGCTACCAACAGAGTTAGTTGCCGTTACTGTGTACTCAGCCGTGTCCTCAACAAGAGACTCTTTCACCTTCAGAGTGTAAGAGTTGTCCTTCGAGATCATCTTGTAATGACTGTCCTTGTCAGTTATAGGTTTTTTGTTCTTTGACCATGTGACCTCCGGCTCTGGATAACCTGTTGTTTTACAGGTGAGCTTGAAGCCTTCACCTGCCTCAACATTAACTGGCTGTAACTTGCCCTTAATATGTGGTGCAACCTTCTTCTTCTCGACACTAACAGTAACCTTCACGATGGTGGTACCTTTGCCAGACTTGGCACTGACTCTGTACTCACCAGCATCATCAGCCGTAGCATCGACGACCTGTAAGTAATACACATCACTGTCCATATCCCAGTCAACTTTGTACTTCTTGTCACCCTTTTTCTTCGGCTTAATCTTATTCGTGTCCTTGAACCAGGTAACCTCTGCCTCCTCTTCAATTTGACAAGTTAACTTAAATGTTTCTCCTTCTGTCACAACCAATGGCTGAGGTTCTTTTGTAAACTTTGGACCTTCTGGCTTCTCCTTTGACTTCTTATCCTTTTCAACTTTTTCTTGTTTTTCTTCTTCTTTCGGTGGTTCCTCTTCCTTTAGCTTTTCTTCTTCCTTAGGTTTTTCTGCTTCTTTTACTTTTTCATCTTCTTTGGGTTTTTCCTCTACGGGTTTTTTTTCTGCCTCCTGCTCTACAGCCTTTTCGGCTGCTTCCTTTGTTACTTCCTTTGTTATCTTCTCTTCCTTTTCAGTCTCTTTCTTCTTTTTTTCCTTTTTCTCTTTCGGTTTTTCTTCTTTTGGCTCTTCCTTTTTTTCCTTCTTCTTTTTCTTCTCTTCCTTTGGCTTATCTTCTGGTTTCTGCTCTTCTTCCTTATCAATTTTGTCCTCCACCACTTCCTTCTTTTTCTTCTTCTCCTTTGGTTTCTTTTCCTTTGGACTTTCTTCCACCTTTTCCACGGCTTCTTCAACAACCTCTTGTGGCTTTTCTTCCTCTCTTATTTCTTCTTTCTGTTTGTCTTCCTTGGGCTTCTCTTCCTTTGACCTTTCCTCTTCAACCCTTTCTTCTTCCATCTTCTCTTCTATCGGCCCTTCCTCTTTAGACTTTTCTCCCTCGGATCTTGGTTCTTTAGGTTTTTCTTTGTTGAGGATTTCTTCAGATGTTTCAATTATTTCTTCCTCTATTACCTTCACTTCTTCAGGAACAGAGACAGCAACATTAACAGTTGCTGAGACGGTTCCGCCGTCATTGCTGGCGACAATGGTGTACTGGCCGGCATCATCTGGCGTGGTATCGCTGATGAGCAACAGATGGACATCATCATTTGAGTCGAAGTCAAGTTTGACACGGTCAGTTGACTTTTCAAACTGCTTACTCCCTTTGAACCAGGTGACCTCAGGCTTTGGTTGTCCTAAGACGCGTGCACCGAGCGTAATGGTCTTTCCCGACTTCACGACGACGGGTTCGGGGAAGAGATCGAACCGAGGCAAAGAGACCGTTTTGTCGGTCACGACTTCCTCCAGTGTGATGTCGCCGAATGCTTCGCTGTCGACGTCCACTGTGGAGTATATTGTCTCCTCAATGATGACGGTCTCTTTCTTTACCACCGTCTCATTTGTCAGCTCCTCATTCTCCTCAAGTGACGTTTTTCCCTCATCCGTCTTATTTTCTTTAATTAATTTGGCTTCCTCTTTCATGGCTTCATCCACCGCAGACGGATTATTCACAGCTAATTTGGTTGCCATTTTGTCATCTTCTTCATCAGCTGCATTGCCTCTTTCTTCTTCATCACCAGTAATGGGTGCCGCCATTTCTTTGACATCCGGCACGTCTTTCTTGCTTTCTTTCATTGCCTCTGATATTTCCGAACTATTTTCTGCAGATGTACCATCCACCAGCGGGTTTGATTTCTCCTCAGCCGTTTCTTTTCTCGATTTCATCAGGATCAGCTGTGGCTTACTGTCCGCCTCTTTTGACTCGATTTCTTCCAACAGCTCCTTGGTGTCTGCGATGTCTATTTCTATGTTCAGATCCTGATCTGCGGAGATCTTCAGTGCCCTAGCAGCTTCTTCCTGTACTATGGCCACTTCCGTTAGACCACCATCCCTGCCATCGGCACCCTGGCGCAGCCTGTTCTCACCGGTATAGGAAATCGTGATGATGTCTTGTTTATCTTTATCTTTGTCCTCGACGATCACCGTCACGGTGACGGTCATCGAGACCTCGCCGTGAATGTTCGACGCTTTGACGGTGTAATCATCGGCATCATCAATGGTGCACTCTTTGATGATGAGCGTATACAAATCGGATGCAACATCCCAGTGGATCTCTATGTGCTGATCCTGTTTCTTGGGCTTTAGCTCTTTATCGCCCTTATACCAAGTGACCTGAGGTTGAGGGTCACCTGCTACTTTGCAGCTAAGTTTTACGGTTTCTCCTTCTTTCACAGTGACAGGCTCGGGGATGACTTCGAATCTTGGTCTTGGCAAATCTTCTACTCTCTCTTCTTGCTCTGCGGCCAGCACTTCTTCCACGGATTCTTTTGGCTTCTGGTCCATTTCCACTTCCTTTGGGGCGGTTTCTTTTATTGGTGGTTTTTCCTTCTTTTCAATTGCTTCTTCTCCATCTTCAGATTCTTCATTTACTTCTATCCCTTTCACTTTCTGTTTTTTAACCTTCTTAATTTTCTTTCCTGATATGTCCACTTCTTCTTTCATCTTAATAATAATCTTTTTCTTCTTCTTCTTTTTCACATCTTTCCCCTCAGATTCTCCTTCACTTGATTCTGACTCACTCGATGTTACTTCAGAGTCAACAAGCTCAGACTCAATTTCTGTTGTCTCTTCTTCAGTAGTAGTAAACTCAACCTCAACTTTATCAATCTTTTCGGATGTCTCCATCACATCAACTTCTGCCTTTTCTATTCTTATAGATTCACTCAATGAACTAATATTCACTGACACTGTACAAGATTCGGAGCCACAATCATTTGTAGCTTTCACTATGTAGTCACCAGAATCTTCAACTGTTGCATTTTTAATTATCAACATGTTTAGGTCATTAGAAGTATCCCAGTCAACCTTCACACGACCTTCTTTCTTTGGTTTGATTTTCTTCTCATCTTTATACCAAGTAATTGATGGATCTGGATTTCCTGTGACCCGACACGTTAAACGGATTGTCTCTCCTTCGTTTACAGTGACTGGCTGCGGTTCTGCGGTGATGACAGGGGCACTAGAGGCACGTGTCGCATCCAGCTGGTCATCAACTGGCTCTTGCTTCACTCTTTCCGTTGGCTCCTTGGCTGGGTATCTTCACAGCGTCGTCCAGCTCAGCCATGTCTTCACTGATGCCGACCTTGTTTTCCGCATAAACCCGAAAGAAATACTGATGGCCTTCCTTAACTTTGGTCACAGTCAAAGTTAAGGTTGTGCCATTTGTCTGTCCGACCTTCTTAAATTTATTTTTCTCGGCTTCTCTCATCACGATCAAGTAAGATGTTAGGTCCGTGTTGCCGGCATCAATCGGTGCATCCCAGCTCAGCGTCACCGAACTACTGTTTACTTCCTTAACAATTAGATTTGTGGGAGCCGATGGCACGGTCTGAGGTTTCTCAGCAGATGGCTGTTGATGCTTTTCAGAAGTGATTTCTTCTTCAGATGTCTGTTCGGGTTTGGGGGCTGTCTGCGCCTCGGTTGTGATTTTGGCTTCAGACTGAGGCTCGGCTTCTGTGACTTTGCTCTCCGTGACCTCTACTTGCTCTTCTACTATTTCCACTTCTTCATCCTTCTTGATCACTTTTGATGTTATTTTTACCGCAGAATCTATCTCAGCAGCTGATTCACTGATGCCAGCACTGTTCTCGGCATAAACCCTGATAAAGTATTCTTTGGCTGGCTCGATGTTAGAAGTAATGGAATATTTCAACGTACCGCCAGACACTTTACCAACTT\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet_out/AcAc_transcriptome_25591.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet_out/AcAc_transcriptome_25591.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,132 @@\n+>Ac1_1/1_1.000_2580\n+AAGACAACTGCTCTTGATAGTTGTCTCGGAAGAGACTTGAAAACATCCAAGATGGTGAACTTTACGGTAGACGAGATCCGTGCGATCATGGACAAGAAGAAGAACATACGTAACATGTCCGTGATTGCTCATGTGGATCATGGCAAGTCGACGCTGACTGATTCGTTGGTGAGCAAGGCTGGCATTATTGCTGGCTCCAAGGCTGGCGAGACCCGCTTCACAGACACAAGGAAGGATGAGCAGGAAAGATGTATTACCATCAAATCAACAGCAATTTCACTCTTTTACCAGCTGCCAGAAAAAGATTTGAAGTTGATCGAGCAGCCAAGAGAGGAGGGAGAGACTGCTTTCCTGATCAACTTGATTGACTCACCTGGTCACGTGGATTTCTCCTCGGAGGTGACTGCTGCCCTTCGTGTTACAGATGGTGCTCTGGTTGTTGTCGACTGTGTGTCGGGCGTGTGTGTACAAACAGAGACTGTGCTGCGTCAGGCCATTGCTGAGCGTATCAAGCCAGTACTGTTCATGAACAAGATGGACTTGGCTCTGCTGACCCTACAGCTTGGTGCTGAGGACCTCTACCAGACCTTCTCCCGTATCATTGAAAGCATCAATGTAATCATTGCCACTTATGCTGACGACGAGGGACCGATGGGTAACATCCATGTTGATCCATCCAAGGGTACAGTTGGCTTTGGATCTGGACTCCATGGCTGGGCATTCACACTGAAGCAGTTTGCCGAGATGTATGCAGACAAGTTCAAGATTGAGGAACCAAAACTGATGAAGAGGCTGTGGGGAGACCAGTTCTACAACCCAAAGGAGAAGAGATGGGGCAAAGAAATGCAGAAGGGCTATTGTCGTGGTTTCACACAATACATCCTTGACCCCATTTACAAGATGTTTGAGTTCTGCATGAAGAAGCCAAAGGAAGAGACACTGAAGCTGGTTGAGAAACTTGGCATCAAACTGACAAGTGATGACAAGGACCTCATAGACAAACAACTGTTGAAGGTTGTCATGCGTAAATGGCTGCCAGCTGGTGATGCTTTGCTTCAGATGATAACCATCCATCTGCCGTCACCAGTAGCGGCTCAGAGGTACCGTATGGAGATGCTGTATGAGGGGCCACATGACGATGAGGCTGCTCTGGGAATCAAGAACTGTGACCCCAATGGACCACTGATGATGTACATCTCCAAGATGGTACCAACATCAGACAAGGGTAGATTCTATGCATTTGGTCGTGTGTTCTCTGGTGTTGTGTCAACAGGTATGAAGGCTAGGATCATGGGTCCCAACTTTATCCCTGGGAAGAAGGAAGATCTCTATGTGAAGGCCATCCAGAGAACAATCCTTATGATGGGTCGTTACATAGAGCCAATTGAAGATGTGCCCTGTGGTAATGTTTGTGGTCTGGTTGGTGTTGACCAGTACATTCTGAAGACTGGAACCATCAGCACGTACGAGCATGCCCACAACTTGAAAGTGATGAAGTTCAGTGTCAGTCCAGTTGTGCGTGTGGCTGTTGAGTGTAAAAACCCAGCTGATCTGCCCAAGCTTGTTGAAGGATTGAAACGTCTGTCAAAATCTGATCCCCTGGTGCAGTGTTCCATTGAGGAATCTGGAGAGCACATTGTTGCTGGAGCTGGTGAACTTCATCTGGAAATCTGCCTCAAGGACTTGGAAGAAGATCATGCCTGCATCCCAATCAAGAAATCTGACCCTGTTGTCTCATATAGAGAGACTGTCAGTAACACATCTGACAGAACCTGCTTGTCAAAATCACCAAACAAGCACAATCGTCTCTTCATGGTTGCTGCACCACTGCCAGATGGCTTACCTGAAGAGATTGATAGGGGAGAGAAGGTCAGTGCTCGTCAGGATCAGAAGGAGAGAGCTAGATACCTGGCCGACACATACGAGTTTGATGTTACTGAGGCTCGTAAGATCTGGTGCTTTGGACCTGATGGCACAGGACCAAACCTGGTCATTGACTGCACAAAGGGTGTCCAGTACCTGAATGAAATCAAAGACAGTGTTGTGGCTGGCTTCCAGTGGGCTAGCAAGGAGGGTGTACTCTGTGAAGAGAACATGAGAGGAATCCGCTTCAACATTCTTGATGTCACACTGCATGCTGATGCTATTCACCGTGGTGGTGGCCAGATCATCCCAACAACAAGAAGATGTCTCTATGCATGTGTGCTGACAGCTGAACCAAGGTTGATGGAACCAATATACCTGGTTGAGATCCAGTGCCCTGAGCAAGCTGTTGGTGGCATTTATGGTGTGCTGAACAGAAGACGAGGTGTTGTCATTGAGGAGAACCAAGTGGTGGGAACCCCGATGTTCCAGGTCAAGGCATACCTTCCTGTAAACGAATCATTTGGTTTCACTGCCGACCTGAGGTCCAACACTGGTGGCCAGGCATTCCCACAGTGTGTGTTTGATCACTGGCAGATCCTCCCAGGCGATCCGTTTGTGGACAACTCCAAGCCTAACATAATCGTCCAAGAGACGAGAAAACGCAAAGGGCTGAAGGAGGGCGTTCCTCCACTGGACAACTTCCTGGACAAGTTG\n+>Ac2_1/1_1.000_5295\n+GAATTTTGGCCGAGATATCAGCTGATGACTGTAGCTTTGGTCTGGGCACTGGCCATTGTTCCCCAGGTGCTTTGTCAACTGATGATGACCACGACACCACCACCAACTCCAATAGCGTGTAGAGAAAATATGTGGGGTTGTGCCGACGGCAAGCAGTGTATACGTGAACTGTATCGTTGTGATGGTGATTACGACTGTGAGGACCGCTCTGACGAGGCCTTTCTTTTGTGTGCCCTCATTGTTTGCGATGAAAACAGCCAGTTTGAGTGTACTGCCAACAGGTTTACTAATAACACTAAGATCTGCATACCTGTTTCTTATTTGTGTGATGAGGACAATGATTGCGGAGATAACTCAGATGAAGATCCAGCCAACTGTCCTACCACATTCCGTCCTCCGACGACTCCACCGCCTTGTGTTCCTGGTTTCGAGTTCTTCTGTCCAGCTAGTCGTGACAGGGGCTGTATACCAATTGGTTTGAAATGTGACACTAAGCATGACTGTATGAATGGTGAAGATGAACAAGGCTGCACCTACAGAAATTGTTCTGATACAACGGAGTTTCAGTGTCATTCTAAGCAATGTATTGATAGCCGTCTGAAGTGTAATGGTTATGCCGACTGTAGGGATGGAAGTGATGAAACACCAGATATATGTGATGTTGCCCCTTTGCAGTGTGCAAAACATGAGTTTCAGTGTAACAATGGAAAGTGTATGGTTTGGTATGAAGTTCTCTGTAACGGAATAGACGACTGTGGTGATAATTCCGATGAAGATATCTGTAACACACTCCACATAAATGAATGTAACAATAAGACATTGCATCAATGTTCTGATAACTGCGAGGAGATGACTTTTGGCTACAGGTGTACTTGTAATCCTGGATACAGCTTAGCAAAAGATGGAAAAACATGCATCAATTCCAATGAATGCCTAGATTCACCAGGTGTGTGTCCACAGATTTGTATGGACACACCAGGAAGTTACAAATGTCAGTGTGCTACAGGCTACAGGGATATAAATGGAGATGGAACAAAGTGTGTTCGTACAGACAAAACCGAACCATATTTGATTTTCGGCAACAAGTACTATATACGCCGCATGGACATTGATGGTAGTAACTATGTCAGTATGTCCAGTGAACATACCTACACACATGTTTTGGACTTTGATTACCGCAATAAGAAGATATACTATGCCGATGCTCCAAATATGAAACAGGCAATAAAGAGAATGAACTTTGATGGCTCTGGGAAGGAGATTATTGAAAAGCATCATGCCACAGGCATCGAAGGAATTGCTGTTGACTGGGTTGGAGACAATATATACTGGACTAGCAACAAACAATGGGGGATG'..b'GCGTTGAGGGAAGCCATGTCTGGTCGGAGTACGCCGTCCAGACCGTCGGGTCAGACGGCAGCCAAACACTTGGGCACGGCGGCCGATAGACCGGCGCATCACACGGCACGGTCAAGGTCGAGGACTCGCCTGGAGAGACAGGACTCGACCGACTCAGAGAACAGCACCCCGACACGGACCGACCAACAGCGCCTACGTCTGCCCACCCCAGTCAGGCGGTCCGTGTCTCTGAAGGAAACCAGAAGCGTGCGCATCGTCGACGGTGACAGTCTGACGCTGCCAAGACGTAGGCCGCAGCCGG\n+>Ac61_1/1_1.000_237\n+ATGAATTGTTGGCAGAGAAGGAAAAGTACAAGACGATCAGCGAAGATTTGGACTCAACTTTTGCCGAGCTGGCTGGATTTTAAGGGTTATCTTCATTTGCCAATTACAAACACCACTACCACGACCATCACTACTACTGTTTCACCAGTGCTAACTGATGCAATATTCACTATTGAGATCATTCACCTATGTCTAATACAACCAAATAGAAAAGAAGGGAGATATTTCTTTAGAATA\n+>Ac62_1/1_1.000_189\n+CATTCTTCAACATGGTCCAACGTTGTAACGGTTTGTGTGGTAACTAGACTGGACTGGACTGGAGCAGGCCCCGTCATCGTCATGTCGAGCCGACTCACGGCGGTGGTCAATCTTCCACCACAGACCTCTTACCATGGCAGATCTGATATATGGACTTCATTAGCCAGATCGTCTCTACAACTTTTAAAC\n+>Ac63_1/1_1.000_279\n+TTACCACACAAACCGTTACAACGTTGGACCATGTTGAAGAATGCCTGGCCAGATATGTCCGGCTCCACGATCACTTCAAAGTCCTTCAGGATCTGCATGTTGGCCTGGCCACACGTGATCAAGTTCTTCAAGGCGTTCTGCGACGCTTGGCTCGGTTCTGAGTTAGTGAAGTCGCCGACCATGGCTACGCTTAAAGACGTGCCATCACGTCCTCAGCATCCTGTCCAGCCACGAGCCATCCTCTGCCTTCGTATATGGCGCCGTCTTGACCAATCAGGA\n+>Ac64_1/1_1.000_1023\n+AACCATATTAAACCCAAGATGGCTCCCAAGATTGGAATCAATGGTTTTGGACGTATTGGAAGGCTGGTGCTGAGAGCAGCTTTGGCCAAGGGCACAGTGGAGGTCGTGGCTGTGAATGATCCCTTCATTGATTTGGATTATATGGTTTACATGTTCAAGTATGACACAGTGCATGGACATTTCAAGGGCACAGTGACTGCTTCTGATGGCAAACTGGTTGTTGATGGAAAAGCTATCACAGTTTTTAACAAGATGAAGCCATCTGAAATACCATGGGGATCTGTTGGAGCTGATTACATTGTAGAGTCTACTGGAGTGTTTACTTCACTGGAGAAGGCTAAGGCTCATCTGGAAGGTGGAGCAAAGAAAGTGATCATCTCGGCTCCATCTGCTGATGCTCCAATGTTTGTGATGGGTGTCAACCAGGAGAAGTATGATCCCAAAATGACAATCATCAGCAATGCTTCCTGCACAACCAACTGCCTGGCTCCTCTGGCTAAGGTCATCAATGACAAATTTGGTATCATTGAGGGCCTCATGACTACAGTGCATGCCTACACAGCCACCCAGAAGACTGTTGATGGTCCAAGTGCCAAAGCCTGGCGTGATGGTCGACATGCTGCACAGAACATCATCCCAGCATCAACTGGTGCTGCCAAGGCTGTTGGAAAAGTCATCCCCGACCTCAATGGCAAGCTCACTGGCATGGCCTTCCGTGTCCCAGTGCCTGATGTTTCTGTTGTTGACTTGACATGCCGTCTCGCCAAGGAGGCCTCCTATGACGAGATCAAAGCTGCTGTGAAGGCTGCCGCAGAAGGACCAATGAAGGGTATACTTGGGTACACTGATGATTTTGTTGTGTCTTCTGACTTCATTGGTGATACACACAGCAGCATCTTTGATGCCAAGGCTGGAATTGCCCTGAGCCCAACCTTTGTCAAACTTGTCTCCTGGTACGACAATGAGTATGGCTACAGCTGCCGTGTCATTGATCTGATAACATATGTTGCTGGTCGTAATGCA\n+>Ac65_1/1_1.000_960\n+GTAGCGGTCACGGCGAGCCTCGTTGTCGTCTCGGCGCAGAGTAGCTCGGTCGGAGAAGGATTCATCATGCCGGAGAAAATGGCTGGATCTAATTGTTTCAAGTACAACTTCGCTCTGGTCAGCCGGATCGCGAACTCGTTCGCCGAGACGTCGAGCTTCGATCTGAAGCCGGGCGCGTCGCCGATCAACATCGAGAAGGCCCGCGCCGAGCACGAGCAGCTGGTCGACGCCCTGAGACGCATCAGCCTCGACGTGATAGAACTGCCGTGCGATGAGAAGCATCCGGACGGCTTGTTCGTCGACGACATAGCCGTCGTCATCAACGGAACGGCACTCATATGCCGACCGCAGTCGCCGCCGAACAAGCCCTCCAGGGAGGGAGAGCTGGCTGTCGTCCGACAGGTGCTAAGAAAGGAACTCGGACTTAAAGTTGTTGAAGTGGAGAACAAAGGAGATGAGGAAACGAAGCTGGAAGGTGGCGATGTCCTTTGGACAGGTAGAGAAATCTTTGTCGGTCTGTCTGAGCGTACCAACATGCAGGGTGCCCACGCCGTTGGCAGGACATTCCCTGAGTATCCAACAACTGTTGTCAAGGTCCACCCACCTGCCATACACCTGAAGGACTACATCAGCATGGCTGGACCAGAGATCATGGCCATTGGCAAAAGCGAAGGAGCCAGGAAGACATTCCAGGAGATGAAGGCATCAGGTGCCCCAGGCTACAAGTACATCATGGTTGAAGAAGATGAGGCAGCTAATGTATTGTACTGTAATGGTACATTGCTACATCTCTCCAGTGACCAAATACCCAAGGGATTTGCTGTCTATGAGAACAAGATCGACTGTCCACGTGTAGCCATTACAATGGAGGAACCACTGAAGAGAGGTGGACGGCTGGGCAGCTGCGTGCTGCTAATCAACCGTGTCAGACATCCTAAAAAGATTCCAACAACAGCACAG\n+>Ac66_1/1_1.000_870\n+TCAGACGTTGGTTTACAATCTTCTTCACCTCATCATATGTCAAGGCATACTTCAGGCGATTTCTCAAGAACACCACCGGACGAGATGGGTGTTCGTGGTCCAAGGAAGCATTTGAAGAGGCTTCATGCCCCTAAACACTGGATGTTGGACAAGCTTGGGGGTGTTTTTGCCCCACGCCCAAGCACTGGTCCACACAAGATGCGAGAGTGTCTCCCTCCGGTGGTGTTCTTGAGAAATCGCCTGAAGTATGCCTTGACATATGATGAGGTGAAGAAGATTGTAAACCAACGTCTGATCAAGGTTGATGGCAAAGTGAGAACTGACAAGACATACCCTGCTGGCTTTATGGATGTGATCACAATAGAGAAGACGGCTGAAAACTTCCGTCTCATCTATGATGTCAAAGGTCGTTTCACCATTCACCGTATCACTTCCCAAGAAGCCAAGTACAAACTGTGTAAGGTAAAGAAGATAATCATTGGACTGAAGGGAGTTCCACATCTGGTCACTCATGATGCTCGTACCATTCGCTATCCAGATCCAATGATCAAGGTCAATGACACAGTTCAGGTTGACATTGCCACAGGCAAGATAAAGGATTTCATCAAGTTTGAATCAGGAAATTTGTGCATGATCACTGGTGGGCACAACTTGGGTCGTGTTGGCCTTGTGACACACAGAGAACGTCATCCTGGTGGCTTTGATATTGTTCACATCAAGGACAGCATGGGCCACTCATTTGCCACACGTTTGAACAACGTGTTCATTATTGGTAAAGGTAACAAGCCGTGGGTGTCATTACCAGCTGGCAAGGGACTGAGGTTGACGATAGCAGAGGAACGTGACAAGAGGATCGCGGCAAAATCCCAG\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet_out/ApAp_transcriptome_35099.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet_out/ApAp_transcriptome_35099.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,130 @@\n+>Ap1_1/1_1.000_256\n+AGCAACAAGACATTCCTTTTTGGTGCTAACTTCTCAATGGATGGCAGATATATCGTGGCCGGCTCACACGAAAACCTGCACCTGTGGAGCACGGAGAACTGCAAGCTGGTCACAACAATCAGACTGCACACCAACGACCACTTCCCAATGGCCGTCTGCTCAGACAGTAACTACATAGCCACCGGCTCAAACATCCACACGGCCATCAAAGTCTGGGACTTGACCAACGTCCAAATGTCCGAGCCGGGCTCCTTGA\n+>Ap2_1/1_1.000_225\n+TTTGTCCAACACCCAGGCATACTTGAAGGAGCCTTTACCCATCTCCTGGGCCTCCTTCTCGAACTTTTCAATGGTTCTCTTGTCGATGCCACCACACTTGTAGATCAGATGGCCAGTGGTGGTAGACTTCCCGGAGTCTACGTGGCCAATAACCACGATGTTGATGTGTTTCTTTTCTGCTCCCATGCTGTGTTTCTACGTGCAACTTCTAGAGAATCAAAATAC\n+>Ap3_1/1_1.000_189\n+TTGCTTTTGCTTAATGTAATAATATGGCTGGTTCCATTGAACTCCCTAGGTGTCAGCACTGTTTTATTGCCTAGACCGTCTTCTCCTTATAACCCCTCTTGCCAGTGCCTAGTGCCGGAGCAAGTTAAAAACTGTTTGAATGCTGGATCAATAGGAAATATCCAGTACATCACATACTGTGTGGAAACA\n+>Ap4_1/1_1.000_330\n+CTCCGTATGGATTGGTGGATCGATCCTCGCCTCCCTGTCCACCTTCCAGCAGATGAGGATCAGCAAGCAGGAGTACGACGAGTCTGGACCATCCATCGTTCACAGGAAGTGCTTCTAAAGATAGTTGTGACCATCCCAACTGCCGTGACCACTCACAACAACAAACAACATTCTGTCTGCTCAGTGGCCCGTGGGCGACCTTTGTTCAGTGCCAGGGAACTCGTCATGACAAAGTCTAAAGAAAGTGCTGATTCCACCGTCAGAAGTTTGCTATACGAAATCCAGTCACACCATTCTGCTCTTCAAACATTACACAAACCAATCTTTTCC\n+>Ap5_1/1_1.000_229\n+AGAATGATCTTCACAAAGGGATTAATGTTACACATTACTGTTCAAAGGACACACAGTGAAACAAGCACCAAACCAAGCTTGCTGGTCACCAGACCACACCAGTTTACATCAACATGCATGGACTGTGAATTCTTTGAAGAGCAATCGAGGGATTTGCTGTCATGTAAACAAAGTAGCAGGCTTCTGAACGTCTACTGTTTCATCCACGCCAACATGAGATGGACTGTTA\n+>Ap6_1/1_1.000_374\n+AAATATACAGATTTAATAACAGCAATTGATAAACACTTTGAAAGCAAATTGTCATCTGTTGAGAAAGATGACATATTATTATCAGAATCTCACTTTGCACAATGTGGTTCTTTGTCTGACACAGTTAGCAGCTATCTTCACACTGTGATGACAGTCTCCAAGTGGAAGAAGAAAGTCAAAGCAATGCAGCAGACACCAGGACAACCACTACTTCTAATTATTTGTAGTGCTGCAAGTCGAGCAGTAGACTTGATAAGAGATTTGAGGTCCTTTTCTCAAGATAATTGTAAAGTTGCAAAGCTATTTGCAAAACACATGAAGCTGGAAGAACAAGTAAAATTCTTGAAGAAAAATGTAATACAGGCAGGAGTTGG\n+>Ap7_1/1_1.000_291\n+CAGAAGGAAAGGCCCAAAGGGTTGTCCCGATGTCCGTCCCGCGGGCCAGACTCGACCCTCTCCGGCAGATCGGCAGCCCCAGTACCACCCTGCCAGATCGTGTTCGGGTGGGTTTTTTATCGACCTGCCGGGGACTGGCCGAGTAGTGACCGATCACGGGCGAACCGGAAACCGACACGACAACCCCGGACATCAGAAGACGGGACGACACACACACGCACGAACGGAGAGATAGACGCAAGACGACTACATCAGCACAGACGTCCGCCGCACACGGACTCGGACGCGGAC\n+>Ap8_1/1_1.000_147\n+GCGCTGATTGTCATATTGTTATATAGTTCACGGCCTGGTCTGTCGGACAATGGCTCATACAACGCAGACTGCCACCTGAGAATATCTGAAAACTGGCAAATGCGTCATTTTACAAATCGCAGCTATCCAATTAATTATTTAGCTGGG\n+>Ap9_1/1_1.000_1956\n+CATTTTCCTTCACGCATTTCATCTGACTTCAAAGTCGCAGAAATGGTAACAACAACAGTGGCATCAGCTCAGGCCGCTGACTCGGACGCCATGGCCCGGTCATACGTGTACGACTTCAAGAACAACACGTTCTCTGTCTGGGATTACGTGGTGTTTGGTGGCGTGCTGGCAGTGTCTGCTGGGATCGGGATATACTACGGCTGTACGGGCGGCAGGCAGAGGACAACATCTGAGTTCCTTATGGCTGACAGAAAGATGCATGTCCTTCCCGTTACCTTGTCACTGCTAGCCAGCTTCATGTCTGCCATTACCTTACTAGGTACCCCAGCTGAAATCTACATGTTTGGCACTCAGTATTGGATGATATGGATTGGATATGTTATTATGATTCCACTAGCTACACACGTTTTCATTCCTGTCTTCTACAATCTACAATTGACAAGTGTATTTGAGTATCTACAAATGAGGTTCGGTACCCACGTCAGGATCTTTGCCTGTCTCTGCTTCATCGTACAAATGATATTATACATGGCCATAGTTTTGTATACACCCTGTTTGGCTCTCTCGGTCGTTACTGGCTTTAATAAGTGGATATCCGTGTGTTTGGTTGGCGTCGTCTGTACCTTTTATACAACAATAGGAGGAATGAAAGCCGTCATGTGGACAGACTCGTTCCAGATCTGCATGATGTTCGCCGGGTTGATAGCTGTGCTCGTTAAAGGATCCATTGACGAAGGAGGCTTCGGTAACATCTGGAGATACATGGAGGAAGGAGACAGGATACAGTTCTGGGACATCGACCCAAGCCCCTTAAAGAGACATTCGCTGTGGGCCTTGATCTTCGGCGGTTGTTTCACGTGGCTTGCCGTCTACGGTGTAAACCAAGCCATGGTACAGAGAGCTTTATGTTGTCCCAGAAAGAAAGACGGACAAATAGCCATGTGGCTCAATCTTCCTGGTTTGACGGCTCTGCTCACTGTATGTGCCCTGTGTGGTATGGTTGTCTACGCAGAGTACAGATACTGTGATCCCTTAATTACCAATAGGATTGAGGCTAAAGATCAGTTACTGCCCCAGTATGTCATGGATCAGTTGTTTTATCCTGGTTTACCTGGTCTATTTACTGCATGTCTCTTCAGCGGAGCTCTAAGTACGATATCCTCAGGACTAAACTCTCTGGCTGCCGTTACACTTCAGGACCTAATCATTGACCGATGTTGTTCAAAAATATCTGAGACCAAGGCCGCCCGCATATCTAAGGCATTAGCCTTCAGCTATGGTCTGCTGATGATTGCTTTGTCGTACGTGGCTTCAAAACTTGGAGGGGTTCTGCAGGCTGCACTTGGTTTGTTTGGGATGATAGGTGGTCCAGTCCTCGGGCTGTTTATTTTGGGAATCATCTACCCTTGGGCTAATCACGTGGGGTCGTTCGTTGGGACGTTTGTCAGTTTGGTTATCACTCTGTGGATTGGCTTTGGTGCTCAGATATACAAGCCTTCAGTGTACAGGCCTCCAGTAAATATAACGGGTTGTCCGCTGAAGGAAGTCAACGAATCCTTCAGTTTCACGACGCTAGCCGCGAATTTCTCTACGACAGTGGCTCCATCTATCCCAGCTAGAGAACGACCAGGATATCTCGTCATTTATGAAGTGTCCTACATGTGGTACAGTCCCATCGCTGTTTTTATCGCAGTCGTCGTAGGCTTGTTGGTTAGCGCATGCACAGGGTTTAACAAACCTTC'..b'ATCACCTGTCTCATGGAGACATTTAAATGGCTCTAACCAAAGAACATTTGGTGAAATAACATCAGATATGAAACATGAGGGAATCAGTGGTGAAAGCATTGAATCATTGCAGGTTGACCAGGAGAATATAGTTGGCCAGATATCAGAAGCTTCTAGATTTATTAAAAATCAGAAGATTACAGAAAATCCTGAAGTATCTATCCAGAGAAAACAGACAGAAGAGGCTGTAGCAGAAGTTGTGCCATCTTCATCCTTCCAGATGTCCCCAAACAGTCACCATGTAACTGGCATCCACACCTTGCAGATGTTGGACACATCAGGCCTATCTGCAGAATATATCAAGTTGATACTTGAAAAGGATATTCAAGGGAGCATAGAAATTGATTTCAAAGCTGATGCAGCCACAGTTAGATTTCAGCATCAACAAGATGCATCTTATTTGCTGCAACGTGGCAGCATCATGATTGAAGGCAGAAGATGCAAGCTGGTCCCTCTGTATACAGCAATTCACGACAGAACAGAAGGCAGCTTTGCTATCAGAGTAGAGGGTTTGAATGAAAACATCACAAAAGATATGTTAGAAATGCTCTTCGCAAATCGTAGAAAGAGTGGTGGATATGACCTGAGGTCAATCTATATGCCGTCAACAGGTGGAGAAGCTATCATCACCTTTCACTGCAGAGATGCTGTCAAAAGTGTTCTTGGAATGCAGAGCAAAAGGCAGCTTAAAATGAAGAATGCTCAGTTGGATATCAAGGAAATGAAGCCATTGCCACCTCCACCATTCATAATTGGGCCAACTGAGTCAAAGAAAATCATCATGACAGAAGCACCCTCTGTTGAGAAGGAGGATCTGGAGCTTTTTCTTTCGGGTGACAGTTCCAACAGTTCAACTAATGAATCTGATTTCATTCCCAGAGTACATATTGCTCAAGTGCAGTATGCTTATAAAAAGAATGTAATACTAATAGAATTCAAGGCAATTCCAGATTATGATGCAATGCTGCATATTTGTGTGACCTTTCCACTAAAAGACCGCATGACAAGTCTACAAAAAGTAGCCATTCCAACTGGAATAATAGTAAATGGAGTTAACAATTTGGATAAAGAGGATTTGGAACTGTACTTTGAAGATCCAAAAAGTGGTGGAGGTGAAATTATTGAGGAAATCAGCTTCCATTACGACAACCAATGTGCTGTCATAAACTTTGACAACTATCAAGTTGTTGAATCTATTCTGAAGCAGAAGCATAATGTCAGGGGCCAAGCTGTTGAAGTAGATGCCTTCTATCCAGCTTTTGGTACTTGGCCTTCTGATTACAATCGTTGGAAACCATGGCATTCCCTTCCACAGCCATTCATCTTCAAGATTCCTGGGCAGGAAATTGTAGACTTCCTTTCATGGAACTCAGAGGCAATTGATAAATGTAACTCGCTTGGAAAAGCACTTGACCTTTTCATTGAACTGGACAGGACAAAGAATTCAGAATTACATATATCATATCTTCATGGTGGTGCTGAAAATATTCCAACACAGAAGGAGTGGGAAGAAAGAGCCAGAGAAGTGATAGATCAACTTATGGATAGCATCTGTGTAAAGAAAATTGCATTATCTGAAGAGTGCTTTGAAAGAATACAAGAAGAAGTGAAAAAGATGATGACAAAATATGGAAGCATTCACTTAGACATACACAAGGATCAGTCTATCATTGTATTCACTGGTTGGAGAGAAGAAATCACCAGATTCTTAGAAACATTACAACCTACTCTTCAACATATAGAAGAAGAATTCATGCGAGAGACTCAGTCCATAACAGAACAAGTACCCCTGAAGCACCATGAACGTATAATAATCAAGACTGGCAACCACACAAAGACACTGAGACAGAAGTGCCCAGGAGTAGAAGTCAAAATAAATAAAAATTGCTTGACCTTAATTGGCCTTCCACAAGAAGTAAATAAAGCCAAGTTATATGTGTATGAAAACATAACGCAAATGATAAAGTGCCGACAATATCAGTTTTCGAAGAAAGTAATCACATTTGTGCAGAGGAAAAGGGTGCACTCGTTTGTTATATCTGAGTTGAAGAAGGCCAGTGTGGTTGTGGTGCCAGAGTTTGCTGACAGTTATATCAATGCCTATGCCATGTCGGACCAAGAACTGAAGGTATATGAAGATATTATGAAGAAATCTATTGTTGAGAGAAGAGTTGCACTGAACAACGAGAGCAAGCTTGTTCTTCAACATTCTGCATGGCAGTCATTCAAGACCGATTTGGTGGCCGGATACAGTGAGAATATACTCATTGAAGAAGATGGGGCTGCCAATGGAATCTGTCTCGTAACTCTATCTCATCTGGCTGACGTGATATTGGAAACTATTAATAACATACTGGAGGAATACAGTGTTTGTCAGACCGAGTATCCAGTCAACCGCCCTATTTGTCGTCTGATATTCGAATTCTACAATGATGAAGTGAAAGCCATTGAAAGTAGTCTGAATTCCTTCCAGTGTAACATCACTCAAAGTGCTAATGGTTTTATGATCAAAGGAAATAAGTCAGCCATCGGGGCAGCAAAACAAGCCTTGCAGAATCTTTGTTCAAAAGTATGCTGGAAAGACCACTTAATTGACAATGAAGAGGTGACACATTACCTTGAGAGCAGTGAAGCAGCAAATCATATCAAACTGCTAGAGATAGCTTCCAAGGTTGTCTGTATTCATTTGAATTCCCAAACATTGACAAATAAGGGAGTGGTGACTAAAGTTGACCCAAATGGCAGAGAACTTTACTCAACCACGATTGAGCAAGCCACCATTAGGATTTTGATTGGAGATATTACCAAACAGAACGTTGATGCCATAGTAAATGCTGCTAATGGACGCCTTAAGATGTCAGGGGGTCTGGCTGCTGCTATCTTAAAAGCAGGTGGTGACGAGATTCAAGCTGAATGCGACAGATACATGGCTGGAAGAAAAGAACTACTTCCTGGAGAAGTGCATGTGTCAAAACCAGGCCGTTTGCCATGCAAGATTATTATCCATGCTGTCGGACCAACTTGGAAAGATGGAAAATCTGGCGAGGAAAATGAACTGTTTGAGGCTGTGGCTGAAAGCTTGGACCGGGCTGACAGAGCTGGCATGCAGAGTATTGCATTACCTGCTATTAGTACCGGCGTGTTTGGCTTTCCACTGCAGAGTGCAACCAAAATCATCTGTGAAGCTGTCATTGAACATTTCAAACAGAACCCAACTTCTGACTTAAAAAGTATACATCTGATAGATAACAGACCTGAATGTGGAGAAAGCCTAGTCAAATCCCTAAAGGCATGTGGACAGCAGTCAGGTAGCGATAAAGCAAAAACATCAACCAGTTGGCAGTTAATCAAAGACAGAATGAAGAAGTGGCTTTCTAGCAGTGATCAGGGGCAAACAACTGATAAAATCCAGACACCTGAAGGTATCACCATCTGGATCAAACAGGGAAGTCTGACAAACGAACAGTGTTCCACATGT\n+>Ap64_1/1_1.000_274\n+ATACTAGGAGCAGTTTTAGTTTCAAATAGCGCTGCCACGCTCTATTTCTCTTCTTATCTCTTTATTGTATCAACAACAATTCTAAGCGCCGTTCTATTAAAAACTAACTCCTTGTTTTCCCTACCACTATTTAAATCATCAACAACTCTATCAACCATTCTATTCCTCTCCTTCATAAACATAGGGGGCCTTCCTCCATTCTTCGGTTTCTTTATTAAAGCTTTCGTAATACTTAACTTACTTTCCAGCAATCTGGCCCCCCTCACCTTCTTCT\n+>Ap65_1/1_1.000_161\n+GGAATGAAACTAATTCTTATAATCCTACTAATCTCTTTTATCATCCCCGCCATTCTATTTTTACTCTCGATCTTTACTACTATGCGCATGCCAGAGAGCCGTGAAAAATTTAGGCCCTACGAGTGCGGGTTTGACCCCAATCACTCGGCCCGAACCCCATT\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet_out/PgPg_transcriptome_90109.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet_out/PgPg_transcriptome_90109.fasta Fri Feb 01 10:22:32 2019 -0500 |
| b |
| b'@@ -0,0 +1,128 @@\n+>Pg1_1/1_1.000_474\n+GAGGTATGTTCGGGTTATAGGTGTGGTCCGACAATGGGTCGAGTAATCAGGAGTCAGCGTAAGGGTGCTGGCAGTGTATTCAAGGCACACACGAAACACAGGAAAGGTGCTGCAAGACTTCGAGCATTTGATTTTTCTGAAAGACATGGCTATATCAAAGGTGTTATAAGGGACATCATTCATGATCCAGGACGTGGCGCTCCATTGGCACGTGTCGTTTTCCGTGATCCATATAGGTACAAGCTGAGACATGAGAACTTCATCGCCTGCGAGGGCATGTACACCGGACAGTTCATTTACTGCGGCAAAAAGGCCACACTCCAGATAGGAAACATCCTTCCCGTCGGTGTGATGCCTGAGGGTACAGTCGTGTGCTCACTGGAAGAGAAGACTGGAGATCGTGGACGACTGGCCAAGTGCTTGGTAACTATGCCACTGTCATCTCCCACAATCCGGAAACAAAAAGGACTAGGG\n+>Pg2_1/1_1.000_1300\n+GCTGTAGGCAACTGTGACAGAACAACAGGAGAGTGTAAGAAATGTATATATAATACAGCTGGCTTCTATTGTGAAAGATGTCTTCCTGGTTACTATGGTGATGCCTTAGCTGAACCGAAAGGGCAATGTAAAGCATGTAATTGTTACCCACCTGGTACTAATGACAGAGCCAGACAAGAAGGCTCCCTGACTTGTGATGAGAGATCTGGCCAGTGTCCGTGTAAACGTCAAGTTATTGGTAAAATGTGTGATACTTGTGAAGATGGCTTCTGGAACATAGACAGTGGACGAGGTTGTGAAGCATGTTTATGTAACCCAACTGGATCACACAACAGGAACTGTGACCTGCGTACTGGACAATGTCAGTGTAAGTCTGGTGTTACTGGCAGAAAATGTGATCAGTGTCTGCCTGACCACTGGGGATTCTCTCGTGATGGATGTAAAGCTTGTAACTGTAATATGGAAGGAGCTGTTAATACTCAGTGTGATTTGAGGACTGGGCAATGTATCTGTAGGCCAAGCATAGAGGGAGAGAAATGTGACAGATGTGTGGAGAATAAGTTTAACATCACTGCAGGATGTATTGATTGTCCTCCATGTTACTCACTTGTCCAAGATCAGGTACACATCCTCAGATCAAAAATAAATGAACTTCGTGAAATTATCCATAACATTGGTGACAACCCACATAAGGTTGATGATGCTGACTTCCGTAGGAAGTTAAGGGCTGTAAATGACTCTGTAAATGATCTGTGGAGAGACGCCATGCATGCTGGTGGTGGTGGAGACTCCTCTCTTGGCCAACAGATGGAGGCACTGCAGCAGGCTATCAGTGACATCATGACTGAATGTGGCCAGATAACAATTGATATAACATATGCCACATCATCATCGGACAGCAGTAAGGTAGATATTACTTATGCCGAGGAGGCAATTGATGAAGCAGAGAAGGCATTACTGGCTGCTGAAACCTACCTTCGTACAGAAGGTAGGAAGGCACTTCATGATGCCATTGAAGAGTTGAGGGATCTTGACGAGAAGTCACAACAACTGACTAAAATAGCAAGAGAAGCTCGGGAGGAGGCTGAAAAACAAGAAAAAGAAGCCAGTATGATAGATGAAACAGCTAACAAGGCATTGAATACATCAAAAGAAGCCTTAGTGTTAATTAATGAGGTACTGAGGAAGCCTGACGATATTGCCGATCAGATAGAAGATCTTAGACGAGAGGTTCTAGACACAGAAGTGGAATATCAGGCCACAAAAGCTGAAGCAGAACGAGCAGAGAAGTTGGCTACTG\n+>Pg3_1/1_1.000_1813\n+TCTACCTGGAGTCTATCTAGGGGGGTGAGGCTTGTCTCTCCGGTGTTTTGTCACCGTGATACTATCTCGCCTTATCACATCCGATCGCCGTCGAGTGACGTCAGCAAAATGAGTGTCAGCGACTTAGAGGCTCGTCGAGAGGCCAGGAGGCGGGCCAGAGAAGAAAAACAATCGGTGCTACTCGGCTCTCCGGCCACCCAATCTGCCATAACGACTGACCACGACGACGAAGATATCGTGGAACGAATTGCGAGGAGGCGAAGAGAACGTCAGGAACGACTCGCAAAACTATCTGCTGATACCAGCTCTGTCGATTACGACATCGAGAAACGTCGCCAGGAAAGACGAGCAGCACGCGAAAACATAATGAGGGGTGAGATCAAGGACGGGTCAAACGACCATGAGAAGGAGAGCTCTTATGCAGAAGAGAAGTCGGCAGACGACACGAAAGAAGAATGGCCAACAGCGCGCGATGAAGAAGAAAATGGAAAGGACGAAGAGAAAGACAAAGGACGAGAAGAAGACGAACAGAGACAGAAAGAAGAGGAGGAAACGGTTAGAATAGAAACACAACAACAGGAAGGTGAGATAAATGAGGAAGAGCAAAATGAAAAGCGAGAATGGAAGATGGGTGGAAAATCTACAGTAGAAGAACAGGAAAACGGTCTGAGTGGTGAAGAAGGTGAGGAAGAGGAGGAAGAAGAGGAAGAAGGAGAAGAGGAGGAGGAGGAGGAAGAAGAAGAAGAAGGGGAAAATTATCAGCAGAGAGAGGATGATTTGGCGGAGGAGGAAAGAAAGATCCAGGAGGAAGAGGATCTCATCAGGGAGGAGGAGCAATTGAAAAGAGAAGAAGAACAACGGTGGAGAGAGATGGAAGAGAAGAGGCAGCAACAAGAGAAGGACGAAATGGAGTTTGAAGAAGACGAGAAGAGACGTAGAAAAGAAGAAGCGGAAATGGACGTGGACGTCGGGGAGAAGAACGAAGATCAGAGTTCTCCCGAAGAGAAGGACAAGGGAAGGACGATTGACGAGAAACGTCAGCAGCTGATGAAACACATGAATGGCTCGATCGATGGAACGACCCCGACACGGCCGAAAAATGACTCCCCTGATACGCCACCTAGCGAGACTAAAAGACGACAGAAGGCGATGGAATGGGAACAACGTCTCAAGAGAACGCCCTCGCAAAGCGAACCAAACGACAGAATCAAACAGATTGAGGAACAACGGGCCGCCGAGCGGAAGGAGCTACAGCGCGCGCGCGAGGCTCGCTGGAAAGAACGGGAAGAGAAGCTCAGACAAGAAGCCGAAACTCGGAAGAAGCGGGAAGAAGACTTGGCTGAGAGACGCCGAAAGGCGGCCGAGGAGAGGAAAACGTTGCGCAAACAATCAGATATCGCTCATAACGAACCACAACCTGAAGGTGGAGAGAATGACGATGGCTTGGCAGATATGGAGAAAGGCAAAAGGAAAGGGTTGGGAGGCCTCTCCCCTGAGAAGAAGAAGCTACTAAAGCAACTGATCATGCAAAAGGCAGCGGAAGACTTAAAGAAGCAACAAGAGGCCGAAGCTGAAGCGAAGAGGAAGATCATCCAGCAGCGTGTTCCAAAACTAGAGATTGATGGATTAGATCAAGGTCGTCTGGAGAAAATCGTACGTGACCTTTATAAAAAGGTCGTTGCCCTTGAGGAGGATAAATATGATTGGGAGGTGAAGCTTAGGAAACAGGACCAAGAGATGAATGAGCTTAACATCAAGGTTAACGATATTAAGGGCAAATTTGTTAAGCCCGTCCTGAAGAAGGTATCGAAGA\n+>Pg4_1/1_1.000_231\n+ATCACGTTATATTTTTATCGCCTTAAATTCGAAGCCAAATCTTATCGAGTGAACTGTGCGTGTATCCCGACTGATACGTGTATCCCAACTGAATGTGTAAGTCGTCTGCCCGCGTGTTGTGTTGTTGCCGCCGTCGTCATCATCCCAGCGCGACTTAACTCCAGCATTCAGCTGACCTGTATGAAATGTGTGCTATTTTTCCAATGTTGCGGTTTGTGTGCGTGTGTGTGT\n+>Pg5_1/1_1.000_1440\n+GTACTCATAGTTGGTGTAGAGACAATGGGCTGTATTTTGGGATCGCTGGCT'..b'AGGCTGCCAATGAGTTTGGATTCAGCGAGCCATCGATGCCCATCATGCTGAAAAAGAAAGAAGAAGTGGAAGAAATAAAGGAAGACACGAGCAGACAAAGGCGTAGAAGTCGTTCATATTCCCGAGAACCCGCTGACAGATGTGTACCAGAACACATGAGAATCCCACCGGAATTCCTTGCCAGCCCAGACGAAAACCAGTATGGTGTCGAAGGTCGTACAATGAGAGTGGTTGCTAACATCAGAGCTTATCCCAAACCTGAGCTATCCTGGTACATGTATGGGAGAAGACTCCAGATGGGTGACAGACTGACCAGCAGTCTCACGGACAAGGGTGAACTGTCACTCGAAATACAGCAGTTCTGTTGGTCAGATGTAGGCGAATACAAAATTGAAATAAGAAATGAATATGGCATGGCCTCACAAGCAATCAAAGTTGACATGGCTGATCCTCCAACATTCCTTGAGCCTTTACATGACCAAATATTCCATCTCCATAGTAACAGCAAGATGGAATGTCGTGTACATGGCATTCCTTATCCAACGGTGACCTTTAAAAAGGATTGGCGTGTCATTGCCGATTCACAAAGGATTAAGATAGTGAGGGAAGAGTATGATCATTGGACTTTAAACATTCGTAACGCTATCCACCCAGATGAAGGTCTGTATGAATGTGTTGCTGAGAATGTTGCTGGTAGGGTGTACTGCTCAGCTAACGTCAAGGTCACAGAGAAACATGGCCTCTGGAGAGATATTAAGTTTAATCCATGTCCAGTCGAGGACTTCTTCCATGTCATTGATGAAATTGGAAGAGGCTCTTATGGCGTAGTTAGACGTGTGATAGACAAGAACTCCGGTAACCAGTATGCTGCTAAAATACTCCGTTACGGAGATCTGATGATCAAGGAGGAGCTGATGACCGAATTAGAGATCCTGGCTCAGCTGGATCATCAACATATCATACAAGTCGTAGACGGCTACGAGGACAAGAAGAGACTGATCATCATCCTAGAAATTGTGACAGGAGGCGAGCTCCTACAGCGTTTAATTAAAGAAGATACACTGACGGAGAGTGAAGTGGCTTTCTACATCAGACAACTACTGCAGGCTGTAGAATATCTACACAGTAAAAATGTCATCCATCTTGACCTGAAGACGGAGAATCTCTACCTGCTGAGTCAATCGTCAGAGAATCTGAAGGTGATAGACTTCAGTTTTGCACGGAAGTACAACCCGGCACGCCGCCTACACGTCAAATATGGGACGCCAGAGTTTGTGAGTCCGGAAGTGTTATGTGAGGAGCCCATCACTCCAGCCGCCGATCTCTGGAGTGTCGGAGTCATCACTTATATACTTCTCAGCGGCATATCACCATTCCATCGAGACACAATCCGTGACACATTGTTGGCTGGTCGAGCAGGAGACTGGAAGTTTGATGAAGAAGCCTTCAGTAACATCTCTTCTGAGACAAAAGACTTCATCTCCCAGTTAATTGTGCTTGACCCAAAAAAACGACTCACAGCCACAGAGGCTTTGGATCATCCATTCATCAACTTTGCCCAACGCCGAGGTCTTGGAGACAGGATTAATCTGGACAGACACAAAGCTTACATGTTTAGGAGGAAGTGGGAGCGTGGCACTAACTTGGTGATGACTCTCGTAAAGCCGATGCCTCTCTCAAACCATTTGATAGAACAGCCACCACCAGAGTTCGAATTTGAACTGGATAACCAGGTACCGATGTTACAGCTGCCAGGAGAGGACCAGCCGACTACTTCGAGTGCCACAGATGGTCTTCAGGTGGAACTTGGTGCAGCTGGAATGTTATCGATAATGGGTCCTCCATCAATGGTATCTGCAGCGCCATCTACTGTTGGTTCCGGTGGCTCCTCTGAGTGGGGCAGAGAATACGAGGATGAGGATACGTGGTATGAGTTTAGCTCGGTCTATCAGACTGGTGTTGATACTCATCTACTGCCATCTAAAGATACTCGCATGGGAGTACGGATGGCTGGATACCGCCGAACACTGGGCAAACCAGATCCAGAACAGCTTCCCGTTACACAGTCAAGTTTCCAGCCGACACGATATCGTGGCTCGATGAAGGAGCGCCAGGATCTGCGAGACCTCGAAAAGGAGCGAGAAGAGAGCGAAGAAGCCGACTCCGAACATCTGAAGCACACGAGACGGGGTCTGTGGCAGGTCAGAAGGATGATAGAGATAAACAAGGCTAGCGAAGGTTTCCCGCCAATATTCAAAGAGAAGATCAAGGACAAGGCGTACAATGTAGGAGACAGCTGTACGCTGAGAGTACACGTGATAGGGAATCCTCCCCCGATATTGTCGTGGTACAGGAATGAGGAGCTCCTCAGTACCGGAGGCAGGGTGAGGATATCGGCATCCTCCGAAGAAGGCGCACATTCCTTGACCGTCCTCCAGACAAAACCAAACGATTTCGGCGTCTACAAGTGTGTGGCCAGGAATAAATATGGTACTGTGACGTGCCGAGCAAGGATGTTATGTGGGGACAATCCAAGTAGACCTGGTCGTCCTCACGTTACTAAAGTTTCCGACGCCGAAGCTTTCATGATTTGGGAGGAACCCGAGTCAGATGGTAACAGTCACATACAAGCTTACAAAGTCGATTGGTTCAAACCCGGTGAACAACGATGGACAACAGCTACTTATTGTATAGATGAGTGTGCTCTTATCAAGGGTCTGAAGCCAGACACCTCGTACAGGTTCCGGGTGTCGGCTATTAACGCCTTTGGAATCAGTCCGTACAGTTGGGCATCTGTTGAAGTTAGAACGAAGAGAAAGGGAGCGGATCCAATAGAGATAGAGGAGGAGACAAAACGAATCCTGCTCCGCTCTCGTCAAGCCACCAACCGTCCGTCTCCAGAATCTAGTCCCCAGACGAGTCCTCACGGATCAATGACGGATCTGACTGAGGAAGCTCTCGACAGGAAGGCCAAGGATCACGGCGTTCTGGATCGGGAGATCATGATCCAAGAGATAGAGCCCGAACGTTTCCTTGCCTTTGGCTCGGATGTTTGGAGGGGACGATACACGTTAGTGAAGAACGTCAAACCGAAGCAGGGACGAAAGATCCGACGTGTGGCGAAGATCCTCTGTTACGACGAGTTTAATCCCGACGACAGTCTCCGGGAGTACGAGATGTTGAAGGGCATAAGACAACGGCACATCGTCCGGTTACACGAGGCATTCCTTCATAACGACTTTGTTTATCTGATCTTCGAGAAGTTGTACGGAGAGAATGTCGCCCGCTCGCTCTCGTTAAAGAACAAGTACAACGAACACCACGTCTCCAGCATTATAAAACAGGTCTTGGATGCTCTCCAGTTTCTGCACCATATCGGTATTGTACACCTGAACCTTCAACCCGACAACGTCATCATGGTATCCAGGCGACGCTTCGACATAAAATTGATCGACTTTGGCCGAGCGCGGAAGATTACGTCATTCGATGGCGTCAAAGTGCCGCGTGAAGGAACCGCCGATTTTATGGCTCCGGAAATGGTAGACAGAGAGTTGGTAGGTGTCGCTGCTGACATTTGGGGCGTAGGTCTACTGGCCTTTGTACTTCTGAGTGGCGTGTCGCCTTTTGAGGGAGATCTCGACGAAGACACGTTCGCCAACATTATACACGTACGCTATGATGCGCACACGTTGTATCATAACGTGACGAAATACGCGCTAAAATTCATCTACCAGACGCTGAAGAGGAATCCAAAGGCTCGTCTGATGACGGAAGAGGCACTCGACCATCGTTGGCTGATGTTGAACGCTCCGATGGTAAAAGTCCGTAAAGCGGCCGTCTTTCCCACCGACAAACTTCGACTGTTTGAGGAGAACTACATCAAGCGCCGCCTGGCGGGCCGAGCTCCGCCCGACCGTCTGATGAACGCCTACGGCATCGGATTGTCGTTCTCGTCGGATGAGGAAGGCGACGATTGGTTGAGGAATGGCAGTAAATAT\n' |
| b |
| diff -r 000000000000 -r 7a813e633d1c test-data/velvet_up.output --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/velvet_up.output Fri Feb 01 10:22:32 2019 -0500 |
| b |
| @@ -0,0 +1,21 @@ +Number of segment pairs = 4032; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4160; number of pairwise comparisons = 0 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS +Number of segment pairs = 4422; number of pairwise comparisons = 1 +'+' means given segment; '-' means reverse complement + +Overlaps Containments No. of Constraints Supporting Overlap + + +DETAILED DISPLAY OF CONTIGS |
