| Next changeset 1:a36a1acd5807 (2023-10-12) |
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Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/cap3 commit 9d6ba79f91bdf48dc01c09c088c63f5ea60d137a |
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added:
cap3.xml test-data/ace.txt test-data/cap3stdout.txt test-data/contigs.fa test-data/contigsandsinglets.fa test-data/contigslink.txt test-data/contigsqual.txt test-data/info.txt test-data/input.fa test-data/singlets.fa |
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| diff -r 000000000000 -r d76a0d8a9eac cap3.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/cap3.xml Sat Sep 02 07:09:11 2017 -0400 |
| [ |
| @@ -0,0 +1,91 @@ +<tool id="cap3" name="cap3" version="2.0.0"> +<description>Sequence Assembly tool</description> + <requirements> + <requirement type="package" version="10.2011">cap3</requirement> + </requirements> + <stdio> + <exit_code range="1:" level="fatal" description="Tool exception" /> + </stdio> + <command detect_errors="exit_code"><![CDATA[ + cap3 "$inputSequences" -o $overlaplength -p $overlapidentity > "$cap3stdout" && + mv "$inputSequences".cap.contigs $contigs && + mv "$inputSequences".cap.contigs.qual $contigsqual && + mv "$inputSequences".cap.contigs.links $contigslink && + mv "$inputSequences".cap.ace $ace && + mv "$inputSequences".cap.info $info && + mv "$inputSequences".cap.singlets $singlets && + cat $contigs $singlets > $contigsandsinglets + ]]></command> + + <inputs> + <param label="Input sequences to assemble" name="inputSequences" type="data" format="fasta" help="Input sequences to assemble" /> + <param label="specify overlap length cutoff > 15 (40)" name="overlaplength" type="integer" size="3" value="40" help="-o option. must be > 15. 40 by default" /> + <param label="specify overlap percent identity cutoff N > 65 (90)" name="overlapidentity" type="integer" size="3" value="90" help="-p option. must be > 65. 90 by default" /> + </inputs> + +<outputs> + <data format="fasta" name="contigsandsinglets" label="${tool.name} on ${on_string}: Contigs and singlets" from_work_dir="${inputSequences}.cap.contigs" /> + <data format="txt" name="cap3stdout" label="${tool.name} on ${on_string}: Standard Output" hidden="true"/> + <data format="fasta" name="contigs" label="${tool.name} on ${on_string}: Contigs" from_work_dir="${inputSequences}.cap.contigs" /> + <data format="txt" name="contigsqual" label="${tool.name} on ${on_string}: Contigs Qual" from_work_dir="${inputSequences}.cap.contigs.qual" hidden="true" /> + <data format="txt" name="contigslink" label="${tool.name} on ${on_string}: Contigs Link" from_work_dir="${inputSequences}.cap.contigs.links" hidden="true" /> + <data format="txt" name="ace" label="${tool.name} on ${on_string}: Ace" from_work_dir="${inputSequences}.cap.ace" hidden="true" /> + <data format="txt" name="info" label="${tool.name} on ${on_string}: Info" from_work_dir="${inputSequences}.cap.info" hidden="true" /> + <data format="txt" name="singlets" label="${tool.name} on ${on_string}: Singlets" from_work_dir="${inputSequences}.cap.singlets" /> +</outputs> + + <tests> + <test> + <param name="inputSequences" value="input.fa" ftype="fasta"/> + <param name="overlaplength" value="40" /> + <param name="overlapidentity" value="90" /> + <output name="contigsandsinglets" file="contigsandsinglets.fa"/> + <output name="cap3stdout" file="cap3stdout.txt"/> + <output name="contigs" file="contigs.fa"/> + <output name="contigsqual" file="contigsqual.txt"/> + <output name="contigslink" file="contigslink.txt"/> + <output name="ace" file="ace.txt"/> + <output name="info" file="info.txt"/> + <output name="singlets" file="singlets.fa"/> + </test> + </tests> + + +<help> +**What it does** + +This tool is a CAP3 wrapper developed for the visitor2 set of worflows + +Under this conditions, it takes as input a set of blast hits in fasta format and performs CAP3 assembly on these sequences + +Standard CAP3 outputs (Standard Output, Contigs Qual, Contigs Link, Ace and Info) are kept hidden in the Galaxy history (feel free to reveal these hidden datasets). + +Standard CAP3 outputs Contigs and Singlets are returned in the history, as well as a merge of these two datasets (Contigs and singlets) + +**Acknowledgments** + +This Galaxy tool makes use of the `package_cap3_3`_ Galaxy package developed by jjohnson. + +It is Copyright © 2014-2015 `CNRS and University Pierre et Marie Curie`_ and is released under the `MIT license`_. + +.. _package_cap3_3: https://testtoolshed.g2.bx.psu.edu/view/jjohnson/package_cap3_3 +.. _CNRS and University Pierre et Marie Curie: http://www.ibps.upmc.fr/en +.. _MIT license: http://opensource.org/licenses/MIT + + +</help> + <citations> + <citation type="bibtex">@article{Huang:1999wb, + author = {Huang, X and Madan, A}, + title = {{CAP3: A DNA sequence assembly program.}}, + journal = {Genome research}, + year = {1999}, + volume = {9}, + number = {9}, + pages = {868--877}, + month = sep + } + </citation> + </citations> + +</tool> |
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| diff -r 000000000000 -r d76a0d8a9eac test-data/ace.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ace.txt Sat Sep 02 07:09:11 2017 -0400 |
| b |
| b'@@ -0,0 +1,296 @@\n+AS 4 13\n+\n+CO Contig1 1372 7 2 U\n+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC\n+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA\n+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT\n+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG\n+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA\n+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT\n+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA\n+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC\n+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC\n+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC\n+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC\n+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC\n+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT\n+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC\n+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC\n+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC\n+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG\n+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG\n+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC\n+\n+BQ\n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 \n+25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 \n+25 25 25 25 25 25 25 25 10 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 \n+20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 15 15 15 15 \n+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 '..b'e_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139\n+BS 74 74 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113\n+BS 75 284 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139\n+\n+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_2/2_Confidence_0.000_Length_284_hit1_IdMatch=98.94,AligLength=284,E-val=2e-139 284 0 0\n+AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG\n+TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG\n+AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG\n+AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG\n+TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT\n+\n+QA 1 284 1 284\n+DS \n+\n+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113 236 0 0\n+ATAGAAGCACTGTGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTG\n+CCTATCTCCAGGAGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTC\n+TCCATGAGTCGGAAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTG\n+ACACTAAGAAAGTTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT\n+\n+QA 1 236 1 236\n+DS \n+\n+CO Contig4 253 2 1 U\n+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA\n+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA\n+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC\n+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA\n+ACAGTTCTTGTTA\n+\n+BQ\n+10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 \n+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 \n+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 \n+15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 \n+15 15 15 15 15 15 15 15 15 15 15 15 15 \n+\n+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 U 1\n+AF gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_2/2_Confidence_0.333_Length_251_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 U 3\n+BS 1 253 gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118\n+\n+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 253 0 0\n+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA\n+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA\n+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC\n+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA\n+ACAGTTCTTGTTA\n+\n+QA 1 253 1 253\n+DS \n+\n+RD gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_2/2_Confidence_0.333_Length_251_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118 251 0 0\n+T\n+GGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCACCG\n+AGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACAATT\n+TCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTCGTT\n+CCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCAACA\n+GTTCTTGTTA\n+\n+QA 2 251 2 251\n+DS \n+\n' |
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| diff -r 000000000000 -r d76a0d8a9eac test-data/cap3stdout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cap3stdout.txt Sat Sep 02 07:09:11 2017 -0400 |
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| b"@@ -0,0 +1,299 @@\n+Number of segment pairs = 342; number of pairwise comparisons = 14\n+'+' means given segment; '-' means reverse complement\n+\n+Overlaps Containments No. of Constraints Supporting Overlap\n+\n+******************* Contig 1 ********************\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+ gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+ gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+ gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+ gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+******************* Contig 2 ********************\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+ gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+ is in gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+******************* Contig 3 ********************\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+******************* Contig 4 ********************\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso+\n+\n+DETAILED DISPLAY OF CONTIGS\n+******************* Contig 1 ********************\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+gi|225356593|gb|FJ15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+gi|225356593|gb|FJ15+ GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+ ____________________________________________________________\n+consensus GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+gi|225356593|gb|FJ15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+gi|225356593|gb|FJ15+ GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+ ____________________________________________________________\n+consensus GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+gi|225356593|gb|FJ15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+gi|225356593|gb|FJ15+ ACATCCTGG\n+gi|225356593|gb|FJ15+ TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+ ____________________________________________________________\n+consensus TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGC \n+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+gi|225356593|gb|FJ15+ GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+ ____________________________________________________________\n+consensus GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC\n+gi|225356593|gb|FJ15+ TCAGATATCCATTTAGTGAATCCTGAGAATCTC"..b'\n+gi|225356593|gb|FJ15+ AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG\n+gi|225356593|gb|FJ15+ ATAGAAGCACTG\n+ ____________________________________________________________\n+consensus AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ TGAATCAGGTTTATGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG\n+gi|225356593|gb|FJ15+ TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG\n+ ____________________________________________________________\n+consensus TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG\n+gi|225356593|gb|FJ15+ AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG\n+ ____________________________________________________________\n+consensus AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG\n+gi|225356593|gb|FJ15+ AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG\n+ ____________________________________________________________\n+consensus AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT\n+gi|225356593|gb|FJ15+ TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT\n+ ____________________________________________________________\n+consensus TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT\n+\n+******************* Contig 4 ********************\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA\n+gi|225356593|gb|FJ15+ GGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA\n+ ____________________________________________________________\n+consensus TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA\n+gi|225356593|gb|FJ15+ CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA\n+ ____________________________________________________________\n+consensus CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC\n+gi|225356593|gb|FJ15+ ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC\n+ ____________________________________________________________\n+consensus ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA\n+gi|225356593|gb|FJ15+ GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA\n+ ____________________________________________________________\n+consensus GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA\n+\n+ . : . : . : . : . : . :\n+gi|225356593|gb|FJ15+ ACAGTTCTTGTTA\n+gi|225356593|gb|FJ15+ ACAGTTCTTGTTA\n+ ____________________________________________________________\n+consensus ACAGTTCTTGTTA\n+\n' |
| b |
| diff -r 000000000000 -r d76a0d8a9eac test-data/contigs.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigs.fa Sat Sep 02 07:09:11 2017 -0400 |
| b |
| @@ -0,0 +1,46 @@ +>Contig1 +GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG +GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG +TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG +GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC +TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC +ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA +ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT +CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG +TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA +TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT +CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA +ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC +CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC +TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC +TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC +TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC +GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT +GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC +TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC +TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC +AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG +AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG +TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC +>Contig2 +TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC +AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA +GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA +GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA +GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC +CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC +TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT +GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG +GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA +>Contig3 +AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG +TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG +AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG +AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG +TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT +>Contig4 +TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA +CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA +ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC +GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA +ACAGTTCTTGTTA |
| b |
| diff -r 000000000000 -r d76a0d8a9eac test-data/contigsandsinglets.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigsandsinglets.fa Sat Sep 02 07:09:11 2017 -0400 |
| b |
| @@ -0,0 +1,91 @@ +>Contig1 +GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG +GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG +TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG +GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC +TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC +ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA +ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT +CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG +TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA +TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT +CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA +ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC +CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC +TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC +TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC +TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC +GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT +GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC +TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC +TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC +AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG +AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG +TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC +>Contig2 +TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC +AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA +GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA +GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA +GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC +CCACTTTATCGTGGATGGTAAAACTGTTTACAAGAAGAAGAACCCCCATGGACTCATGAC +TGGAGTTCCAGGAACAACCCTATTTGACACTGTGAAATCTGTAATAGTCTGGAATGAAAT +GTTGGATCAGGCTGGTGCAGGTTCCATAGACCTTTTAAATGAAGCTCAAGTAGTTGAATG +GATGAAGAGACAAGGCTTAGTTGTCAAAGAGGGAA +>Contig3 +AACGTAAAACAAACGACATGGATGCATCTAACCCTATTATTTCAAGCGATAGAAGCACTG +TGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTGCCTATCTCCAGG +AGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTCTCCATGAGTCGG +AAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTGACACTAAGAAAG +TTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT +>Contig4 +TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA +CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA +ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC +GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA +ACAGTTCTTGTTA +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0 +ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA +GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT +TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA +TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA +TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG +AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC +CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG +AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA +AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC +TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA +TATTCAA +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0 +GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA +CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA +TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC +TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC +TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG +ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC +ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA +GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_14_Transcript_1/1_Confidence_0.000_Length_210_hit1_IdMatch=98.1,AligLength=210,E-val=3e-98 +TGTCCCGTTGCACCCCCCATCCATTAACAATCGGGGTGGGCATACTCATGTCACTCGCCA +GATGGGCGGAGTACCTCACCCTCCTCTTGGTCTAATACCCATAGCTCAGAAGTACGGGGT +AGAGATCTTGGACCAGAAACATGTCTACACAGGAGGCACTTGGGATGGCTTTCTTAATAG +ACTCGCCCAACAGATGGGCCGGACAACGGT +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_24_Transcript_1/1_Confidence_0.000_Length_280_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129 +ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT +GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA +GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG +CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG +TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128 +GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG +GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT +ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC +CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG +CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171 +GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG +ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA +CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA +TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG +AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT +GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC |
| b |
| diff -r 000000000000 -r d76a0d8a9eac test-data/contigsqual.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/contigsqual.txt Sat Sep 02 07:09:11 2017 -0400 |
| b |
| @@ -0,0 +1,127 @@ +>Contig1 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 +25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 +25 25 25 25 25 25 25 25 10 30 30 30 30 30 30 30 30 30 30 30 +30 30 30 30 30 30 30 30 30 30 30 30 30 30 30 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 +20 20 20 20 20 25 25 25 25 25 25 25 25 25 25 25 25 25 25 25 +25 25 25 25 25 25 25 25 25 25 25 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 +>Contig2 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 0 15 +15 15 15 15 15 15 10 10 10 10 10 10 10 10 10 +>Contig3 +10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 +10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10 +10 10 10 10 10 10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 0 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 +>Contig4 +10 10 10 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 15 +15 15 15 15 15 15 15 15 15 15 15 15 15 |
| b |
| diff -r 000000000000 -r d76a0d8a9eac test-data/info.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/info.txt Sat Sep 02 07:09:11 2017 -0400 |
| b |
| @@ -0,0 +1,23 @@ +No file of quality values (.qual) is found +No file of constraints (.con) is found. +Number of overlaps saved: 12 +ComputeOverlap done +IdentifyChimeras done +Number of overlaps removed: 0 +RemovePoorOverlaps done +ASSEM done +ComputDistForContigs done +PresentLayout done +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 395, length: 395, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 197, length: 197, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 224, length: 224, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 1372, length: 1372, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 402, length: 409, right size 7 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 421, length: 421, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 627, length: 627, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 515, length: 515, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 506, length: 506, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 284, length: 284, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 1, right clip: 236, length: 236, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 4, right clip: 253, length: 253, right size 0 +Clip gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_iso left clip: 2, right clip: 251, length: 251, right size 0 |
| b |
| diff -r 000000000000 -r d76a0d8a9eac test-data/input.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.fa Sat Sep 02 07:09:11 2017 -0400 |
| b |
| b'@@ -0,0 +1,159 @@\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_4/7_Confidence_0.286_Length_409_hit1_IdMatch=96.58,AligLength=409,E-val=0.0\n+TTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTTCTGGCTGCA\n+GTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTGTCCTGCAAT\n+GTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCATCTCCAGTA\n+GTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCTCCAACTTTA\n+TCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTAACGACGGCT\n+TGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATCCGAACTACT\n+TTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTTTAAGAG\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_3/7_Confidence_0.286_Length_395_hit1_IdMatch=97.97,AligLength=395,E-val=0.0\n+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC\n+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA\n+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0\n+ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA\n+GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT\n+TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA\n+TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA\n+TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG\n+AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC\n+CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG\n+AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA\n+AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC\n+TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA\n+TATTCAA\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_11_Transcript_1/2_Confidence_0.667_Length_236_hit1_IdMatch=98.73,AligLength=236,E-val=2e-113\n+ATAGAAGCACTGTGAATCAGGTTTACGCGAAGATGGTGAGGAGAAAACGGCAAGATCTTG\n+CCTATCTCCAGGAGTTGGTGAGGACAGCCCATCGAGAGATTCTCCCCCAAGGAGAACTTC\n+TCCATGAGTCGGAAGCCAAACAGTATGTAGCCGAATATAAGGCTCGACTACCTGTGGTTG\n+ACACTAAGAAAGTTGGCGAACTGCCAACTGAGGTCTTCCAGGTAGCACTCCCAAGT\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0\n+GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA\n+CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA\n+TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC\n+TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC\n+TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG\n+ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC\n+ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA\n+GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_2/7_Confidence_0.143_Length_224_hit1_IdMatch=97.77,AligLength=224,E-val=3e-104\n+ACATCCTGGGTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTT\n+GGCCGTACCTCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGG\n+ACATATGCCATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGAT\n+ACTCCTGCAACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTAC\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_21_Transcript_2/2_Confidence_0.333_Length_515_hit1_IdMatch=97.28,AligLength=515,E-val=0.0\n+TGGATTTTCATCCATTGCTGGAGGGCTTACTAGGATGGTCGACTGGATGTATGCCTGCCC\n+AAAGCGGCGGGGACGGGTTGTCTGTTACGGTGACGATGCATGTATAACATTTTGGAGCCA\n+GGGCGTCCTCTATCGGGTGGATCCAGATTTTAAACAAATGGACGGGTCCATAGATAGAGA\n+GGATGCAAGAATCACCATTGAGTGGGTCCTCCACCATCTCAGAAAGGATTTAGGTGTAGA\n+GGAGACCCCTGCTTTTTGGAAGACAGTTGCAGCAGTGTGGCTTGATATGGCCATTGACCC\n+CCACTTTATCGTGGATGGTAAAA'..b'80_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129\n+ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT\n+GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA\n+GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG\n+CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG\n+TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_6/7_Confidence_0.143_Length_1372_hit1_IdMatch=97.59,AligLength=1372,E-val=0.0\n+GTTGCATATTCAACCTGCCGAGCCCAGGAAGACTCAGGCGGGGGAGGCACTACATTAGGG\n+GTCGCAAAGCTAGACTTCTTGTATGGGATGTTGTTAACCTCCAAAATAGCTGCACAGATG\n+TATTCCTTAGCCAGTTTGGCAGAGGAAGACCAGGCTTCTCCCAACAGCTTCACATCCTGG\n+GTATGGTGGCTGTGGGCGTAGAGCCTAACTCCAACAGGATTGGCAGCATTTGGCCGTACC\n+TCAGATATCCATTTAGTGAATCCTGAGAATCTCCCGCTGACCATTGCATGGACATATGCC\n+ATGGCATCCTCTGCTGTATTTATATCGTGGGGAGGTGGATGGAGGTTCGATACTCCTGCA\n+ACGTCCAGGTTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAAAGCTGACGTT\n+CTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTCTCTTTGACTG\n+TCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTCTCCAAGTTCA\n+TCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTAGGCACTAGCT\n+CCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGTAAGCCATCTA\n+ACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACTTTCTGTGATC\n+CGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGGTCTAAGAGCC\n+TCAAACACTTTGTACTCATCATTCAGATTCGCCTCAGGAGGAGGAGGGCATCCTACAACC\n+TCCTTGACATCATAGTCGTTGGATTGGACTGTCAAATTTATCTGCCTCACAGCCACTCTC\n+TGCTCCCTCTTAAACTCGTCCAGGAATCCTGACAATGTGGGGAACAGATTAATCCATCCC\n+GCTTTGTCATCCTCTCCATCTGAATAGAGGTCTAGACAGAAGTCCCGAGAGGGGAATCCT\n+GACGAATCTGGATATTCAAAGTCCTGGAGGGTTATATGTTCTGGCTTCGTTCCGGTTTGC\n+TCTTGCGTTTGCATGACAATAATCTCGCCGGGGATTGTGTTAACCACAGCGTGTATTGTC\n+TCTTCGATCCGAGGTATGCTGAATCCCATTGTTATCATTAAACCCCTCATACGGTCATAC\n+AGAGTTCTTTGGCGTGCCGTTCTAGATACTGCCTTTTCAAAGGGATTATCCTTCTGGCAG\n+AGCATCATCTCAAGAGCATCGCTCTCAGGCATTGTGGGGACATGTATCACACGGTGTCTG\n+TGGTACACTCCCATAATTTGTACGCCAAGAAATTTGTGGTCCGTAATTAGAC\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128\n+GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG\n+GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT\n+ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC\n+CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG\n+CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_19_Transcript_5/7_Confidence_0.286_Length_421_hit1_IdMatch=96.67,AligLength=421,E-val=0.0\n+TACTCCTGCAACGTCCAGATTAATGAGCTCAGGTTGGGTTTTTACAATCTCCCGTCTCAA\n+AGCTGACGTTCTGGCTGCAGTAGTCTTATCAATCAGATTACGCTTTTCCTCCATTTCTTC\n+TCTTTGACTGTCCTGCAATGTGGGGAAAGGAGTCACTAGTGGGTATAAGGAAATCAAGTC\n+TCCAAGTTCATCTCCAGTAGTGAAATAGCCCCCTTTAGCAGCACCCACAACAATTTGGTA\n+GGCACTAGCTCCAACTTTATCGGCAACAGTACCAACCTGAGAAACACCTCCAACTGAGGT\n+AAGCCATCTAACGACGGCTTGAGCCATATTTGGTAGGAATTTCTCAGGGATGTCACCACT\n+TTCTGTGATCCGAACTACTTTGGGTCTGGGGTTCGGTTCTGAATACTGGACTTGCTGAGG\n+T\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_9_Transcript_1/2_Confidence_0.667_Length_253_hit1_IdMatch=98.0,AligLength=250,E-val=3e-118\n+TACGGTGCCCCTAAGAGAATCGAACTCAAACTCTCCAGTTGTGTAGTAACCAGAGAGCCA\n+CCGAGGAGGGACGGGGTGGTGATTATGAAAAGATGATGGGTTTTGGGGAGAGGTTATACA\n+ATTTCAAAATCTTGAACGGCCACTGGGTCTTCAGATATCACTTTGAAAGGACTGAGTGTC\n+GTTCCATCAGGCATACCCTCAAGTTTGGTCCTAATCTTAGCTGTGTCCTTGCTGAGAGCA\n+ACAGTTCTTGTTA\n+>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171\n+GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG\n+ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA\n+CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA\n+TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG\n+AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT\n+GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC\n' |
| b |
| diff -r 000000000000 -r d76a0d8a9eac test-data/singlets.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/singlets.fa Sat Sep 02 07:09:11 2017 -0400 |
| b |
| @@ -0,0 +1,45 @@ +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_29_Transcript_1/1_Confidence_0.000_Length_607_hit1_IdMatch=97.7,AligLength=608,E-val=0.0 +ACGCCCGAGAGCGTGGTCTTGGGCATGGCACTGTAGGCGACCTGACTCCCAGACTTTCGA +GGGCGATTTCGCCCTCTTCGACGGGGTCCTTGAACCATTGAGCAATTCTTTCCCACAATT +TGACGAGAAGATACACTCTGTACGGTAACCTTGGGGGAACGACGGTTTCTGGTGGAAAGA +TTGTTTCCACTGTTGTTTGATATGCGCTTTGTAGTTGTGACGATGGTGGCCATGGCATAA +TATTTACAAATTGTATTCTTGATTTGAGTTTGGGTTGTTTGATGTTATAGGGTCGGCAAG +AGCTTACTTGCAGTTCTCTTCCTCTTTTTGCGGTCGAGAGTCTTTTTGTTGAGTCTCGTC +CTTTGTTCTGCGGTCAGCAGTGATCTCTTCGATGCTACTTTAGGAGGTGGAAACCGGGAG +AATAAGTCTTGAATTCTCACACGGTAGTCATCAGGATTTTTATGACTAACCTCTCTAATA +AGCATCTGCACCTGGCGGGGACAGTGCCCCGGGAATTGCTGCATTATACTGTGAAACAGC +TCCAAATCCAGGGTTTCATGAACGGGCACAATCTGTGGCACAGCTTTAGGGGCAGTTGCA +TATTCAA +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_27_Transcript_1/1_Confidence_0.000_Length_471_hit1_IdMatch=97.66,AligLength=471,E-val=0.0 +GCAAAAAGAATGCCTCTGATAGGGCAATCATAAAACTGTTAAACAAATACATGCCTAGGA +CAGGAAATAAGAACTGGCCTGGTGTCCATACAACCCCGGAAGAAGGCATACTTGATGGTA +TTAAGATAACGGCCAAATCCAGTGCAGGCGCTCCCTATTGGAGACACAAGGGGGAATGCC +TAGACCATATAATTGATACTGGACTTCCTGTTGTGCTAAAGCATATAAAGGAAGGAACCC +TCAATCAGTTGTGGCGGGAAAACCCTGAGATGTTCCTCGTTGAAGTTAAGAACAAACTTG +ATAGATACGAGGTTTCGAAGCTTAAAGAGAAGACTAGACCCTATGTGTGTGTACCTGCGC +ACTGGGCTCTCCTATTCTCGTGCTTGACTCAAGGATTCCAAGAAGGACTTCAAGTTTTTA +GTAACTTGGACCCCAGTACAGAATGCTCGAATGCATATGGATTTTCATCCA +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_14_Transcript_1/1_Confidence_0.000_Length_210_hit1_IdMatch=98.1,AligLength=210,E-val=3e-98 +TGTCCCGTTGCACCCCCCATCCATTAACAATCGGGGTGGGCATACTCATGTCACTCGCCA +GATGGGCGGAGTACCTCACCCTCCTCTTGGTCTAATACCCATAGCTCAGAAGTACGGGGT +AGAGATCTTGGACCAGAAACATGTCTACACAGGAGGCACTTGGGATGGCTTTCTTAATAG +ACTCGCCCAACAGATGGGCCGGACAACGGT +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_24_Transcript_1/1_Confidence_0.000_Length_280_hit1_IdMatch=96.79,AligLength=280,E-val=4e-129 +ACCATTTGTCCCCCATGGTGCATTTTCATGGTAAGGTAGTCACTGTTCCAGGAACCATCT +GAGGTGGTAAAAAGGTCCTGGAAACCAGTATCTGGAGTGATATCCTCGTCAATGGAGACA +GCTCCTAATTCAGCACCTTCAAACTCAATCACCCATTCGAGTGTGACAGTGAAGGTGGTG +CTTCCTGTGTATCCACCGGTGGTAGAGGCAACAACCACATTGATGAAGCCATGATTGGCG +TCATCAGGGTTGCCTTTGGTGAGATACCACTTACGGGTGG +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_22_Transcript_1/1_Confidence_0.000_Length_289_hit1_IdMatch=95.5,AligLength=289,E-val=1e-128 +GGCCTGCAGGCCATAACTCGGTTGAGGTTTTGAGTGTCATTGCCTGAGATATTGTTGGCG +GGGTCTGGAGACCATCCTATGGCAAGGGATCCAAAAGTATTTGCACTTCCAGATCCCACT +ACCAGCACTCGGAGTTTCTTGGGTCGCCAGCGGGAATATAGCTTACTCTGCTGCTGAAGC +CTAGAATCACTCATAGCCGTTGGACATATGGCTTGAGCAAAAAGGCTAGCTCCCACTGCG +CGCTGCGGTTGTACCTCAATAACGCCTATAATGTCCACGCCCGAGAGCG +>gi|225356593|gb|FJ150422.1|_Drosophila_A_virus_isolate_HD,_complete_genome--Locus_20_Transcript_1/1_Confidence_0.000_Length_352_hit1_IdMatch=98.01,AligLength=352,E-val=8e-171 +GCATTCACTGCTCTAAGTTGCTCGGTCAGCTGGTCAATGCGGCGAAGTAGATTAGTTTCG +ACAGTCTGAACTGCTTCATCAGCCACCCTAAATTTAGGGATGGGAGGGCTAATGACAGGA +CCTTGGGTGTAATACTTGAGACATTTGCCAGTATCTCCAGTGCGGATATAATCTTTTGCA +TCTGTGTAACTGGCAAACATAACAAAACCTGGGATAGAGTAACCTTGTATAACTGCAAAG +AAGTTTGCTGTCTTCAAGGTCGTCTTGTCCTCAAGGTAGTAGGTTACATTTGTCCCTGGT +GCATTTGTATACACATAAGCCTGGTGGGCAGCCGAAAAGGGGACCATTTGTC |