| Next changeset 1:82f2b6f20fa2 (2019-01-26) |
|
Commit message:
planemo upload commit b288d4f48e58e291bda17c5945c281348ee072c7 |
|
added:
macros.xml snippy-core.xml snippy.xml snippy_core_wrapper.pl test-data/S1.tgz test-data/S2.tgz test-data/core/core.txt test-data/fna_ref/snps.gff test-data/fna_ref/snps.txt test-data/gbk_ref/snps.gff test-data/gbk_ref/snps.txt test-data/map_qual/snps.gff test-data/map_qual/snps.txt test-data/min_cov/snps.gff test-data/min_cov/snps.txt test-data/min_frac/snps.gff test-data/min_frac/snps.txt test-data/mutant_R1.fastq test-data/mutant_R2.fastq test-data/wildtype.fna test-data/wildtype.gbk |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Fri Feb 16 13:40:16 2018 -0500 |
| [ |
| @@ -0,0 +1,25 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">snippy</requirement> + <yield /> + </requirements> + </xml> + + <xml name="version_command"> + <version_command><![CDATA[snippy --version]]></version_command> + </xml> + + <token name="@VERSION@">3.2</token> + + <xml name="citations"> + <citations> + <citation type="bibtex">@UNPUBLISHED{Seemann2013, + author = "Seemann T", + title = "snippy: fast bacterial variant calling from NGS reads", + year = "2015", + note = "https://github.com/tseemann/snippy", + url = "https://github.com/tseemann/snippy"}</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 snippy-core.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snippy-core.xml Fri Feb 16 13:40:16 2018 -0500 |
| [ |
| @@ -0,0 +1,76 @@ +<tool id="snippy_core" name="snippy-core" version="@VERSION@"> + <description> + Combine multiple Snippy outputs into a core SNP alignment + </description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + + perl '$__tool_directory__/snippy_core_wrapper.pl' + '$is_reference' + --indirs '${" ".join(map(str, $indirs))}' + + ]]></command> + + <inputs> + <param name="indirs" type="data" multiple="true" format="zip" label="Snippy input zipped dirs" help="Select all the snippy inputs for alignment" /> + <param name="is_reference" type="boolean" checked="true" truevalue="--noref" falsevalue="" label="Exclude reference" help="Don't include the reference file in the alignment." /> + <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection"> + <option value="outaln" selected="True">A core SNP alignment in the fasta format</option> + <option value="outfull" selected="False">A whole genome SNP alignment (includes invariant sites)</option> + <option value="outtab" selected="False">Tab-separated columnar list of core SNP sites with alleles and annotations</option> + <option value="outtxt" selected="False">Tab-separated columnar list of alignment/core-size statistics</option> + </param> + + </inputs> + + <outputs> + <data format="fasta" name="alignment_fasta" label="${tool.name} on ${on_string} core alignment fasta" from_work_dir="core.aln"> + <filter>outputs and 'outaln' in outputs</filter> + </data> + <data format="fasta" name="full_alignment_fasta" label="${tool.name} on ${on_string} full alignment fasta" from_work_dir="core.full.aln"> + <filter>outputs and 'outfull' in outputs</filter> + </data> + <data format="tabular" name="alignment_table" label="${tool.name} on ${on_string} core alignment table" from_work_dir="core.tab"> + <filter>outputs and 'outtab' in outputs</filter> + </data> + <data format="txt" name="alignment_summary" label="${tool.name} on ${on_string} core alignment summary" from_work_dir="core.txt"> + <filter>outputs and 'outtxt' in outputs</filter> + </data> + </outputs> + + <tests> + <test><!-- Test #1 - test with 2 zipped directories --> + <param name="indirs" value="S1.tgz,S2.tgz" /> + <param name="is_reference" value="false" /> + <param name="outputs" value="outtxt" /> + <output name="alignment_summary" ftype="txt" file="core/core.txt" /> + </test> + </tests> + + <help><![CDATA[ +**snippy-core @VERSION@** + +Combine multiple Snippy outputs into a core SNP alignment + +If you call SNPs for multiple isolates from the same reference, you can produce an alignment of "core SNPs" which can be used to build a high-resolution phylogeny (ignoring possible recombination). A "core site" is a genomic position that is present in all the samples. A core site can have the same nucleotide in every sample ("monomorphic") or some samples can be different ("polymorphic" or "variant"). If we ignore the complications of "ins", "del" variant types, and just use variant sites, these are the "core SNP genome". + + +**Inputs:** + +Multiple Snippy output directories. (At least 2 of) + +**Options:** + + - noreference Exclude reference (default '0'). + +**Note:** + +snippy **must** have been run with --cleanup False + + ]]></help> + + <expand macro="citations" /> +</tool> |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 snippy.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snippy.xml Fri Feb 16 13:40:16 2018 -0500 |
| [ |
| b'@@ -0,0 +1,246 @@\n+<tool id="snippy" name="snippy" version="@VERSION@">\n+ <description>\n+ Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.\n+ </description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements" />\n+ <expand macro="version_command" />\n+\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ #if $ref.is_of_type("fasta")\n+ cp \'$ref\' \'foo.fna\' &&\n+ #end if\n+ #if $ref.is_of_type("genbank")\n+ cp \'$ref\' \'foo.gbk\' &&\n+ #end if\n+ snippy\n+ --outdir \'out\'\n+ --cpus "\\${GALAXY_SLOTS:-1}"\n+ #if $ref.is_of_type("fasta")\n+ --ref \'foo.fna\'\n+ #end if\n+ #if $ref.is_of_type("genbank")\n+ --ref \'foo.gbk\'\n+ #end if\n+ --mapqual $adv.mapqual\n+ --mincov $adv.mincov\n+ --minfrac $adv.minfrac\n+ #if $adv.rgid\n+ --rgid \'$advanced.rgid\'\n+ #end if\n+ #if $adv.bwaopt\n+ --bwaopt \'$advanced.bwaopt\'\n+ #end if\n+\n+ #if str( $fastq_input.fastq_input_selector ) == "paired"\n+ --pe1 \'$fastq_input.fastq_input1\'\n+ --pe2 \'$fastq_input.fastq_input2\'\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "paired_collection"\n+ --pe1 \'$fastq_input.fastq_input1.forward\'\n+ --pe2 \'$fastq_input.fastq_input1.reverse\'\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "single"\n+ --se \'$fastq_input.fastq_input1\'\n+ #end if\n+ #if str( $fastq_input.fastq_input_selector ) == "paired_iv"\n+ --peil \'$fastq_input.fastq_input1\'\n+ #end if\n+\n+ &&\n+\n+ gunzip out/snps.depth.gz\n+\n+ &&\n+\n+ #import re\n+ #set $dir_name = re.sub(\'[^\\w_]\', \'_\', $fastq_input.fastq_input1.element_identifier)\n+ mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&\n+\n+ tar -czf out.tgz ${dir_name}\n+\n+\n+ ]]></command>\n+\n+ <inputs>\n+\n+ <param name="ref" type="data" format="fasta,genbank" label="Reference File (either in fasta or genbank format)" help="Fasta or Genbank file to use as the reference" />\n+\n+ <conditional name="fastq_input">\n+ <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">\n+ <option value="paired">Paired</option>\n+ <option value="single">Single</option>\n+ <option value="paired_collection">Paired Collection</option>\n+ <option value="paired_iv">Paired Interleaved</option>\n+ </param>\n+ <when value="paired">\n+ <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select first set of reads" help="Specify dataset with forward reads"/>\n+ <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>\n+ </when>\n+ <when value="single">\n+ <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>\n+ </when>\n+ <when value="paired_collection">\n+ <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>\n+ </when>\n+ <when value="paired_iv">\n+ <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>\n+ </when>\n+ </'..b'lue="mutant_R2.fastq" />\n+ <param name="outputs" value="outgff,outsum" />\n+ <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />\n+ </test>\n+\n+ <test> <!-- test 2 - gbk ref default -->\n+ <param name="ref" value="wildtype.gbk" ftype="genbank" />\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n+ <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n+ <param name="outputs" value="outgff,outsum" />\n+ <output name="snpsum" ftype="tabular" file="gbk_ref/snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="gbk_ref/snps.gff" />\n+ </test>\n+\n+ <test> <!-- test 3 - gbk mapqual=40 -->\n+ <param name="ref" value="wildtype.gbk" ftype="genbank" />\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n+ <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n+ <param name="outputs" value="outgff,outsum" />\n+ <param name="mapqual" value="40" />\n+ <output name="snpsum" ftype="tabular" file="map_qual/snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="map_qual/snps.gff" />\n+ </test>\n+\n+ <test> <!-- test 4 - gbk mincov=15 -->\n+ <param name="ref" value="wildtype.gbk" ftype="genbank" />\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n+ <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n+ <param name="mincov" value="15" />\n+ <param name="outputs" value="outgff,outsum" />\n+ <output name="snpsum" ftype="tabular" file="min_cov/snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="min_cov/snps.gff" />\n+ </test>\n+\n+ <test> <!-- test 5 - gbk minfrac=0.7 -->\n+ <param name="ref" value="wildtype.gbk" ftype="genbank" />\n+ <param name="fastq_input_selector" value="paired" />\n+ <param name="fastq_input1" ftype="fastqsanger" value="mutant_R1.fastq" />\n+ <param name="fastq_input2" ftype="fastqsanger" value="mutant_R2.fastq" />\n+ <param name="minfrac" value="0.7" />\n+ <param name="outputs" value="outgff,outsum" />\n+ <output name="snpsum" ftype="tabular" file="min_frac/snps.txt" lines_diff="6" />\n+ <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />\n+ </test>\n+\n+ </tests>\n+\n+\n+ <help><![CDATA[\n+\n+**Snippy @VERSION@**\n+\n+ Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels).\n+\n+**Author**\n+\n+ Torsten Seemann\n+\n+**Inputs**\n+\n+ - NGS Reads in fastq format (single or paired end)\n+ - Reference file in either fasta or genbank format\n+\n+If the reference file is supplied in genbank format, snpeff will be called to determine the effect of any snps found.\n+\n+**Advanced options**\n+\n+ - mapping quality - Integer - Minimum mapping quality to allow (default \'60\')\n+\n+ - minimum coverage - Integer - Minimum coverage of variant site (default \'10\')\n+\n+ - minimum fraction - Float - Minumum proportion for variant evidence (default \'0.9\')\n+\n+ - rgid - String - Use this @RG ID: in the BAM header (default \'\')\n+\n+ - bwaopt - Extra BWA MEM options, eg. -x pacbio (default \'\')\n+\n+**Further information**\n+\n+ For a much more in depth description of snippy and how it works, see https://github.com/tseemann/snippy\n+\n+ ]]></help>\n+ <expand macro="citations"/>\n+\n+</tool>\n' |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 snippy_core_wrapper.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/snippy_core_wrapper.pl Fri Feb 16 13:40:16 2018 -0500 |
| [ |
| @@ -0,0 +1,82 @@ +#!/usr/bin/env perl + +#-------------------------------------- +# +# snippy_core_wrapper.pl +# +# This is an intermediary script between snippy-core.xml and snippy-core +# It: +# - Copys the supplied zipped snippy output files to the working dir +# - Untars them to their datafile name +# - Builds the snippy-core command +# - Runs the snippy-core command +# +#-------------------------------------- + +use warnings; +use strict; +use File::Copy; +use File::Basename; + +my(@Options, $indirs, $noref); +setOptions(); + +my @list_of_dirs = split /\s+/, $indirs; + +#The list of final directories to be passed to snippy-core will be stored here. +my @snippy_outs; + +foreach my $d (@list_of_dirs){ + print STDERR "$d\n"; + my $bn = basename($d); + my ($name, $dir, $ext) = fileparse($d, '\..*'); + copy($d, $bn); + print STDERR "$d, $bn, $name, $dir, $ext\n"; + `tar -xf $bn`; +} + +my $test_list = `ls -d */`; +$test_list =~ s/\///g; +print STDERR "$test_list\n"; + +@snippy_outs = split /\s+/, $test_list; + + +my $commandline = "snippy-core "; + +$commandline .= "--noref " if $noref; +$commandline .= join(" ", @snippy_outs); +print STDERR "snippy-core commandline: $commandline\n"; + +my $ok = system($commandline); + +#---------------------------------------------------------------------- +# Option setting routines + +sub setOptions { + use Getopt::Long; + + @Options = ( + {OPT=>"help", VAR=>\&usage, DESC=>"This help"}, + {OPT=>"noref!", VAR=>\$noref, DEFAULT=>0, DESC=>"Don't include the reference in the alignment."}, + {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."}, + ); + + &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage(); + + # Now setup default values. + foreach (@Options) { + if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) { + ${$_->{VAR}} = $_->{DEFAULT}; + } + } +} + +sub usage { + print "Usage: $0 [options] -i inputfile > ... \n"; + foreach (@Options) { + printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC}, + defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : ""; + } + exit(1); +} |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/S1.tgz |
| b |
| Binary file test-data/S1.tgz has changed |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/S2.tgz |
| b |
| Binary file test-data/S2.tgz has changed |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/core/core.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/core/core.txt Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,3 @@ +ID Aligned Bases Reference bases % Aligned Bases +S1 2732313 3000464 91.06 +S2 2731269 3000464 91.03 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/fna_ref/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fna_ref/snps.gff Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,16 @@ +##gff-version 3 +Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 +Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 +Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 +Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 +Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 +Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 +Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/fna_ref/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/fna_ref/snps.txt Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,9 @@ +DateTime 2017-07-12T04:51:24 +ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq +Reference /home/ubuntu/snippy/test-data/wildtype.fna +ReferenceSize 200694 +Software snippy 3.2-dev +Variant-DEL 5 +Variant-MNP 1 +Variant-SNP 9 +VariantTotal 15 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/gbk_ref/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gbk_ref/snps.gff Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,16 @@ +##gff-version 3 +Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR +Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 +Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/gbk_ref/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/gbk_ref/snps.txt Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,9 @@ +DateTime 2017-07-12T04:52:49 +ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq +Reference /home/ubuntu/snippy/test-data/wildtype.gbk +ReferenceSize 200727 +Software snippy 3.2-dev +Variant-DEL 5 +Variant-MNP 1 +Variant-SNP 9 +VariantTotal 15 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/map_qual/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map_qual/snps.gff Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,16 @@ +##gff-version 3 +Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR +Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 +Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/map_qual/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/map_qual/snps.txt Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,9 @@ +DateTime 2017-07-13T05:37:56 +ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq +Reference /home/ubuntu/snippy/test-data/wildtype.gbk +ReferenceSize 200727 +Software snippy 3.2-dev +Variant-DEL 5 +Variant-MNP 1 +Variant-SNP 9 +VariantTotal 15 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/min_cov/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/min_cov/snps.gff Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,13 @@ +##gff-version 3 +Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR +Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 +Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/min_cov/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/min_cov/snps.txt Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,9 @@ +DateTime 2017-07-12T04:54:55 +ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq +Reference /home/ubuntu/snippy/test-data/wildtype.gbk +ReferenceSize 200727 +Software snippy 3.2-dev +Variant-DEL 4 +Variant-MNP 1 +Variant-SNP 7 +VariantTotal 12 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/min_frac/snps.gff --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/min_frac/snps.gff Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,17 @@ +##gff-version 3 +Wildtype snippy:3.2-dev variation 24388 24388 . . 0 note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR +Wildtype snippy:3.2-dev variation 29479 29479 . . 0 note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ +Wildtype snippy:3.2-dev variation 47299 47299 . . 0 note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein +Wildtype snippy:3.2-dev variation 102969 102969 . . 0 note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103048 103048 . . 0 note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A +Wildtype snippy:3.2-dev variation 103379 103379 . . 0 note=del GAA=>GA GA:11 GAA:0 +Wildtype snippy:3.2-dev variation 106602 106602 . . 0 note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 106722 106722 . . 0 note=ins GTTTTTA=>GTTTTTTA GTTTTTTA:11 GTTTTTA:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY +Wildtype snippy:3.2-dev variation 109833 109833 . . 0 note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase +Wildtype snippy:3.2-dev variation 114540 114540 . . 0 note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase +Wildtype snippy:3.2-dev variation 129881 129881 . . 0 note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type +Wildtype snippy:3.2-dev variation 138877 138877 . . 0 note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 138920 138920 . . 0 note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125 hypothetical protein +Wildtype snippy:3.2-dev variation 160547 160547 . . 0 note=del GTC=>GC GC:18 GTC:0 +Wildtype snippy:3.2-dev variation 160552 160552 . . 0 note=del CTA=>CA CA:20 CTA:0 +Wildtype snippy:3.2-dev variation 190866 190866 . . 0 note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/min_frac/snps.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/min_frac/snps.txt Fri Feb 16 13:40:16 2018 -0500 |
| b |
| @@ -0,0 +1,10 @@ +DateTime 2017-07-12T04:56:36 +ReadFiles /home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq +Reference /home/ubuntu/snippy/test-data/wildtype.gbk +ReferenceSize 200727 +Software snippy 3.2-dev +Variant-DEL 5 +Variant-INS 1 +Variant-MNP 1 +Variant-SNP 9 +VariantTotal 16 |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/mutant_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutant_R1.fastq Fri Feb 16 13:40:16 2018 -0500 |
| b |
| b'@@ -0,0 +1,49920 @@\n+@mutant-no_snps.gff-24960/1\n+AATGTTGTCACTTGGATTCAAATGACATTTTAAATCTAATTATTCATGAATCGAACTAGTACGAAATGCAATGAGCATCTTGTCTAGTTCGATTTTTTAATGTCTAAAAATGTCGTATATGTAATCAGAGTAGAAAGTGTTGAGGCGTTT\n++\n+5??A9?BBBDDDBEDDBFF+FGHHIIHHHEIHIIHIIAHDHIIHIG#IIHIFHHHFGIII*IHHHIHFIIHGICIHHIHFFFHHHIIIIIHIHDHIIIAHHH?GHHHHHF@HGGH6GGHEEGBGGGGGFGFE6FGFEFE?GF5EGGEEAC\n+@mutant-no_snps.gff-24958/1\n+CAAAGTCGTTGGTCATATAAAAAACCGCGTACAGTCAACTATAGATACAATCAAGATAAACTCATGCACAGATTGGGAGATATTTTAGTGCAATATGGAATTCAACATGACACAGGGTTATTACCACATGAATGGCATTATCACATTTCG\n++\n+?A????@?DDDABDE9FGGGFGICFHIIIBGHIIIGICHHIFH=IHAFIHIHHHHIFCIIEIHAIFGIHIDDIHEIIFIIIIHHHICIIIHIH=@HFHEHBFHIHHHH-HHHFCBHHDGHHEHGEH<GDEEEFHDEGGDGE*FGBGG,GD\n+@mutant-no_snps.gff-24956/1\n+TATAAATTCAACTTTGCAACAGAACCATCTAATCTTCAACAAACTGGCCCGTTTGTTGAACTACTCTTTAATAAAATAATTTTTCCGTTCCCAATTCCACATTGCAATAATAGAAAATCCATCTTCATCGGCTTTTTCGTCATCATCTGT\n++\n+?????BBADD5DDDDDGFGCFFEECFBBICIII,IIHIICHIHIIFHHHHHIHIIIIIIIAHHIHHH5FHDHHHHFIIHFGF5IIIHIIHHI@<IHHHHHDHDHFHHIGGEHHFHGEEFBHH?HH*FEGBHGH@EDG?C*FEGBGEGGGG\n+@mutant-no_snps.gff-24954/1\n+CATGATCAAAAAGCAGCTGATTTATTATTACAAGCACAACGTTTTGGTGTAAAAGAAGATGGTTCAGCAAGTAAAGAACTTGTAGATAGTTATAAATCAGAAATTCTTGTTAAAAAAGACTCAAAAATTAAAAGCTTGAAAGATTTAAAA\n++\n+<A?=?<?BBDDDDDDDFGGGAFEHIIIBIFH/CFCHFFIH9IHIHIIIHHIIIIIHHIHH>FHDHHHHIH+IFHIIGHHICHHIHHHIHFHHHCHHHFFHHFGHHCHIH<HHGGHHBEHGFE9HFGGAHGGF;:EGCGGGGFEE,B:AEG\n+@mutant-no_snps.gff-24952/1\n+CTCAATATCATCGGTGGATTTATTCATCCATCATCTGGTCGTGTCATTATTGATAACGAAATTAAACAACAGCCGTCTCCAGATTGTTTAATGCTATTTCAACATCATAATCTGCTGCCATGGAAAACGATTAATGACAACATTAGGATT\n++\n+=?<????BDDDDDDDDFGCFFFHB>H0FHHHIIIHDIHIHHH.CHIHHIIDEIHFIIFEHIIFIHIIGGIIIFIIHHHFDCHGIIHIIHIHHHHFEHCHHIDHCHFHFHHFHFHHFBGEHGHEEFGFHGHGF*?GGEE88DEGF6FGBA*\n+@mutant-no_snps.gff-24950/1\n+TTTCTTTCTTTAAAAATGGTCTCATAAAATGGTTTCGACTGTATTCTTTGCATGTCACCAATTACATAAAACTCTTTTTTAGCCCTTGTCACTGCAACATTTAACAAGTTTGGTTTTTCGCATGACCAGTTCACAGCACCATCTTGAGTA\n++\n+A5???BBBD@DDDDDDGGFGGFHEFB+HIIGIIIGHGIIFIHIHCI>IIFHHHAHIDHFICHHIFICHHIIHHHIHHIHCFIHIIIH=HHIH<HEFEFHHFHIHHHFDHHEIGHHFGDFHHEEHGF=HGHGGEFFCEGEDFFCGAGEG8G\n+@mutant-no_snps.gff-24948/1\n+ACATCGATGTTATTAAAGGCATTATCGCCTTTTCATCAAACAAAAAAAATAATTCAGAATTAGATGAGCTATATTCCATTTATATGAATGATGATTCTATCACATCCATTGTTCACCCTGACTTAATAGAAAGTATAGAGCTTATCCATA\n++\n+?AA?ABBBDDEBDDDDFCFGCCICFHHFFHIHHIEFHHHIGHCIIIH,IIIAIHEEEHHGIFHH5IHHHAHHHHHHGIHFHFGHIHHIIIFIDIEDHHH?H.HFH.HHH?HDFEHAHD:G=EEDEFEHCHHHHGDFGGCEG@FDE?EGEE\n+@mutant-no_snps.gff-24946/1\n+GATCCGATTCAAATTGAACCTGTTGTTACTTTAGAAAGCCATTTAATTGATAATATTCGTAAAAATTATAATGTTCCGGAATATCTAGTTTCTAAAGAAGCTTCTGTGCAGTCTGTCGCTGACAACGCTAATCAATATGGCTTTTGGAAA\n++\n+?A???BABDBADDDDDCGCGGGHHIIIFHCHIIFHH/IIHI=IGIEIIIIIHIAIIIHIEIHIIHHDHD?ICBIHIIEIIAHFIH?HHHHHHHHDFIFHCFHEGHHFFHEIHHEGGEH*HFGF>EFEEGCFHGFEE8FFGGFEFGG8HG9\n+@mutant-no_snps.gff-24944/1\n+CCGATTGGCGTCGTAGGTGCTGTTGTTGCTTGGAACTTCCCAATGCTATTAGCTGCATGGAAGATTGCGCCAGCCATTGCTGCAGGTAATACAATTGTGATTCAACCTTCGTCTTCAACACCATTAAGTTTATTGGAAGTTGCTAAAATT\n++\n+??A??7B>DDDDDDDDAGCFG-HFHEIH.HHICHIHHIHIIIIGHHDHFFIIFFFHHIIHHHAH=IIHHHHFEEHHHH>IIIIIF7HHIH*G.@I>IHHH.6HEDEHHHHHGHGGHG,GFGGGGGGGFEDHEDGFEGC@GHG@GCGGGGB\n+@mutant-no_snps.gff-24942/1\n+TCACTACATTATTTTAAATATCTTTTACTTCTGCAGAAACTTTCATCCCATTTTGAACATCCATATTTTTGAACGGGACAGTTAACACATATTGTTTTAAATAATAATTAAGCGTCTCTAAACTAAGCGTGTTATATCTTGTATTATCAC\n++\n+?AA??=BBDDB<BDDEFFFDGCH0E-HFHHIIHI=CI/HHHIHHGDHIGIID@FEFFHHIEGHHDHH@IEH>IFHBHDIHCHIEIIHIHHHHIGECIHDHIHHH.FHFGHIGIHHHGHGHGEGGGGGGFHDFGGBGBGHFEGGEGG=EFG\n+@mutant-no_snps.gff-24940/1\n+GACTTAATTTCACAATATGCTCAACTGTCTCACGATCTTTAACGTGTGGCACAATAATACCTCTCGCACCCATATCCAACACTTTAATGATATCTCTATCTATCACTGCAGTGACACGTACAATTGGTATAATATGCGCTGCTTCAGCTG\n++\n+?????BBB@D@9DDEDGGFFGGIHHHIHIFHIIIHIIGIIIIIHFIIIGHDFFIHHHHIEHHIHBHHIIAHHIFIIIIIFD4HHICIHHIHCGHHH=ICHIHGHHFHHDHHFHFHGGGHHGGHH*FE:EEHDGEGGGGEGCBGGFFEG@E\n+@mutant-no_snps.gff-24938/1\n+ATGAGTATGGATGTTATGGGAATTTCAAAAGAAGAATTAAGAGATGAAGTCGATTATGGTGGCGTAGGTACTTATATTGGACATGCTGAGCAAGCAAATCATAACTTATTTATCTAATCAATAAAATCTATTTTAAAAAGGAGTTTTTTT\n++\n+????=B>BDDDDDDDDFFFGGGIHCIIFFHIII0HIIIH?HGIHIHI>7GHI>HFEHDHHHFHHFIFIHIIE-IHIHFIHHHFHFHIHHDCGGHHHHI'..b'GGGGEG\n+@mutant-no_snps.gff-24/1\n+ACAATCTACTGTATCTGAAGATGGTACTGAACAACAACGTGAAGCGGTTGTAAATGATGAAACACCAGGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGTAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGA\n++\n+9??AA?BBDDDEDDD=?GGGGGIICIHAIFFIHHIHHHHH=EHHHGIHIFGIEEHF9IGIFHIIIIGHHHIHIFAGHIIGIEI?GHGGHHFH=FHI?HGHFDIIF5FHHD,HFHHGFHHHGAFGEGFEFHGG(GGEGG8F::CE*GGEGG\n+@mutant-no_snps.gff-22/1\n+ACGACACAATTTATTCCCCATTGGGAACAACCAGAGCATATTCAGTCACTTACGTTTCATAGTGCTTTTGCAACACTTCAACAACACTTACCTGAAATGAAGCGATATGCAGATATCATTGTGGTTTGTTACCATGGTGGATTTGAAAAG\n++\n+???A?BBBD<EDDDBBGFGGGGFCH-IIAHFIIHIHHHIFHII@HIFHFFIICFIHFHFFDHI/IHGHFFHIEGIHE-IHFIEH=:IFH+HHHHHHD?HFFF8HHHIHHH.=HDFHECHHCGGG,EHCEGFGGF,EE)=@G?CFEFEFGE\n+@mutant-no_snps.gff-20/1\n+AGGAGTATCCGCTTGTTAAATGTACATAGCTTATATTTAGCTGTTTAACATGCCACATAATGATTCGAATTATTCCAAGTCCCGCACCTCAGAATCAAAAAACATTCGAGTGATAAAATTTTAAAAATCAAAAATATAAAAATGATCTAA\n++\n+?AA??ABABDDDDDDEGFGGFFEIHHHHIHHHGHIIIHBIIIGEGHCIIIIHFIEHHHFHIIIAFHIIIIIHH0HIHIIHHHIIFDHHHIIHHHHHEFHIEGHHG=HIHGHFHGF?HHHEGGG?F2GGEEFFGHE;.G.GEF@=?ECGEG\n+@mutant-no_snps.gff-18/1\n+ATAAAGTTACTTAATCATTCTCATCATACAATAATTTTTACTCGAATTGGAAAAATTATAAAAATTAAACATAGAAACAACTTGAACATTGGTTTTATGCAAGATCAGTAGAGATAACTGTAAAATGTTCTTAATATTGTCAAAATGTAA\n++\n+?AA??AB?D9<DBDDDFCGFFFHHIIFIIHIHGHHIIHBGHDHHHIII-HHHIIIHIIHHFCIHIGHHIHI@HHHFHHCHIHIIFHGIHHFHIIEHGHA)CI=HGHHH=H,.FHHGD@GGHHDGGFB+HD+,@;GFGFAGFBGGGFE;GG\n+@mutant-no_snps.gff-16/1\n+GTATTTTCGGTGCATTAAAATTGATTGAAACGACACATATGCCAAAATCACAAACACCAAATATTAATAAAGGTATTCGCCGTTCATTTCAATGTCTATTATGCACACAACAAACATGTCGATTTATTATCGTTGGCGTTTTAGCAAACT\n++\n+??=9?5BBBDDDDDDDGFGFFFCHIHCHIFHH+HHFHFFIIEHHHEGFHFHIHHGHIHIIHFFHIHIFIIIHCH-HHGIIHGHEIIHIEHHHHIGGHAHD5GHCHHHEIHIGHGHHFAGFFDD2.FFFFHFFEEGIGEAGG?EGG*EG@G\n+@mutant-no_snps.gff-14/1\n+TTAAATATTATGCAAGATCAACAAACGTTAGCGGGCATTACGGCGAATGCGCTTGCTAAACTTGATAGCATCATTAATGAGGAACAGCCGGATATGATTTTAGTACATGGTGATACTACAACGACTTTTGTAGGAAGCTTGGCAGCATTT\n++\n+?????BBBDDBDED<BAFFGF@EEHIHHIHIHCHIHIHHHIHHIIHAIIHHFHIHFHHHGDFIFIHHHIIEIHHHFBHAIEHFIHHIIFHFHHIHGHFIHE,FHHHHHHHHHGHFHGEHHGH>EHGGFHFH+FEGABEGGBEEGEGEGG2\n+@mutant-no_snps.gff-12/1\n+TTTCACAAAACTACTCAATTTATTAAAACATGAACAAGTGACTTACCTCATAGATGCTAATCCATCTATATTAACACCATCTTTTTATGAGCATCTTCGACAATATGATGCACAATTTATGATTCGTATCGATCATAGTACATCAATTGA\n++\n+A??==BBBDDDD@D<DGFFGFGIFHIIHHFHHIIIIFFHIHFHHIHFHIIH9GFGI=ICHFHEBFIIHIHGHIHIIIEFIIHIEI+III7HFHHGHHFDGHHHHIHEHHGHHHFHHEHGEHHFFGHBH;EDGGGEGFGFE(*8GEGGFGC\n+@mutant-no_snps.gff-10/1\n+TCACCATAATGATGAGCCGCTTCCTTTGTTGGCGGTACTTGTTGCTTATCTGTTGTTGCTTTGTCTATCGTTGTTACTGCATGTGCTTTCATTGGTGTATGTTGCTCAGCCGCGCTCGAGACTCGCCATAATCCCATTGCACTAAAAAGC\n++\n+?A??ABBBBDDDEDD<FGGGFFHEIFHHHIEIIH9HIIFIDHHAHIDIIIHIFICIDHGHHHHDIHHIGIIHHFHIIHHIHIHIIHHIFIHHG=HFHH?HEHEH-HE*DHHHHFFFHHFEHHH6HGEFHEEBCFGCAGCEFGGCBCG@<G\n+@mutant-no_snps.gff-8/1\n+ATGGTGTACTTAGCTTAAGTAAGAATCCTGATATTTCAATTGCTGAGTTAATGGAAGATATTGAAGGTCCTGATTTCCCAACTGCTGGACTTATTTTAGGTAAGAGTGGTATTAGACGCGCATATGAAACAGGTCGTGGTTCAATTCAAA\n++\n+?????BB?DEEDDDDBF?FGCGIIHIIIIIICHIHHIIIHIIFHFIHHIIFBIIIFIHIHHHHIHIHHIHFH5HAFHIHGHIHHIEIHIHIFHGFIDIHIEHHEDHGGDHHHHBFFFDH6HGEEHGD@FGHGFEGFG=H1GGGFGEG@EG\n+@mutant-no_snps.gff-6/1\n+TTACCTTTGCCTAACTTTTCCCCCAGTGCACCGAATGGTTCGGCTACAGAATACCCTGTAATTCTGTGTTCACTTAATGCGGCTGGCATTTCTGCTGGCGACATTTCATGATAGCTAAAATGCCCCGGTTTAATCTTTAATTGTTCTCGT\n++\n+??<??BBBDDDDDDDDCGFEGGICIIHIFIIIGIIHIHIHFI:IHIHIIIIHHHHHGIHHHFHIFFHIHGHICHHHGIGAH@HEHDHI7IHHFIHHFHFHCHHEI=HFH?FHCHHHHFG+EHGGH7H8HDGHGEBGEGHEHEG@@FG?GD\n+@mutant-no_snps.gff-4/1\n+CCAAACCAAGATAATCCATTAACAGAAGGCAAAACACCAATCTTACTATTTGATGTTTGGGAGCATGCCTACTATCTGAAATATCAAAATAAACGTCCAGACTATATGACTGCATTTTGGAATATTGTTAACTGGAAAAAAGTTGATGAA\n++\n+??????BBDDBD@DDDFFGFECHIIIIH>IDGHIH@IGIIII>:IIHE,CHFFIE.H-HHIHIEFGF5HIIHIIHIHIIHIHIEFIFHIHFHFIHHGIHIIEHHIIGHHE?HHH;HGEFFHG*;GGFHGHHF?ED=EGGCGG8EF?C5EG\n+@mutant-no_snps.gff-2/1\n+AATTTAAATTTAACTGGGTGGTCATTGTATCGCAATATATTATTTCCCGGGGCATTTAAACAAATCATGGCTGGGATACATATGGCGGTAGGAACAAGTTGGATATTTTTAGTTTCTGGTGAAATGATTGGTGCACAATCGGGATTAGGT\n++\n+????A9BBDDDDDDDDFGGFEGFHHIHHHIHCHIGH,EGIIIFHIHIFEHHGFIHIIE5CIHFHHHIHHIFHIHIIII5IFHGHHIFF?FGIHHHIICFHCHI7HHHHHHHHGHFHHGDHGFHEHEDHFFEFGEFG@EEGC-EGHGGGEG\n' |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/mutant_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutant_R2.fastq Fri Feb 16 13:40:16 2018 -0500 |
| b |
| b"@@ -0,0 +1,49920 @@\n+@mutant-no_snps.gff-24960/2\n+TCCATTCATCGGTACAACTGTATTTGGTGGATTATCATTAGCGTTAGGTGCAGCGTTATTAGCTGGACGTCGTCGCGAACTATAAAAACAAACAATACACAACGATAGATATCATTTTATCCAAACCAATTTTAACTTATATACGTTGAT\n++\n+????9BBB@DBD@B<DGFFEFAIHFHEH>FIHHHHICIHFIIIIC9H9H8FCCAHHI=DIG?HEHC?I5HEIGEHHFHHIH?=HEIFA/H<HHHHHIIG,HHH-+HHF@FEHGFFHEH*FF;HDHGGHGDHD*GE-E-EFEGD;;G*EG-\n+@mutant-no_snps.gff-24958/2\n+TGTAAAACTTTCTTTTTGTGTCCATATTTGATAAAAATCATTTAAACTACATATTTGATGTGCTTCGTTTGTAGAGAAACACGTCACTAATGTACGCCAGTCTAAACGTAGTGATATCTTTTCGATATCAATACCAACTGGTTCTTTATC\n++\n+?????B?BDDDDDBDDFFGGC+IIHIHE+FHICIEHIHAD+IIHAHHHIEHBEGIIFGDGIHD-HHHF.HH5HHHH6FH-HCC(HCI@HDHHIHHHFC-FIHGHDDFFH,FEDGEHHE+FFG(FFF9HG=DGGGE;)GEFGG':ED*CF2\n+@mutant-no_snps.gff-24956/2\n+CTACGTGAATCAAAAACAATGGATTCAATTTTGGAAAAAGGCAATGAAATTAGACTATGATCCAAATGTAAAAGTTCAAATGATTCGACCGAAAAATAATTATACATCGGATATACAATCGGCAGTTGACGAAACTGCAAAATAGCCTGT\n++\n+A??,9B7B-DDDBD9DGGGGGEFFG/H>IF/IHIIIH+FHH.H-HHHFEGFIHHFCHAEHHFHDCH+HHFEDFIE-FIGHFIHCH@FHEHEHII+CG,I+FCDH+GHFFECHCH4H+FFD9G;7F=D1?@8FEEDEG;GEE2CF'EE*G*\n+@mutant-no_snps.gff-24954/2\n+AGAAATTGTGTCATTCGGAATAGCTTGTGTTAATTTTAAAATTCGTGTGTCTTTAAATACATTTGGTTGGTCTTTTTTCACAGTATTACGTGCATCGTTAAATACAGCTGCAGCATCTACATCTCCATTTAATAATGAGATAACTGCTTG\n++\n+??9??BA<D@DBDEBDGFGFCFIHIIII.CHHIIGHEIHIIH9HHFHEHFH/IHHHFHHGHECH5HEFFIBFHD+@HHFFI5GIHDH>HBHHGHEHGHHHH+D=DDDHHHEHHHHE*DFHE=FHHGEEECDHCF+FGCEGGGFFEC5EEE\n+@mutant-no_snps.gff-24952/2\n+GATAAATAGCTTCATCAATATCGTGAGTGACTAATATAATAGTTGATTCCGTTTTATGTTTTAGTTGTACTAGTTGATCTTGAAGTTTATAGCGTGTAAATGCATCTAATGCATCTAATGGCTCATCCATCAATATAACGTTAGGCTTAT\n++\n+A???,>BB9BBDDBDDCCGCCGH8HHHEIHFIHI+HCHIE9FIIHHEII+9CIHEFFIHEHI5=I5H5HGFIHEHF55D-5ED,-HGGG9H=+HCIIH+HCEHIHFEHFGHFH#FHFHEH,:42HD)G**FBE9?(EEFG*EEGEGGHG9\n+@mutant-no_snps.gff-24950/2\n+TGAGCCGAGTTCATTTGTAATATCACCATTTTCAGCAGTACAAAAACAGGTTAAACGTATATTAAAGCAACAACTACCGACTAGAATTGATATTGAACGTACAAAAATTAATCAATGGGTCGATAAATCCATTGGTACTGTTCATACTTT\n++\n+??,??BBBDDD@DDD+8AGFFFIHF-HHHHGIFHHIDHHICA+H-HH9IGFCIFHBFCHIHDI5HHII@HHEHHIHFHHD+EFIHC4IFIIA>IDHGCHHHFHG.HDFE-HEEBCHEDHH@HHDG>5CEGG=8GF=EGFGGEABEE?GG3\n+@mutant-no_snps.gff-24948/2\n+AAATTAAAATGAAGTGTTCTCGGTCAGCATTTCCTATGAAGTCACGCATAATATCAGCAGCGTCTTGTGGTTCTTCAATACGTCTTTTTAAATACCAAAGTGTATCTTCTTTAACCATTCGGACTTTGACAACATGTATTCTTTTTCTAC\n++\n+?????B>BDBDDBDDDC>FFFEHIHI8IIECEHI+-HDIGHHCHEHCGHGH?HE9EAA=IFDDI-D+HFHAIFFHHII5HGIHEDHHFIHFFIHFIHFHDCHDGBI=6HCHF;EHE=DH.H=EHGGHF?FGEE4GF2HF*>DECF;FGEE\n+@mutant-no_snps.gff-24946/2\n+CAATACTTTTTCGCCATGCTCTTTCACAAATTGTTTTTGTACTGAGTTTCCTTTAACGTCATACCAACCGGTCTTACCTACGTTTGTAATATTACTAGGTAGCACCATTTTATTATTATAAGCAATTTGATTAGCTATCGTGAACATGGG\n++\n+?=???/BBBBDDBDBDGFCF.+CFHIFHICHIGG@HHIFIDBHHIIDHCGFDGHH5FIHFBFDHHFEEAH5FHHIHGCFHHIIBFHDIHIEHEHF7HHFIEFF6.EHGF?D?ICEEHFDFFFBG,FHH@@HEFCFFEB@*EE=EFEGE**\n+@mutant-no_snps.gff-24944/2\n+AACTGAATACCTTCAACTGCAAGGTCTAAATTAGCATCATCTAATATGATATTGGCGCTTTTACCACCAAGCTCTAAAGTAGCAGGTACTAGATGTTTCGCTGCAGCTTCGGCATCTTGATAACCTACATCAGTTGAGCCCGTAAATGAT\n++\n+,9?????>DDBDDDD@GFF8GFI/-IHHHEIHFHFIHHDH.HCHBHI>IEBIHIIHIGEHH5B@HG>D-EH5III-HHAF<FEHEDFEHHHHHIHDGHFG.@HI+FIGC=#EFE+HFE+D*HGGHEHD>EGAEE=FG95(B6CGEDEGGE\n+@mutant-no_snps.gff-24942/2\n+CATCAAAGTTTGATTCAGCACACCAACAAATGCACCAATCATTACGACAGCTATAACACGGTTCCGTTGTTTCAAATCTATATTAAAGGCATATACATTCCTCAAATTTTGACGTCTCCCTCTCTTTTAAGTGGAACCTACTATCATTTA\n++\n+=<A??BBB<DBBBD@DFFFFGGHIBCFEFIIH/IGIHIDHHHI9F?HIGIHFH5AHDH8HG+EHIHEFGHID*IEFIIFFHIHG+IEEHFIIFEHEIHHFEHHEGIHGHAHG<H+=GEFBGE@9GGEFF8*GGG?CFGGE6G2@E8D=EG\n+@mutant-no_snps.gff-24940/2\n+TCGATTATTAAGTGACTCCGAGTTAAGAATTCATCATGTTACAAATCCATTAGGTGTAGGAGGTATTACTGATGCAACAACTATCTCTGAAACATAGATTAAACAATGGTGATTCAGTTTATGGCATTTTTAATTCTATACCGGACCCAT\n++\n+?????B>BDD-DDD-DFFAGEFIEAFIHFII@HHI-H>HHHHEDHEH/IIHCDHFF)DIE@IFHHEHCFFHIAICHEIHCIHFACIHD7GHDEIIIDH.HIHH@HHHIHHBHDGHFFEHFHCG??F+E=5(=GFDEE?E;GGGACFGG.E\n+@mutant-no_snps.gff-24938/2\n+CTCTAATACCTGAAGCAAAATCAGCATGAATATGTGTTTCTGCAGCTTTAGTAATTGTGAATCCTTCTTTATCTGCAACTTTTAAATATTTTGTTAAATCTCGTATAGGGTCAATAATCATTGCTTCTCCTGTACGTTGACATCCAATTC\n++\n+???A?BBBD?DDBDD@6GFCGFHFCIIC/FIIHGIGFHI+HIHIHHAHHHIF=HHEFHGG'FFHIF@?H5@FIIFHGHE5ECHFHEHDICHIH@HFGH"..b"G<GF;E\n+@mutant-no_snps.gff-24/2\n+GTGGTGCCACCATCAAGACTTATCAATGAAATACCTTACGCAATGAAACAATTAGAAAGTTAGTCATTACTAATCATTGAATATAGTATAGCATTACTTTCTAGCATAAAAATAAGACCCCCCTACATATAGGGAAGTCTTATTTTTTTA\n++\n+9???,<?BDDBBBB<DGGGGFGIHEIHBCFIFIHIII-FEHHHI9HIHHHG0HEH+@ECFH.HHHGFHHHHAGF7HIIFHHIHHCFHEHHHFHE)GHF.ECHFHDGDCGGHEFFHGHEHF,FHHHHDGEE)FBEAE*EFE/EGEGF:F,/\n+@mutant-no_snps.gff-22/2\n+TACTCAAGACAACTTTGCCTACAGTTGTACCTCTCGTACCAGGTTGAATCACAGCCGTTTGCTTAAACCTTTCAGCAATTTGTCGATGTTGGTGACCCGTAATAAAGATATCTATATCTTTAGAAAACGCTTCTAACATGCCATATCCTT\n++\n+=????B/?DBDBEDDEAA+CEGFHFHIH.HIFHH7IF?@FHIHGHGFHHF.IEFEHIEFIIEDGIEFEFFHIFCF>HHIECI@HFGDEHHDHIGDHHH5CIH3FHFGF?FHEFHHHE=04GDHGG0EFFFGF:G*GAEDD)2GEGFAAGC\n+@mutant-no_snps.gff-20/2\n+GAATCTTAGAACCTTCCATTTGACCATCCCTTATTAAAAAACAAGCTGCAGCAAGTGAAGCTAGACCAGATCCGATTAAGTAAGCGGATTTGTTTTCTACATTTTCAGGTTTTTTAGGGCGCGCAAATGCTTCATAATTTCCATAACTGT\n++\n+A????BBBBD-DDDDDGGFGFGFIIHC-EFIEDGI=EHHHGHHIGGGEF+?+HGHH+IHEFHGHIFHCIFIDBF5HIHIDH5DFH++HIHIFEFIDHHFH,EHCHHHGFHHIH+EF,E=+.HEEEEF3(HF+BECID8EGHCGGD-EEEE\n+@mutant-no_snps.gff-18/2\n+AATTAATTCATAAGAGTAAATGCCAATAGATGGCATACCGATTCCTGAACCCATGACAGAAACTTTTTTACCTTTATATGTTCCGGTAAAACCAAACATATTTCGCACTGTATTGAACTGTTCCACATCGTCCAAATATGTTTCTGCAAT\n++\n+????,?>=B<BB?DBDG-F-GGCHH6I/AHIHIHHIHHA'IHFIIHHHHCHF-IIH+IH@GHIF?GFIDHI;*A;IHIHF=GIAGHIGHHH6DGHEIICBG+DGAFFHD4FFGDFIHEFFH*G;F@EE9FFFFG4GAEGEE=G8EE8EGE\n+@mutant-no_snps.gff-16/2\n+AAAAATTCTACATTCGTCGCTAAACCTTGCGGTATCGCACTACAACCACATGCAATCGTGGCAAATATATATACTGATTTAACATATGATTTATCATTAAAGCGACCCCATAAAGGCGCGCTTAATATCGAAGCCGTCCAAAATGCGGAC\n++\n+??,??7BBDDD-,-BDGC/?AGCHHIH?HH,/D9HHAHHHIHHIHIHG@HHDHHHEHEFFIFFAGIIHFHDF5IEHII3IHHDCG-G7FIFEEHGHHFF.IHF+HHHFHHFBEHEHHHH.GDE++HGGBBG?G=AEGGGEECFGH*EFGE\n+@mutant-no_snps.gff-14/2\n+AACTGTTGTTGACAATGCGTCGATAACTGTATTTCCGGTAATGAAGATACTCTCTTTGTCTTTGTTTTCAAAAAGTAAATTTTTAGCTGCAATTACTGTTGGCGCAAAATTCAATTCAGCAATATTACTTACCATGACTCGATTTAATTC\n++\n+??A??B9B@D5?DDDDGFGFC-IHHC;III+FHIHGHIIIHI-HHGDE.=HD?HHHIHHHHH5EHHHFHHDFHD=?HFFHFBIHIHEHH*HEHHHFGDH8HIGFDHGHHHHF;HHIEDHHDE@HHGEEH;FG6(BDFGBEFGGGFGG,4E\n+@mutant-no_snps.gff-12/2\n+CATATATTTGTGCCTTTGGATTAAATTGATAAATGAGTTCATTTTTCTTATTGACCAAGTCAACAGATAATCCCGTATCTGGTCTTGGATAATAGTTATGACAAAATGAAAGTAATGTAAAATCATTCAATTGTTGATGTAACCTTGTTA\n++\n+??9??B/BD<ADDDDBF?G+FG,HIEFHI;HHHIIFHIFIIHHIGBEIEEIHDIEBDHH8HHHFFHHIF(HFHFFIHHIIIIHCIIFCHAEFHIH.GFIHFHEH@HHHEHHDHDFH@HHHHC=F@GGG@FFFDGEEEE@GBG(.8EGB@G\n+@mutant-no_snps.gff-10/2\n+GATACGGATAAAGCTATTCCAACGCCAATATATACAATATAAATGAGAGTCACCCGATAAAGTTCCGCACTGCTGTGAAACGACTTTATCGGGTGTTTTTTTATGTTGTTGGTGGGAAATGGCTGTTGTTGAGGTTAAGGTTCTAGTTGA\n++\n+???<?BB=@DDDDD-DGCF.FGIF90HHBHHHGFHE-FGDIIHHHHDFIHFFGFHHF@DHHHI9?HFAIHFIH5HCIIHHF-=IFHHHIHEHHEHHH,HHHAHFD?H4IDHFDHEGHHEGGGB@HHHGHFEGG+;+?G7;)GECGGGEGC\n+@mutant-no_snps.gff-8/2\n+AAGAGGTGTTTGTTTGTATAAGTTATTTAAAATGACACTAGCATTGGCATCCTTACGCACATCAATAACGACACGCACACCAGTACGTAAACTTGTTTCATCACGTAAATCAGTAATACCGTCAATTTTCGTGTCACGAACAAGCTCTGC\n++\n+<????>+BBDDBDDDDFFGFFG>FFIHC-7ICF/HIEHHH.IH+HFHAIGGFDHHHGFHHHHHIHFHHIEFIE@I-HHCFCHIFEHIHBHFHD.HHFEHEHIDH-DHHH=,=HHG=GFHHDDFFE+DGEH*HGDGGEGEEGEFFE?G.GG\n+@mutant-no_snps.gff-6/2\n+GCATCAACTTTAATAGAGCTCGCGATGAAATCAAAGCAGAAGGGCTCGAATATAAAAGCTGTGGCATTGGGGCATCATGAAGGCAATGTCATTATGGGACAAAAAGGTATGCACTTAAATGAATTTAATAATAATGGCGATGATTACCAT\n++\n+595??BBBDDDDDD<DCFFCGFHHIH>HHIHI9IHHHEEHIIHGGHCH/IIHGEFDIGHHFGEGEHCI-GHIFCFIHHHIGGHII-EHH+DIGHGHEHHF?FEHHHGFF=CHGHHFH8?E:EEFHHEBF2FFEGB3FGE*GFGEEGGEG2\n+@mutant-no_snps.gff-4/2\n+TACTTATTTTGTCAATTTATTTAATGTCAATATGTTGATTAATCAATAGTGTTGTCTGATGTATATAGCATTTAAGTCATCGTTATAGTCAACAATAATAAGGTATTTCGAGTTGAAATTTATCGTATTATTTTTCCACTTTTAAGCGCT\n++\n+?<???B>BDDDDBD<DGFCFF86HHHHHH-F(DHHHHHBHHHEIGFGDHHHEHHIC@HIHHCHIHAEFIFIFC=DHGHIDFFH-7GED5AIHFHHAHHGGDEHFF65HHH?6EH=F=EGBFFHH+E+GDFCFG8)D?0@G)D*D*=G=EE\n+@mutant-no_snps.gff-2/2\n+CTCGGATAATACGTCCCTTCATCAACTTCTACTAAATGAGGATCTAATTGTTCTTTGATAAGTGTTTCTAAAGTCATCATCATCTCTCCTTATTCACCAAATCTTCTAAGTATAAACTGCTCAATATAACTAATGAATCGATCAATAATA\n++\n+????<>B?6BDDDDDDFGGGFGHIHHHFHIAFIG5,H/FHG>@FHIH9HHHDGGDABIGHIH>I-AIHCBFHEGI+FH;4EIEHFHIHHFEH-FF4HCHHF.FHGFHH?HHFGDCHH?FEFHHF@CGGEEFGEHEID,GEGGGE(8EGBG\n" |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/wildtype.fna --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wildtype.fna Fri Feb 16 13:40:16 2018 -0500 |
| b |
| b'@@ -0,0 +1,3291 @@\n+>Wildtype\n+ATGTCGGAAAAAGAAATTTGGGAAAAAGTGCTTGAAATTGCTCAAGAAAAATTATCAGCT\n+GTAAGTTACTCAACTTTCCTAAAAGATACTGAGCTTTACACGATCAAAGATGGTGAAGCT\n+ATCGTATTATCGAGTATTCCTTTTAATGCAAATTGGTTAAATCAACAATATGCTGAAATT\n+ATCCAAGCAATCTTATTTGATGTTGTAGGCTATGAAGTAAAACCTCACTTTATTACTACT\n+GAAGAATTAGCAAATTATAGTAATAATGAAACTGCTACTCCAAAAGAAGCAACAAAACCT\n+TCTACTGAAACAACTGAGGATAATCATGTGCTTGGTAGAGAGCAATTCAATGCCCATAAC\n+ACATTTGACACTTTTGTAATCGGACCTGGTAACCGCTTCCCACATGCAGCGAGTTTAGCT\n+GTGGCCGAAGCACCAGCCAAAGCGTACAATCCATTATTTATCTATGGAGGTGTTGGTTTA\n+GGAAAAACCCATTTAATGCATGCCATTGGTCATCATGTTTTAGATAATAATCCAGATGCC\n+AAAGTGATTTACACATCAAGTGAAAAATTCACAAATGAATTTATTAAATCAATTCGTGAT\n+AACGAAGGTGAAGCTTTCAGAGAAAGATATCGTAATATCGACGTCTTATTAATCGATGAT\n+ATTCAGTTCATACAAAATAAAGTACAAACACAAGAAGAATTTTTCTATACTTTTAATGAA\n+TTGCATCAGAATAACAAGCAAATAGTTATTTCGAGTGATCGACCGCCAAAGGAAATTGCA\n+CAATTAGAAGATCGATTACGTTCGCGCTTTGAATGGGGGCTAATTGTTGATATTACGCCA\n+CCAGATTATGAAACTCGAATGGCAATTTTGCAGAAGAAAATTGAAGAAGAAAAATTAGAT\n+ATTCCACCAGAAGCTTTAAATTATATAGCAAATCAAATTCAATCTAATATTCGTGAATTA\n+GAAGGTGCATTAACACGTTTACTTGCATATTCACAATTATTAGGAAAACCAATTACAACT\n+GAATTAACTGCTGAAGCTTTAAAAGATATCATTCAAGCACCAAAATCTAAAAAGATTACC\n+ATCCAAGATATTCAAAAAATTGTAGGCCAGTACTATAATGTTAGAATTGAAGATTTCAGT\n+GCAAAAAAACGTACAAAGTCAATTGCATATCCACGTCAAATAGCTATGTACTTGTCTAGA\n+GAGCTTACAGATTTCTCATTACCTAAAATTGGTGAAGAATTTGGTGGGCGTGATCATACG\n+ACCGTCATTCATGCTCATGAAAAAATATCTAAAGATTTAAAAGAAGATCCTATTTTTAAA\n+CAAGAAGTAGAGAATCTTGAAAAAGAAATAAGAAATGTATAAGTAGGAAACTTTGGGAAA\n+TGTAATCTGTTATATAACAGTACTAATAATAACAATCATTTTTTACATTTCTATATGCTA\n+ATGTGGCAAGATGAGCAAAACTCATTTTGTGGATAATGTTTAAAAGTCATACACGCCATA\n+CACAAGTTATCAACATGTGTATAACTTCGCCAAATCTATGTTTTTAAGACTTATCCACCA\n+ATCCACAGCACCTACTACTATTACTAAGAACTTAAAACCTATATAATTATATATAAACGA\n+CTGGAAGGAGTTTTAATTAATGATGGAATTCACTATTAAAAGAGATTATTTTATTACACA\n+ATTAAATGACACATTAAAAGCTATTTCACCAAGAACAACATTACCTATATTAACTGGTAT\n+CAAAATCGATGCAAAAGAACATGAAGTTATATTAACTGGTTCAGACTCTGAAATTTCAAT\n+AGAAATCACTATTCCTAAAACTGTAGATGGCGAAGATATTGTCAATATTTCAGAAACAGG\n+CTCAGTAGTACTTCCTGGACGATTCTTTGTTGATATTATAAAAAAATTACCTGGTAAAGA\n+TGTTAAATTATCTACAAATGAACAATTCCAGACATTAATTACATCAGGTCATTCTGAATT\n+TAATTTAAGTGGCTTAGATCCAGATCAATATCCTTTATTACCTCAAGTTTCTAGAGATGA\n+CGCAATTCAATTGTCGGTAAAAGTGCTTAAAAACGTAATTGCACAAACGAATTTTGCAGT\n+GTCCACCTCAGAAACACGCCCAGTACTAACTGGTGTGAACTGGCTTATACAAGAAAATGA\n+ATTAATATGCACAGCGACTGACTCACACCGCTTGGCTGTAAGAAAGTTGCAGTTAGAAGA\n+TGTTTCTGAAAACAAAAATGTCATCATTCCAGGTAAGGCTTTAGCTGAATTAAATAAAAT\n+TATGTCTGACAATGAAGAAGACATTGATATCTTCTTTGCTTCAAACCAAGTTTTATTTAA\n+AGTTGGAAATGTGAACTTTATTTCTCGATTATTAGAAGGACATTATCCTGATACAACACG\n+TTTATTCCCTGAAAACTATGAAATTAAATTAAGTATAGACAATGGGGAGTTTTATCATGC\n+GATTGATCGTGCATCTTTATTAGCACGTGAAGGTGGTAATAACGTTATTAAATTAAGTAC\n+AGGTGATGACGTTGTTGAATTGTCTTCTACATCACCAGAAATTGGTACTGTAAAAGAAGA\n+AGTTGATGCAAACGATGTTGAAGGTGGTAGCCTGAAAATTTCATTCAACTCTAAATATAT\n+GATGGATGCTTTAAAAGCAATCGATAATGATGAGGTTGAAGTTGAATTCTTCGGTACAAT\n+GAAACCATTTATTCTAAAACCAAAAGGTGACGACTCGGTAACGCAATTAATTTTACCAAT\n+CAGAACTTACTAAAAATAAATATAAATAAAGGATGACGTGATTAATTAAAACGTCATCCT\n+TTATTTTTTGGCAAAAATAATTCTAGATTCGTATGTAAAATAAATTTGACAGCATTTTAA\n+ACAGCAAATAAAAGACGCCAATTAAATTTATGACAAATGTATCCAGAATTTAATAAGTGT\n+GCTTATATGCCCTTTAAATTCAAAATTTTAATAGTCAATAACAAGTTGAATATAAAAGTT\n+AAACGCCGTTAAATAGCGTTAAAAAATTGAAAATGACAGTATTGCCAAAAAATAAGAATT\n+AATTATTTATATGTAAACGGTTTCCACCTCTATTTTAAATGAAATTTGTGACAAAAAAAG\n+GTATAATATATTAATGACATACAAAGAAATGGAGTGATTATTTTGGTTCAAGAAGTTGTA\n+GTAGAAGGAGACATTAATTTAGGTCAATTTCTAAAAACAGAAGGGATTATTGAATCTGGT\n+GGTCAAGCAAAATGGTTCTTGCAAGACGTTGAAGTATTAATTAATGGAGTGCGTGAAACA\n+CGTCGCGGTAAAAAGTTAGAACATCAAGATCGTATAGATATCCCAGAATTACCTGAAGAT\n+GCTGGTTCTTTCTTAATCATTCATCAAGGTGAACAATGAAGTTAAATACACTCCAATTAG\n+AAAATTATCGTAACTATGATGAGGTTACGTTGAAATGTCATCCTGACGTGAATATCCTCA\n+TTGGAGAAAATGCACAAGGAAAGACAAATTTACTTGAATCAATTTATACCTTAGCTTTAG\n+CAAAAAGTCATAGAACGAGTAATGATAAGGAACTCATACGTTTTAATGCTGATTATGCTA\n+AAATAGAAGGTGAGCTTAGTTATAGACACGGCACGATGCCATTAACAATGTTTATAACTA\n+AAAAAGGTAAACAAGTCAAAGTGAATCACTTAGAGCAAAGTCGTCTAACTCAATATATTG\n+GACACCTCAATGTGGTTCTATTTGCGCCAGAAGATTTGAATATTGTAAAAGGCTCTCCTC\n+AAATAAGACGACGCTTTATAGATATGGAGTTGGGCCAAATTTCTGCTGTTTACTTAAATG\n+'..b'ACGCTAACAATATTGAGCAATTAATATTTTTTAGGA\n+AATGAGTATGAAGGGGGATTTAATTGATGATTTTAAAATTCAAAATTTAAGGGGAGAGCG\n+AACTATCAATGATGCTGCAAAACACAATCGCAATGAAAAAACAGGCGCGTCACCTTATGA\n+AGGTATACGCACCTGTTTATAGTAAGCATTATTTAGCTTCAAATAATTGATCGCCAAATG\n+AAATGTTGCCATGTTCACCTTGTTTAAAATCAAGGTTTGTAATGTTTCCTTGTGTAACGA\n+TAATAGGCGTAATATCACTCTTTGCATGATTGCGGATGTAGTCTAAATCAAAGTTGATTA\n+ATAAATCACCTTGTTTAACTTCTTGACCTTCCTCAACATGTAAAGTAAAGCCTTCTCCGT\n+TTAATTTAACAGTGTCTAAACCGATGTGGATTAATAGTTCTAAACCACTATCTGATACAA\n+GACCAATTGCATGTTTTGTTGGGAAAATCATTTGTACTTTACCGTTGAATGGTGCACGAA\n+CTTCACCTTGTGAAGGTTTAATAGCGATACCGTCACCCATCATTTTTTCGCTGAACACTT\n+GATCAGGCACTTCTGATAATGGTGTTACTTCACCAGTTAATGGTGCATGCACGATATGGC\n+TCAATTCGCTTGTTGCAGATTTATCTTCTGCAACAACAACGGTTTCGTCTTTATCGTCTT\n+CCATAGTAGTAGGGTTTTCTACTACTTGACCATTCATAATCTGTTGCATTTCATGTTTGA\n+TTTGGTCAGATTTTGGACCAAAAATTGCTTGCATATTATTGCCGACTTCTAATACACCAG\n+ATGCGCCTAAATCTTTCAAACCAGGAACATCAACTTTAGATTTGTCGTTAACTTCAACAC\n+GTAGACGTGTGATACAAGCGTCTAAATGTTTAATGTTTGCTTTGCCACCCATAGCTTCTA\n+ATACTGCATATGGTAATTCAGTTGCTGAAGCAGTAGCCGCTTGTGATTGTTTATCTTCAC\n+GACCTGGTGTTTTGTATTTTAATTTTACAATTAGGAATCGGAATACGAAGTAGTAAATGA\n+CTGCGTATACAAGACCTACAGGAATGACTAACCACCATTGTGTCTTATTAGGTAGTATAC\n+CGAGTAAGAAGTAGTCGATGAAACCACCTGAGAATGTATAACCTAGATGAAGATCTAATA\n+AGTACAATGTTAAGAATGATAAACCATCAAGTACTGCGTGAATAAAGAATAATAATGGTG\n+CTACGAATAAGAATGAGAATTCTAAAGGTTCTGTAATACCAGTTAAGAATGATGTTAAAG\n+CAGCAGAACCCATTAAACCGGCTACTACTTTCTTGTTTTCAGGTTTAGCTGTGTGATAAA\n+TTGCTAAAGCTGCTGCAGGTAAACCGAACATCATAACAGGGAATTCACCTTGCATGAATT\n+TACCAGCTGTTAAATGTGCACCTTCACGAATTTGTTCGATAAAGATACGTTGGTCACCGT\n+GAATAATTTCACCTGCTGCATTTTTCCATGAACCAAACTCGAACCAGAACGGTGCGTGGA\n+AAATGTGATGTAGACCGAATGGAATTAATAAACGCTTGATGAAACCAAATAAGAATACGG\n+CAACACCAGTATTTGAGTCTAATAATCCTGTACTGAATGCATTTAATCCTGTTTGGATTG\n+TTGGCCAGATTAATGCCATTGGGAATGCTAAAATAAATGATGTTGTAGCCATCATAATAG\n+GTACGAAACGCTTACCAGCGAAGAAACCTAAATAAGATGGTAAGTTAATGTTATAGAACT\n+TGTTATAACACCAAGCTGCCAGGGCCCCGATTATAATACCGCCGAACACACCTGTTTGTA\n+ATGTTGGGATACCTAAAATGCTAGCGTAACCACTCGCTGGATCACCAATGTTCTTAGGTG\n+TTACTTGTAAAAAGTCACCCATTGTTTTGTTCATGATTATGTAACCGACGAATGCTGCGA\n+TAGCTGCTACACCATCACCGCCAGCTAATCCGATTGCGACACCTAATGCGAAAATCATAG\n+GCAAGTTATCAAAAATGATACCACCAGCACCTGTCATTAATTTAGCGACAGTTTGTACGC\n+CACCATTTTGTATAAAAGGCAAGTAGTGTTGTAATGCTTCGCCTTGCATAGCTGTACCGA\n+TAGCTAATAACAGACCCGCTGCTGGTAAAATCGCAACAGGTAACATTAGTGCCTTACCAA\n+TACGTTGCAATTGACCGAAAAGTTTCTTCCTCACTTGTCCAACCTCCAAAGTTGTATTTA\n+TTATTTAAGATTCAATAAAAAAGACACGAGCAAATAGACTGTGTTGGTAACCATCACAGC\n+TTAATTTAACTCATGCCTAATCTTACTTAGTAACACGTTGGTGTATGTAATTAATGTAAA\n+AGAAGCAATTGACTAAGTAGTATATAAAACGGATACGTTAGTTTATCTAGCTTACCATCA\n+CATCTTATTGAATCTTATTTGTTTGCGACTCCTATTTTAGCATGGTGAAGTATGCGTTTT\n+CAATACAATTATTAAATTCAATTTCAAATCTCTTAATTGTTCACAGATTATTATTAAAAC\n+ATAATATAAGATAATCCTGAATAAAATGTATAAAAGTTGTTGTAACAATTCAGCAATAGC\n+AACTGTTTTCGAGCGTTAAATGATAAGAAAAATATGTCGTTTAAAAAAATTAACTTGTGA\n+CAGAAATATGTAAGATTATTACAATGAACAGGCTTTATCTGATTAATATTGTAATGTGTT\n+TTCTCTTATAGTAAAATGTAAGCGATTACACAACTCAACTATATTTTCCTAATAATTATA\n+TTGTTAAGGAGGGCTACTTTGACAGGCTTTTCAGTGTATTTAGGACAACTTTTAGATGAA\n+GCGTATATTAAGCGAATGATTAAACAAGGTTACCAAATGATTTTTACATCTGTACAAATA\n+CCAGAAGAAGATGACGAGACAAAATATCATTATTTCACAAAACTACTCAATTTATTAAAA\n+CATGAACAAGTGACTTACCTCATAGATGCTAATCCATCTATATTAACACCATCTTTTTAT\n+GAGCATCTTCGACAATATGATGCACAATTTATGATTCGTATCGATCATAGTACATCAATT\n+GAGGCAATCGAAGCGATAATGGCACAGGGTTTAAAGTGCTGTTTGAATGCAAGTATTATT\n+TCCCGGGAATTGTTAACAAGCTTACATCAACAATTGAATGATTTTACATTACTTTCATTT\n+TGTCATAACTATTATCCAAGACCAGATACGGGATTATCTGTTGACTTGGTCAATAAGAAA\n+AATGAACTCATTTATCAATTTAATCCAAAGGCACAAATATATGGTTTTATTGTAGGGAGT\n+GGTTTGCGAGGTCCTTTGCATAAAGGCTTGCCAACAATTGAAGCAACGAGACATAGTCAT\n+CCTGTCGTTGCAGCTAAATTATTACAAGAAACTGGTGTATCTGAAGTGTTAGTTGGAGAC\n+TCATTGATTGAAATAAGGCAGGCAAAACAACTTATAGATTTTTGTAAGCATAGGCATTTC\n+ACGTTATGTATTGAAGAAGTGTTTGATACGACAGTGACTTACCTTTTCGATATGTGTCAT\n+AAAGTACGTCCGGATAATCCGGAGAATGTCATTCGTTCGGAAACGTCAAGACAAATATGT\n+CCGCATTCGATTCAACCACAGTTTACGACGCAACGACGCATTGGTTTAGTAACCGTTGAT\n+AATTTGAATAACGGACGTTATCAAGGTGAAATGCAAATTGTGAGACAAACGCTTAGTGCA\n+CATGACAGTGTGAATGTTGTTGCACAAATTATTAAAGAAGACTTACCACTGTTAAGTTGT\n+ATCGAGCCGAATGATACATTTGATTTTCAAAAAACTAGGGAGTGTAAGAAGTGA\n' |
| b |
| diff -r 000000000000 -r c9a8ef2aa380 test-data/wildtype.gbk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/wildtype.gbk Fri Feb 16 13:40:16 2018 -0500 |
| b |
| b'@@ -0,0 +1,5750 @@\n+LOCUS Wildtype 197394 bp DNA linear 13-JUN-2016\n+DEFINITION Staphylococcus aureus strain WT.\n+ACCESSION \n+VERSION\n+KEYWORDS .\n+SOURCE Staphylococcus aureus\n+ ORGANISM Staphylococcus aureus\n+ Unclassified.\n+COMMENT Annotated using prokka 1.12-beta from\n+ https://github.com/tseemann/prokka.\n+FEATURES Location/Qualifiers\n+ source 1..197394\n+ /organism="Staphylococcus aureus"\n+ /mol_type="genomic DNA"\n+ /strain="WT"\n+ CDS 1..1362\n+ /gene="dnaA"\n+ /locus_tag="WILD_00001"\n+ /inference="ab initio prediction:Prodigal:2.6"\n+ /inference="similar to AA sequence:UniProtKB:P68866"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="Chromosomal replication initiator protein DnaA"\n+ /translation="MSEKEIWEKVLEIAQEKLSAVSYSTFLKDTELYTIKDGEAIVLS\n+ SIPFNANWLNQQYAEIIQAILFDVVGYEVKPHFITTEELANYSNNETATPKEATKPST\n+ ETTEDNHVLGREQFNAHNTFDTFVIGPGNRFPHAASLAVAEAPAKAYNPLFIYGGVGL\n+ GKTHLMHAIGHHVLDNNPDAKVIYTSSEKFTNEFIKSIRDNEGEAFRERYRNIDVLLI\n+ DDIQFIQNKVQTQEEFFYTFNELHQNNKQIVISSDRPPKEIAQLEDRLRSRFEWGLIV\n+ DITPPDYETRMAILQKKIEEEKLDIPPEALNYIANQIQSNIRELEGALTRLLAYSQLL\n+ GKPITTELTAEALKDIIQAPKSKKITIQDIQKIVGQYYNVRIEDFSAKKRTKSIAYPR\n+ QIAMYLSRELTDFSLPKIGEEFGGRDHTTVIHAHEKISKDLKEDPIFKQEVENLEKEI\n+ RNV"\n+ CDS 1640..2773\n+ /gene="dnaN"\n+ /locus_tag="WILD_00002"\n+ /EC_number="2.7.7.7"\n+ /inference="ab initio prediction:Prodigal:2.6"\n+ /inference="similar to AA sequence:UniProtKB:P99103"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="DNA polymerase III subunit beta"\n+ /translation="MMEFTIKRDYFITQLNDTLKAISPRTTLPILTGIKIDAKEHEVI\n+ LTGSDSEISIEITIPKTVDGEDIVNISETGSVVLPGRFFVDIIKKLPGKDVKLSTNEQ\n+ FQTLITSGHSEFNLSGLDPDQYPLLPQVSRDDAIQLSVKVLKNVIAQTNFAVSTSETR\n+ PVLTGVNWLIQENELICTATDSHRLAVRKLQLEDVSENKNVIIPGKALAELNKIMSDN\n+ EEDIDIFFASNQVLFKVGNVNFISRLLEGHYPDTTRLFPENYEIKLSIDNGEFYHAID\n+ RASLLAREGGNNVIKLSTGDDVVELSSTSPEIGTVKEEVDANDVEGGSLKISFNSKYM\n+ MDALKAIDNDEVEVEFFGTMKPFILKPKGDDSVTQLILPIRTY"\n+ CDS 3163..3399\n+ /locus_tag="WILD_00003"\n+ /inference="ab initio prediction:Prodigal:2.6"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="hypothetical protein"\n+ /translation="MVQEVVVEGDINLGQFLKTEGIIESGGQAKWFLQDVEVLINGVR\n+ ETRRGKKLEHQDRIDIPELPEDAGSFLIIHQGEQ"\n+ CDS 3396..4508\n+ /gene="recF"\n+ /locus_tag="WILD_00004"\n+ /inference="ab initio prediction:Prodigal:2.6"\n+ /inference="similar to AA sequence:UniProtKB:P9WHI9"\n+ /codon_start=1\n+ /transl_table=11\n+ /product="DNA replication and repair protein RecF"\n+ /translation="MKLNTLQLENYRNYDEVTLKCHPDVNILIGENAQGKTNLLESIY\n+ TLALAKSHRTSNDKELIRFNADYAKIEGELSYRHGTMPLTMFITKKGKQVKVNHLEQS\n+ RLTQYIGHLNVVLFAPEDLNIVKGSPQIRRRFIDMELGQISAVYLNDLAQYQRILKQK\n+ NNYLKQLQLGQKKDLTMLEVLNQQFAEYAMKVTDKRAHFIQELESLAKPIHAGITNDK\n+ EALSLNYLPSLKFDYAQNEAARLEEIMSILSDNMQREKERGISLFGPHRDDISFDVNG\n+ MDAQTYGSQGQQRTTALSIKLAEIELMNIEVGEYPILLLDDVLSELDDSRQTHLLSTI\n+ '..b' 194281 tttggtcaga ttttggacca aaaattgctt gcatattatt gccgacttct aatacaccag\n+ 194341 atgcgcctaa atctttcaaa ccaggaacat caactttaga tttgtcgtta acttcaacac\n+ 194401 gtagacgtgt gatacaagcg tctaaatgtt taatgtttgc tttgccaccc atagcttcta\n+ 194461 atactgcata tggtaattca gttgctgaag cagtagccgc ttgtgattgt ttatcttcac\n+ 194521 gacctggtgt tttgtatttt aattttacaa ttaggaatcg gaatacgaag tagtaaatga\n+ 194581 ctgcgtatac aagacctaca ggaatgacta accaccattg tgtcttatta ggtagtatac\n+ 194641 cgagtaagaa gtagtcgatg aaaccacctg agaatgtata acctagatga agatctaata\n+ 194701 agtacaatgt taagaatgat aaaccatcaa gtactgcgtg aataaagaat aataatggtg\n+ 194761 ctacgaataa gaatgagaat tctaaaggtt ctgtaatacc agttaagaat gatgttaaag\n+ 194821 cagcagaacc cattaaaccg gctactactt tcttgttttc aggtttagct gtgtgataaa\n+ 194881 ttgctaaagc tgctgcaggt aaaccgaaca tcataacagg gaattcacct tgcatgaatt\n+ 194941 taccagctgt taaatgtgca ccttcacgaa tttgttcgat aaagatacgt tggtcaccgt\n+ 195001 gaataatttc acctgctgca tttttccatg aaccaaactc gaaccagaac ggtgcgtgga\n+ 195061 aaatgtgatg tagaccgaat ggaattaata aacgcttgat gaaaccaaat aagaatacgg\n+ 195121 caacaccagt atttgagtct aataatcctg tactgaatgc atttaatcct gtttggattg\n+ 195181 ttggccagat taatgccatt gggaatgcta aaataaatga tgttgtagcc atcataatag\n+ 195241 gtacgaaacg cttaccagcg aagaaaccta aataagatgg taagttaatg ttatagaact\n+ 195301 tgttataaca ccaagctgcc agggccccga ttataatacc gccgaacaca cctgtttgta\n+ 195361 atgttgggat acctaaaatg ctagcgtaac cactcgctgg atcaccaatg ttcttaggtg\n+ 195421 ttacttgtaa aaagtcaccc attgttttgt tcatgattat gtaaccgacg aatgctgcga\n+ 195481 tagctgctac accatcaccg ccagctaatc cgattgcgac acctaatgcg aaaatcatag\n+ 195541 gcaagttatc aaaaatgata ccaccagcac ctgtcattaa tttagcgaca gtttgtacgc\n+ 195601 caccattttg tataaaaggc aagtagtgtt gtaatgcttc gccttgcata gctgtaccga\n+ 195661 tagctaataa cagacccgct gctggtaaaa tcgcaacagg taacattagt gccttaccaa\n+ 195721 tacgttgcaa ttgaccgaaa agtttcttcc tcacttgtcc aacctccaaa gttgtattta\n+ 195781 ttatttaaga ttcaataaaa aagacacgag caaatagact gtgttggtaa ccatcacagc\n+ 195841 ttaatttaac tcatgcctaa tcttacttag taacacgttg gtgtatgtaa ttaatgtaaa\n+ 195901 agaagcaatt gactaagtag tatataaaac ggatacgtta gtttatctag cttaccatca\n+ 195961 catcttattg aatcttattt gtttgcgact cctattttag catggtgaag tatgcgtttt\n+ 196021 caatacaatt attaaattca atttcaaatc tcttaattgt tcacagatta ttattaaaac\n+ 196081 ataatataag ataatcctga ataaaatgta taaaagttgt tgtaacaatt cagcaatagc\n+ 196141 aactgttttc gagcgttaaa tgataagaaa aatatgtcgt ttaaaaaaat taacttgtga\n+ 196201 cagaaatatg taagattatt acaatgaaca ggctttatct gattaatatt gtaatgtgtt\n+ 196261 ttctcttata gtaaaatgta agcgattaca caactcaact atattttcct aataattata\n+ 196321 ttgttaagga gggctacttt gacaggcttt tcagtgtatt taggacaact tttagatgaa\n+ 196381 gcgtatatta agcgaatgat taaacaaggt taccaaatga tttttacatc tgtacaaata\n+ 196441 ccagaagaag atgacgagac aaaatatcat tatttcacaa aactactcaa tttattaaaa\n+ 196501 catgaacaag tgacttacct catagatgct aatccatcta tattaacacc atctttttat\n+ 196561 gagcatcttc gacaatatga tgcacaattt atgattcgta tcgatcatag tacatcaatt\n+ 196621 gaggcaatcg aagcgataat ggcacagggt ttaaagtgct gtttgaatgc aagtattatt\n+ 196681 tcccgggaat tgttaacaag cttacatcaa caattgaatg attttacatt actttcattt\n+ 196741 tgtcataact attatccaag accagatacg ggattatctg ttgacttggt caataagaaa\n+ 196801 aatgaactca tttatcaatt taatccaaag gcacaaatat atggttttat tgtagggagt\n+ 196861 ggtttgcgag gtcctttgca taaaggcttg ccaacaattg aagcaacgag acatagtcat\n+ 196921 cctgtcgttg cagctaaatt attacaagaa actggtgtat ctgaagtgtt agttggagac\n+ 196981 tcattgattg aaataaggca ggcaaaacaa cttatagatt tttgtaagca taggcatttc\n+ 197041 acgttatgta ttgaagaagt gtttgatacg acagtgactt accttttcga tatgtgtcat\n+ 197101 aaagtacgtc cggataatcc ggagaatgtc attcgttcgg aaacgtcaag acaaatatgt\n+ 197161 ccgcattcga ttcaaccaca gtttacgacg caacgacgca ttggtttagt aaccgttgat\n+ 197221 aatttgaata acggacgtta tcaaggtgaa atgcaaattg tgagacaaac gcttagtgca\n+ 197281 catgacagtg tgaatgttgt tgcacaaatt attaaagaag acttaccact gttaagttgt\n+ 197341 atcgagccga atgatacatt tgattttcaa aaaactaggg agtgtaagaa gtga\n+//\n' |