| Previous changeset 11:e19d9742c99b (2016-04-28) Next changeset 13:72156de89c7a (2016-05-23) |
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Commit message:
planemo upload for repository https://github.com/portiahollyoak/Tools commit 5d021f520b653582862ec98dd812a051b804aa50 |
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modified:
scripts/TEMP_Absence.sh scripts/TEMP_Insertion.sh scripts/pickUniqMate.pl scripts/pickUniqPairFastq_MEM.pl scripts/pickUniqPos_MEM.pl temp.xml |
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added:
scripts/pickOverlapPair.ex_MEM.pl test-data/chr2l_bwa_mem.bam test-data/dm6_chr2l.twobit test-data/median_insert_size test-data/test_TE_annotation.gff3 test-data/test_chromosome.absence.refined.bp.summary test-data/test_chromosome.insertion.refined.bp.summary test-data/test_consensus.fa |
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removed:
test-data/README test-data/dm3_chr2L.2bit test-data/test_TE_annotation.bed test-data/test_chromosome.sites test-data/test_chromosome.sorted.bam test-data/test_chromosome.sorted.bam.bai test-data/test_concensus.fa |
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| diff -r e19d9742c99b -r ca36262102d8 scripts/TEMP_Absence.sh --- a/scripts/TEMP_Absence.sh Thu Apr 28 07:57:12 2016 -0400 +++ b/scripts/TEMP_Absence.sh Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -26,7 +26,8 @@ -r Annotated transposon positions in the genome (e.g., repeakMask) in bed6 format with full path -t 2bit file for the reference genome (can be downloaded from UCSC Genome Browser) -f An integer specifying the length of the fragments (inserts) of the library. Default is 500 - -c An integer specifying the number of CUPs used. Default is 4 + -x The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA MEM. + -c An integer specifying the number of CPUs used. Default is 4 -h Show help message EOF @@ -34,7 +35,7 @@ } # taking options -while getopts "hi:c:f:o:r:s:t:" OPTION +while getopts "hi:c:f:o:r:s:t:x:" OPTION do case $OPTION in h) @@ -61,6 +62,9 @@ t) REF=$OPTARG ;; + x) + SCORE=$OPTARG + ;; ?) usage && exit 1 ;; @@ -73,6 +77,7 @@ fi [ ! -z "${CPU##*[!0-9]*}" ] || CPU=4 [ ! -z "${INSERT##*[!0-9]*}" ] || INSERT=500 +[ ! -z "${SCORE##*[!0-9]*}" ] || SCORE=0 [ ! -z $OUTDIR ] || OUTDIR=$PWD mkdir -p "${OUTDIR}" || echo -e "\e[1;31mWarning: Cannot create directory ${OUTDIR}. Using the direcory of input fastq file\e[0m" @@ -93,6 +98,7 @@ checkExist "touch" checkExist "awk" checkExist "grep" +checkExist "twoBitToFa" checkExist "bwa" checkExist "samtools" echo -e "\e[1;35mDone with testing required softwares/scripts, starting pipeline...\e[0m" @@ -134,5 +140,11 @@ perl $BINDIR/refine_breakpoint.ex.pl # Estimate excision sites frequencies -perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup +if [[ $SCORE -eq 0 ]] +then + perl $BINDIR/pickOverlapPair.ex.pl $i.excision.cluster.rpmk.refined.bp > $i.excision.cluster.rpmk.refined.bp.refsup +else + perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.excision.cluster.rpmk.refined.bp $SCORE > $i.excision.cluster.rpmk.refined.bp.refsup +fi + perl $BINDIR/summarize_excision.pl |
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| diff -r e19d9742c99b -r ca36262102d8 scripts/TEMP_Insertion.sh --- a/scripts/TEMP_Insertion.sh Thu Apr 28 07:57:12 2016 -0400 +++ b/scripts/TEMP_Insertion.sh Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -29,7 +29,7 @@ -m Number of mismatch allowed when mapping to TE concensus sequences. Default is 3 -x The minimum score difference between the best hit and the second best hit for considering a read as uniquely mapped. For BWA mem. -f An integer specifying the length of the fragments (inserts) of the library. Default is 500 - -c An integer specifying the number of CUPs used. Default is 8 + -c An integer specifying the number of CPUs used. Default is 8 -h Show help message EOF @@ -157,7 +157,7 @@ perl $BINDIR/get_class.pl $i.uniq.transposons.filtered.wGap.bed $i > $i.uniq.transposons.filtered.wGap.class.bed perl $BINDIR/make.bp.bed.pl $i.uniq.transposons.filtered.wGap.class.bed $ANNO $FAMI -#rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai +rm $i.unpair.sam $i.unpair.uniq.bed $i.unpair.uniq.?.fastq $i.unpair.uniq.?.sai rm $i.unpair.uniq.transposons.sam $i.unpair.uniq.transposons.unpair.sam $i.uniq.transposons.filtered.woGap.bed $i.uniq.transposons.filtered.wGap.bed @@ -167,8 +167,12 @@ #Estimate insertion frequencies +#if [[ $SCORE -eq 0 ]] +#then perl $BINDIR/pickOverlapPair.in.pl $i.insertion.refined.bp $INSERT > $i.insertion.refined.bp.summary - +#else +# perl $BINDIR/pickOverlapPair.ex_MEM.pl $i.insertion.refined.bp $INSERT $SCORE > $i.insertion.refined.bp.summary +#fi ################################ ##End of processing insertions## |
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| diff -r e19d9742c99b -r ca36262102d8 scripts/pickOverlapPair.ex_MEM.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/pickOverlapPair.ex_MEM.pl Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -0,0 +1,135 @@ +#!/share/bin/perl +use Bio::Seq; +use List::Util qw(sum); + +die "perl $0 <*.excision.cluster.rpmk.refined.bp>\n" if @ARGV<0; + +my $title=$ARGV[0]; +if ($title =~ /annotation/) { + $title =~ s/excision.cluster.annotation.refined.bp/sorted.bam/; +} +else {$title =~ s/excision.cluster.rpmk.refined.bp/sorted.bam/;} +#system("samtools index /home/wangj2/scratch/bill/bill_genomic/$title"); + +my %chrs=(); +system("samtools view -H $title > header"); +open (input, "<header") or die "Can't open header since $!\n"; +while (my $line=<input>) { + if ($line =~ /^\@SQ/) { + my @a=split(/\t/, $line); + for my $j (0..$#a) { + if ($a[$j] =~ /^SN:/) { + $a[$j] =~ s/^SN://; + $chrs{$a[$j]}=1; + } + } + } +} +close input; +system("rm header"); + +open (input, "<$ARGV[0]") or die "Can't open $ARGV[0] since $!\n"; +my $header=<input>; +while (my $line=<input>) { + chomp($line); + my @a=split(/\t/, $line); + + my $left=0; + my $right=0; + if ($a[4] eq "") {$left=$a[1];} + else { + my @t=split(/\,/, $a[4]); + my @p=split(/\(/, $t[$#t]); + $left=$p[0]; + } + if ($a[5] eq "") {$right=$a[2];} + else { + my @t=split(/\,/, $a[5]); + my @p=split(/\(/, $t[0]); + $right=$p[0]; + } + + my $leftlower=$left-500; + my $leftupper=$left+500; + my $rightlower=$right-500; + my $rightupper=$right+500; + my $chr_num=$a[0]; + $chr_num =~ s/chr//; + if (($chrs{$a[0]} == 1) && (! defined $chrs{$chr_num})) {$chr_num=$a[0];} + system("samtools view -Xf 0x2 $title $chr_num\:$leftlower\-$leftupper $chr_num\:$rightlower\-$rightupper > temp.sam"); + + open in,"temp.sam"; + my %ps=(); + my %me=(); + my %uniqp=(); + my %uniqm=(); + my $ref_sup=0; + + while(<in>) + { + chomp; + my @f=split/\t/,$_,12; + ## read number 1 or 2 + my ($rnum)=$f[1]=~/(\d)$/; + + ## XT:A:* + my $xt=""; + my @a=split(/\s+/, $_); + my $as=0; + my $xs=0; + for my $i (11..$#a) { + if ($a[$i] =~ /^AS:i:/) { + $a[$i] =~ s/AS:i://; + $as=$a[$i]; + } + elsif ($a[$i] =~ /^XS:i:/) { + $a[$i] =~ s/XS:i://; + $xs=$a[$i]; + } + if (($xs > 0) && ($as-$xs <= $ARGV[2])) {$xt="R";} + elsif ($as > 0) {$xt="U";} + } + + ## Coordinate + my $coor=$f[3]; + if ($f[1]=~/r/) + { + if ($xt eq "U") {$uniqm{$f[0]}=1;} + my (@cigar_m)=$f[5]=~/(\d+)M/g; + my (@cigar_d)=$f[5]=~/(\d+)D/g; + my (@cigar_s)=$f[5]=~/(\d+)S/g; + my (@cigar_i)=$f[5]=~/(\d+)I/g; + my $aln_ln=sum(@cigar_m,@cigar_d); + $me{$f[0]}=$f[3]+$aln_ln-1; + } + elsif ($f[1]=~/R/) { + $ps{$f[0]}=$f[3]; + if ($xt eq "U") {$uniqp{$f[0]}=1;} + } + +# ${$pe{$f[0]}}[$rnum-1]=[$xt,$coor]; + } + close in; + + foreach my $id (keys %ps) + { +# my @rid=@{$pe{$id}}; + +# if(($rid[0][0] eq "U" && $rid[1][0] eq "M") || ($rid[0][0] eq "M" && $rid[1][0] eq "U")) +# { +# $soft_clip++; +# print "$id\n"; +# } + + if ((defined $me{$id})&&((defined $uniqp{$id})||(defined $uniqm{$id}))) + { + if (((($ps{$id}+5)<=$right)&&($me{$id}>$right)&&($uniqm{$id}==1)) || ((($me{$id}-5)>=$left)&&($ps{$id}<$left)&&($uniqp{$id}==1))) { + $ref_sup++; + } + } + } + + print "$a[0]\t$a[1]\t$a[2]\t$a[3]\t$left\t$right\t$ref_sup\n"; + system("rm temp.sam"); +} + |
| b |
| diff -r e19d9742c99b -r ca36262102d8 scripts/pickUniqMate.pl --- a/scripts/pickUniqMate.pl Thu Apr 28 07:57:12 2016 -0400 +++ b/scripts/pickUniqMate.pl Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -19,7 +19,7 @@ while(<in>) { chomp; - my @f=split/\t/,$_,12; + my @f=split/\s+/,$_; # headers if(/^\@SQ/) { @@ -32,50 +32,62 @@ # unmapped next if $f[2] eq "*"; - # alignments - if($f[11]=~/XT:A:/) + my $mm=200; + my $xa=""; + for my $q (11..$#f) { - my ($rnum)=$f[1]=~/(\d)$/; - # CIGAR - my (@cigar_m)=$f[5]=~/(\d+)M/g; - my (@cigar_d)=$f[5]=~/(\d+)D/g; - my (@cigar_s)=$f[5]=~/(\d+)S/g; - my (@cigar_i)=$f[5]=~/(\d+)I/g; - my $aln_ln=sum(@cigar_m,@cigar_d); - - my $strand="+"; - if($f[1]=~/r/) - { - my $seq=Bio::Seq->new(-seq=>$f[9]); - $f[9]=$seq->revcom->seq; - $strand="-"; - } + if($f[$q]=~/NM:/) + { + $mm=$f[$q]; + $mm =~ s/NM://; + } + + if($f[$q]=~/XA:Z:/) + { + ($xa)=$f[$q]=~/XA:Z:(.*);$/; + last; + } + } + + if ($mm > 5) {next;} - # align to the junctions - if(($f[3]+$aln_ln-1)>${$ref[$ref{$f[2]}]}[1]) - { - if(($f[3]+($aln_ln-1)/2)>${$ref[$ref{$f[2]}]}[1]) - { - $f[2]=${$ref[$ref{$f[2]}+1]}[0]; - $f[3]=1; - $aln_ln=$aln_ln-(${$ref[$ref{$f[2]}]}[1]-$f[3]+1); - } - else - { - $aln_ln=${$ref[$ref{$f[2]}]}[1]-$f[3]+1; - } - } + my ($rnum)=$f[1]=~/(\d)$/; + # CIGAR + my (@cigar_m)=$f[5]=~/(\d+)M/g; + my (@cigar_d)=$f[5]=~/(\d+)D/g; + my (@cigar_s)=$f[5]=~/(\d+)S/g; + my (@cigar_i)=$f[5]=~/(\d+)I/g; + my $aln_ln=sum(@cigar_m,@cigar_d); + + my $strand="+"; + if($f[1]=~/r/) + { + my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); + $f[9]=$seq->revcom->seq; + $strand="-"; + } + + # align to the junctions + if(($f[3]+$aln_ln-1)>${$ref[$ref{$f[2]}]}[1]) + { + if(($f[3]+($aln_ln-1)/2)>${$ref[$ref{$f[2]}]}[1]) + { + $f[2]=${$ref[$ref{$f[2]}+1]}[0]; + $f[3]=1; + $aln_ln=$aln_ln-(${$ref[$ref{$f[2]}]}[1]-$f[3]+1); + } + else + { + $aln_ln=${$ref[$ref{$f[2]}]}[1]-$f[3]+1; + } + } + + $pe{$f[0]}{$rnum}=$f[2].",".$strand."$f[3]".";"; + + # XA tag + my @xa=split(";",$xa); + $pe{$f[0]}{$rnum}.=join(",",(split/,/)[0,1]).";" foreach @xa; - $pe{$f[0]}{$rnum}=$f[2].",".$strand."$f[3]".";"; - - # XA tag - if($f[11]=~/XA:Z:/) - { - my ($xa)=$f[11]=~/XA:Z:(.*);$/; - my @xa=split(";",$xa); - $pe{$f[0]}{$rnum}.=join(",",(split/,/)[0,1]).";" foreach @xa; - } - } } close in; |
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| diff -r e19d9742c99b -r ca36262102d8 scripts/pickUniqPairFastq_MEM.pl --- a/scripts/pickUniqPairFastq_MEM.pl Thu Apr 28 07:57:12 2016 -0400 +++ b/scripts/pickUniqPairFastq_MEM.pl Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -30,13 +30,13 @@ $xs=$a[$i]; } if (($xs > 0) && ($as-$xs <= $ARGV[2])) {$xt="R";} - else {$xt="U";} + elsif ($as > 0) {$xt="U";} } ## revcom the read mapped to the reverse strand if($f[1]=~/r/) { - my $seq=Bio::Seq->new(-seq=>$f[9]); + my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); $f[9]=$seq->revcom->seq; $f[10]=reverse $f[10]; } |
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| diff -r e19d9742c99b -r ca36262102d8 scripts/pickUniqPos_MEM.pl --- a/scripts/pickUniqPos_MEM.pl Thu Apr 28 07:57:12 2016 -0400 +++ b/scripts/pickUniqPos_MEM.pl Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -27,14 +27,14 @@ $xs=$a[$i]; } if (($xs > 0) && ($as-$xs <= $ARGV[1])) {$xt="R";} - else {$xt="U";} + elsif ($as > 0) {$xt="U";} } my $strand="+"; ## revcomp if($f[1]=~/r/) { - my $seq=Bio::Seq->new(-seq=>$f[9]); + my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); $f[9]=$seq->revcom->seq; $strand="-"; } |
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| diff -r e19d9742c99b -r ca36262102d8 temp.xml --- a/temp.xml Thu Apr 28 07:57:12 2016 -0400 +++ b/temp.xml Fri Apr 29 05:47:54 2016 -0400 |
| [ |
| @@ -1,4 +1,4 @@ -<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.2"> +<tool id ="run_TEMP" name="Run TEMP" version=" 0.1.4"> <description></description> <requirements> <!-- The following are classical toolshed packages and should be removed @@ -17,44 +17,35 @@ <exit_code range="1:" /> </stdio> <command><![CDATA[ - ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && ln -f -s "$alignment" alignment.sorted.bam && - bash $__tool_directory__/scripts/TEMP_Insertion.sh -x 30 -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && - bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && - mv alignment.insertion.bp.bed $insertion_bed && - mv alignment.insertion.refined.bp $insertion_bed_refined && + bash $__tool_directory__/scripts/TEMP_Insertion.sh -x "$minimum_score_difference" -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$te_locations" -m "$mismatches" -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && + bash $__tool_directory__/scripts/TEMP_Absence.sh -x "$minimum_score_difference" -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && + zip archive.zip *insertion* *excision* *absence* && mv archive.zip $archive && mv alignment.insertion.refined.bp.summary $insertion_summary && - mv alignment.absence.refined.bp.summary $absence_summary && - zip archive.zip *insertion* *excision* *absence* && - mv archive.zip $archive + mv alignment.absence.refined.bp.summary $absence_summary ]]></command> <inputs> <param format="bam" name="alignment" type="data" label="Alignment bam file"/> <param format="twobit" name="reference2bit" type="data" label="Reference twobit file"/> <param format="fasta" name="consensus_te_seqs" type="data" label="Consensus TE Seqs fasta file"/> - <param format="bed" name="bed_te_locations" type="data" label="TE Locations bed file"/> - <!-- - <param format="tabular" name="te_families" type="data" label="TE Families"/> - <param format="gff" name="gff_te_locations" type="data" label="Reference TE insertion Locations with Family ID names GFF file"/> - --> + <param format="bed" name="te_locations" type="data" label="TE Locations bed file"/> <param format="txt" name="median_insertsize" type="data" label="Median Insert Length"/> + <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/> + <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"></param> </inputs> <outputs> - <data format="bed" type="data" name="insertion_bed" label="Insertion BED file" /> - <data format="bed" type="data" name="insertion_bed_refined" label="Insertion BED file (refined)" /> <data format="bed" type="data" name="insertion_summary" label="Insertion summary file" /> <data format="bed" type="data" name="absence_summary" label="Absence summary file" /> <data format="zip" type="data" name="archive" label="Compressed output files" /> </outputs> <tests> <test> - <param name="alignment" value="test_chromosome.sorted.bam" ftype="bam"/> - <param name="reference2bit" value="dm3_chr2L.2bit" ftype="twobit"/> + <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/> + <param name="reference2bit" value="dm6_chr2l.twobit" ftype="twobit"/> <param name="consensus_te_seqs" value="test_consensus.fa" ftype="fasta"/> - <param name="bed_te_locations" value="test_TE_annotation.bed" ftype="bed"/> - <output name="insertion_bed" file="test_chromosome.insertion.bp.bed" ftype="bed" /> - <output name="insertion_bed_refined" file="test_chromosome.insertion.refined.bp" ftype="bed"/> + <param name="te_locations" value="test_TE_annotation.gff3" ftype="bed"/> + <param name="median_insertsize" value="median_insert_size" ftype="txt"/> <output name="insertion_summary" file="test_chromosome.insertion.refined.bp.summary" ftype="bed"/> <output name="absence_summary" file="test_chromosome.absence.refined.bp.summary" ftype="bed"/> </test> @@ -71,6 +62,41 @@ For TE insertion analysis run TEMP_Insertion.sh in script. For TE absence analysis run TEMP_Absence.sh in script. +Output files +------------- + + +For TE insertion analysis there are 14 columns in the summary file:: + + Column 1: The chromosome where the detected insertion happens. + Column 2: The coordinate of the start position of the detected insertion. + Column 3: The coordinate of the end position of the detected insertion. + Column 4: The TE family that the detected insertion belongs to. + Column 5: The direction of the insertion. “Plus” means that the TE is integrated with the plus strand of the genome while “minus” means the TE is integrated with the minus strand. + Column 6: The class of the insertion. “1p1” means that the detected insertion is supported by reads at both sides. “2p” means the detected insertion is supported by more than 1 read at only 1 side. “Singleton” means the detected insertion is supported by only 1 read at 1 side. + Column 7: The total number of read pairs that support the detected insertion. + Column 8: The estimated population frequency of the detected insertion. + Columns 9 & 10: The coordinate of a junction and the number of the reads supporting it. If the junction is not found column 9 will be the arithmetic mean of the start and end coordinates and column 10 will have the value 0. + Columns 11 & 12: Same as Columns 9 & 10 except for the junction on the other strand. + Column 13: The number of reads supporting the detected insertion at the 5’ end of the TE (not including junction spanning reads). + Column 13: The number of reads supporting the detected insertion at the 3’ end of the TE (not including junction spanning reads). + + +For TE absence analysis there are 9 columns in the summary file:: + + Column 1: The chromosome where the detected absence happens. + Column 2: The coordinate of the start position of the detected absence. + Column 3: The coordinate of the end position of the detected absence. + Column 4: The TE family that the detected insertion belongs to. + Column 5: Junctions at 5’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands. + Column 6: Junctions at 3’ of the excised TE. The two numbers are the coordinates of the junctions on the two strands. + Column 7: The number of reads supporting the absence. + Column 8: The number of reads supporting the reference (no absence). + Column 9: Estimated population frequency of the detected absence event. + ]]> </help> + <citations> + <citation type="doi">10.1093/nar/gku323</citation> + </citations> </tool> |
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| diff -r e19d9742c99b -r ca36262102d8 test-data/README --- a/test-data/README Thu Apr 28 07:57:12 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,7 +0,0 @@ -This is a small simulated dataset for testing if TEMP is properly installed and demonstrating how it works. - -10 TE insertions and 5 TE excisions were generated in the chr2L:2000000-3000000 region of the Drosophila Melanogaster Reference Genome (dm3), and pair-end Illumina reads were simulated with insert size 500, read length 90 and error-rate of 0.0005. Those reads were mapped to the dm3 reference genome and the alignments were in the file "test_chromosome.sorted.bam". - -The 10 simulated insertions and 5 excisions were listed in the file "test_chromosome.sites". -The concensus sequences for those 10 TEs were in the file "test_concensus.fa". -The annotated TE insertions in the reference genome were listed in the file "test_TE_annotation.bed". |
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| diff -r e19d9742c99b -r ca36262102d8 test-data/chr2l_bwa_mem.bam |
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| Binary file test-data/chr2l_bwa_mem.bam has changed |
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| diff -r e19d9742c99b -r ca36262102d8 test-data/dm3_chr2L.2bit |
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| Binary file test-data/dm3_chr2L.2bit has changed |
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| diff -r e19d9742c99b -r ca36262102d8 test-data/dm6_chr2l.twobit |
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| Binary file test-data/dm6_chr2l.twobit has changed |
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| diff -r e19d9742c99b -r ca36262102d8 test-data/median_insert_size --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/median_insert_size Fri Apr 29 05:47:54 2016 -0400 |
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| @@ -0,0 +1,1 @@ +500 |
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| diff -r e19d9742c99b -r ca36262102d8 test-data/test_TE_annotation.bed --- a/test-data/test_TE_annotation.bed Thu Apr 28 07:57:12 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,115 +0,0 @@ -chr2L 1301606 1302488 FBgn0001167_gypsy . - -chr2L 2094501 2094580 FBgn0000155_roo . - -chr2L 2100429 2109522 FBgn0000155_roo . - -chr2L 2112167 2118361 FBgn0003007_opus . - -chr2L 2118446 2119772 FBgn0003007_opus . - -chr2L 2159453 2159556 FBgn0000155_roo . - -chr2L 2267349 2267457 FBgn0000155_roo . + -chr2L 2294096 2299243 FBgn0000349_copia . - -chr2L 2378805 2378893 FBgn0000155_roo . + -chr2L 2530303 2530389 FBgn0000155_roo . + -chr2L 2565592 2569028 FBgn0000005_297 . + -chr2L 2565667 2565886 FBgn0000004_17.6 . + -chr2L 2565869 2566006 FBgn0063450_Tom1 . + -chr2L 2565871 2566024 FBgn0061485_rover . + -chr2L 2565920 2566024 FBgn0063917_McClintock . + -chr2L 2566158 2569026 FBgn0000004_17.6 . + -chr2L 2566674 2566848 FBgn0061485_rover . + -chr2L 2567367 2569022 FBgn0061485_rover . + -chr2L 2567598 2567816 FBgn0063917_McClintock . + -chr2L 2567665 2569027 FBgn0044355_Quasimodo . + -chr2L 2568060 2569027 FBgn0026065_Idefix . + -chr2L 2568062 2569018 FBgn0063917_McClintock . + -chr2L 2568070 2569004 FBgn0063447_accord . + -chr2L 2568121 2568988 FBgn0004082_Tirant . + -chr2L 2568137 2569006 FBgn0063432_gypsy5 . + -chr2L 2568137 2568942 FBgn0040267_Transpac . + -chr2L 2568153 2569001 FBgn0063782_accord2 . - -chr2L 2568154 2568990 FBgn0023131_ZAM . + -chr2L 2568193 2568993 FBgn0003007_opus . + -chr2L 2568251 2568697 FBgn0000006_412 . + -chr2L 2568264 2568985 FBgn0063434_gypsy3 . + -chr2L 2568264 2568985 FBgn0003490_springer . + -chr2L 2568308 2568520 FBgn0067387_gypsy10 . + -chr2L 2568308 2568517 FBgn0067384_gypsy7 . + -chr2L 2568308 2568878 FBgn0063431_gypsy6 . + -chr2L 2568308 2568703 FBgn0001167_gypsy . + -chr2L 2568313 2568828 FBgn0002697_mdg1 . + -chr2L 2568313 2568526 FBgn0000199_blood . + -chr2L 2568329 2568982 FBgnnnnnnnn_HMS-Beagle2 . + -chr2L 2568329 2568982 FBgn0001207_HMS-Beagle . + -chr2L 2568378 2568648 FBgn0063897_Stalker4 . + -chr2L 2568378 2568878 FBgn0063433_gypsy4 . + -chr2L 2568384 2568646 FBgn0063435_gypsy2 . + -chr2L 2568384 2568796 FBgn0002698_mdg3 . + -chr2L 2569006 2569756 FBgn0063917_McClintock . + -chr2L 2569007 2571200 FBgn0000004_17.6 . + -chr2L 2569010 2571603 FBgn0000005_297 . + -chr2L 2569018 2569804 FBgn0061485_rover . + -chr2L 2569064 2570806 FBgn0044355_Quasimodo . + -chr2L 2569064 2569752 FBgn0026065_Idefix . + -chr2L 2569859 2571024 FBgn0061485_rover . + -chr2L 2569987 2570809 FBgn0026065_Idefix . + -chr2L 2570511 2570703 FBgn0063917_McClintock . + -chr2L 2571048 2571200 FBgn0063917_McClintock . + -chr2L 2571264 2571483 FBgn0000004_17.6 . + -chr2L 2571466 2571603 FBgn0063450_Tom1 . + -chr2L 2571468 2571592 FBgn0061485_rover . + -chr2L 2661257 2663012 FBgn0001249_I-element . + -chr2L 2713413 2713444 FBgn0063371_transib2 . - -chr2L 2772652 2776969 FBgn0000005_297 . + -chr2L 2772727 2772946 FBgn0000004_17.6 . + -chr2L 2772929 2773066 FBgn0063450_Tom1 . + -chr2L 2772931 2773084 FBgn0061485_rover . + -chr2L 2772980 2773084 FBgn0063917_McClintock . + -chr2L 2773736 2773910 FBgn0061485_rover . + -chr2L 2774429 2776968 FBgn0061485_rover . + -chr2L 2774429 2776968 FBgn0000004_17.6 . + -chr2L 2774660 2774878 FBgn0063917_McClintock . + -chr2L 2774727 2776980 FBgn0044355_Quasimodo . + -chr2L 2775122 2776985 FBgn0026065_Idefix . + -chr2L 2775124 2776969 FBgn0063917_McClintock . + -chr2L 2775132 2776531 FBgn0063447_accord . + -chr2L 2775183 2776509 FBgn0004082_Tirant . + -chr2L 2775199 2776553 FBgn0063432_gypsy5 . + -chr2L 2775199 2776494 FBgn0040267_Transpac . + -chr2L 2775215 2776321 FBgn0063782_accord2 . - -chr2L 2775216 2776513 FBgn0023131_ZAM . + -chr2L 2775255 2776055 FBgn0003007_opus . + -chr2L 2775313 2775759 FBgn0000006_412 . + -chr2L 2775326 2776047 FBgn0063434_gypsy3 . + -chr2L 2775326 2776047 FBgn0003490_springer . + -chr2L 2775370 2775579 FBgn0067384_gypsy7 . + -chr2L 2775370 2775765 FBgn0001167_gypsy . + -chr2L 2775375 2775890 FBgn0002697_mdg1 . + -chr2L 2775375 2775588 FBgn0000199_blood . + -chr2L 2775391 2776044 FBgnnnnnnnn_HMS-Beagle2 . + -chr2L 2775391 2776044 FBgn0001207_HMS-Beagle . + -chr2L 2775429 2775767 FBgn0010302_Burdock . + -chr2L 2775440 2775710 FBgn0063897_Stalker4 . + -chr2L 2775440 2776515 FBgn0063433_gypsy4 . + -chr2L 2775442 2775582 FBgn0067387_gypsy10 . + -chr2L 2775446 2775858 FBgn0002698_mdg3 . + -chr2L 2776093 2776340 FBgn0000199_blood . + -chr2L 2776099 2776519 FBgnnnnnnnn_HMS-Beagle2 . + -chr2L 2776156 2776324 FBgn0063436_gtwin . + -chr2L 2776156 2776516 FBgn0063431_gypsy6 . + -chr2L 2776179 2776389 FBgn0003007_opus . + -chr2L 2776938 2777318 FBgn0063917_McClintock . + -chr2L 2776958 2777320 FBgn0000004_17.6 . + -chr2L 2776962 2777324 FBgn0061485_rover . + -chr2L 2776962 2777324 FBgn0000005_297 . + -chr2L 2776975 2777315 FBgn0044355_Quasimodo . + -chr2L 2777321 2779175 FBgn0000005_297 . + -chr2L 2777323 2778772 FBgn0000004_17.6 . + -chr2L 2777510 2778596 FBgn0061485_rover . + -chr2L 2777559 2778381 FBgn0026065_Idefix . + -chr2L 2777565 2778378 FBgn0044355_Quasimodo . + -chr2L 2778083 2778275 FBgn0063917_McClintock . + -chr2L 2778620 2778772 FBgn0063917_McClintock . + -chr2L 2778836 2779055 FBgn0000004_17.6 . + -chr2L 2779038 2779175 FBgn0063450_Tom1 . + -chr2L 2779040 2779164 FBgn0061485_rover . + -chr2L 2933353 2935475 FBgn0003122_pogo . - -chr2L 2945631 2945785 FBgn0000155_roo . + -chr2L 2963474 2963538 FBgn0000155_roo . + |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_TE_annotation.gff3 --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_TE_annotation.gff3 Fri Apr 29 05:47:54 2016 -0400 |
| b |
| b'@@ -0,0 +1,934 @@\n+chr2L\tFlyBase\tIdefix\t9726\t9859\t.\t+\t.\tID=FBti0060580;Name=Idefix{}2519;Alias=Idefix#20,TE60580;derived_cyto_location=21A5-21A5\n+chr2L\tFlyBase\tINE-1\t9888\t9949\t.\t-\t.\tID=FBti0059810;Name=INE-1{}1749;Alias=INE-1#4,TE59810;derived_cyto_location=21A5-21A5\n+chr2L\tFlyBase\tINE-1\t24236\t24462\t.\t+\t.\tID=FBti0059812;Name=INE-1{}1751;Alias=INE-1#5,TE59812;derived_cyto_location=21B1-21B1;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tINE-1\t27530\t27788\t.\t-\t.\tID=FBti0059814;Name=INE-1{}1753;Alias=INE-1#6,TE59814;derived_cyto_location=21B1-21B1;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tjockey\t47514\t52519\t.\t+\t.\tID=FBti0019092;Name=jockey{}277;Alias=jockey{}277,TE19092;gbunit=AE003590;derived_cyto_location=21B1-21B1,21A3-21A3;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tINE-1\t60240\t60580\t.\t+\t.\tID=FBti0059816;Name=INE-1{}1755;Alias=INE-1#7,TE59816;derived_cyto_location=21B1-21B1;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tINE-1\t60663\t60773\t.\t+\t.\tID=FBti0059818;Name=INE-1{}1757;Alias=INE-1#8,TE59818;derived_cyto_location=21B1-21B1;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tX\t64316\t64936\t.\t+\t.\tID=FBti0019093;Name=X{}278;Alias=X{}278,CG18303,TE19093;gbunit=AE003590;derived_cyto_location=21B1-21B1,21A4-21A4;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tINE-1\t65664\t65698\t.\t-\t.\tID=FBti0059819;Name=INE-1{}1758;Alias=INE-1#9,TE59819;derived_cyto_location=21B1-21B1;derived_comput_cyto_location=21B1\n+chr2L\tFlyBase\tINE-1\t116518\t116976\t.\t+\t.\tID=FBti0060557;Name=INE-1{}2496;Alias=INE-1#10,TE60557;derived_cyto_location=21B2-21B2;derived_comput_cyto_location=21B2\n+chr2L\tFlyBase\tMcClintock\t123547\t123635\t.\t-\t.\tID=FBti0060562;Name=McClintock{}2501;Alias=McClintock#15,TE60562;derived_cyto_location=21B2-21B2;derived_comput_cyto_location=21B2\n+chr2L\tFlyBase\tINE-1\t172692\t172724\t.\t+\t.\tID=FBti0060558;Name=INE-1{}2497;Alias=INE-1#11,TE60558;derived_cyto_location=21B4-21B4;derived_comput_cyto_location=21B4\n+chr2L\tFlyBase\tINE-1\t173743\t173778\t.\t-\t.\tID=FBti0060559;Name=INE-1{}2498;Alias=INE-1#12,TE60559;derived_cyto_location=21B4-21B4;derived_comput_cyto_location=21B4\n+chr2L\tFlyBase\tI\t176393\t176512\t.\t-\t.\tID=FBti0019095;Name=I{}279;Alias=I{}279,TE19095;gbunit=AE003590;derived_cyto_location=21B4-21B4,21B3-21B3;derived_comput_cyto_location=21B4\n+chr2L\tFlyBase\tINE-1\t178279\t178467\t.\t+\t.\tID=FBti0060560;Name=INE-1{}2499;Alias=INE-1#13,TE60560;derived_cyto_location=21B4-21B4;derived_comput_cyto_location=21B4\n+chr2L\tFlyBase\tINE-1\t179822\t179909\t.\t+\t.\tID=FBti0060561;Name=INE-1{}2500;Alias=INE-1#14,TE60561;derived_cyto_location=21B4-21B4;derived_comput_cyto_location=21B4\n+chr2L\tFlyBase\tblood\t347941\t355383\t.\t-\t.\tID=FBti0019096;Name=blood{}280;Alias=blood{}280,TE19096;gbunit=AE003589;derived_cyto_location=21C1-21C1,21C2-21C2;derived_comput_cyto_location=21C1\n+chr2L\tFlyBase\tINE-1\t451600\t451692\t.\t-\t.\tID=FBti0063763;Name=INE-1{}5702;Alias=INE-1#10915,TE63763;derived_cyto_location=21C7-21C7;derived_comput_cyto_location=21C2\n+chr2L\tFlyBase\tINE-1\t634184\t634245\t.\t-\t.\tID=FBti0060585;Name=INE-1{}2524;Alias=INE-1#28,TE60585;derived_cyto_location=21E2-21E2;derived_comput_cyto_location=21E2\n+chr2L\tFlyBase\troo\t686974\t695955\t.\t-\t.\tID=FBti0019098;Name=roo{}281;Alias=roo{}281,TE19098;gbunit=AE003588;derived_cyto_location=21E2-21E2,21D2-21D2;derived_comput_cyto_location=21E2\n+chr2L\tFlyBase\tBari1\t770516\t772243\t.\t-\t.\tID=FBti0019099;Name=Bari1{}282;Alias=Bari1{}282,TE19099;gbunit=AE003588;derived_cyto_location=21E2-21E2,21D2-21D2;derived_comput_cyto_location=21E2\n+chr2L\tFlyBase\troo\t976935\t984512\t.\t+\t.\tID=FBti0019100;Name=roo{}283;Alias=roo{}283,TE19100;gbunit=AE003587;derived_cyto_location=21E2-21E2,21E1-21E1;derived_comput_cyto_location=21E2\n+chr2L\tFlyBase\troo\t996780\t1005816\t.\t-\t.\tID=FBti0019101;Name=roo{}284;Alias=roo{}284,TE19101;gbunit=AE003587;derived_cyto_location=21E3-21E3,21E2-21E2;derived_comput_cyto_location=21E3\n+chr2L\tFlyBase\tblood\t1220184\t1227592\t.\t+\t.\tID=FBti0019102;Name=blood{}285;Alias=blood{}285,TE19102;gbunit=AE003587;derived_cyto_location=21F2-21'..b'8;Alias=HMS-Beagle#1508,TE60549;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tHMS-Beagle\t22409494\t22409773\t.\t-\t.\tID=FBti0060684;Name=invader1{}2623;Alias=invader1#1573,TE60684;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tinvader1\t22409895\t22410321\t.\t+\t.\tID=FBti0060551;Name=HMS-Beagle{}2490;Alias=HMS-Beagle#1509,TE60551;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tHMS-Beagle2\t22410897\t22411176\t.\t-\t.\tID=FBti0060686;Name=invader1{}2625;Alias=invader1#1574,TE60686;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tHMS-Beagle\t22411294\t22411721\t.\t+\t.\tID=FBti0060390;Name=HMS-Beagle2{}2329;Alias=HMS-Beagle2#100081,TE60390;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tinvader1\t22412695\t22413121\t.\t+\t.\tID=FBti0060565;Name=HMS-Beagle{}2504;Alias=HMS-Beagle#1511,TE60565;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tHMS-Beagle\t22413694\t22413973\t.\t-\t.\tID=FBti0060688;Name=invader1{}2627;Alias=invader1#1575,TE60688;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tinvader1\t22414091\t22414518\t.\t+\t.\tID=FBti0060391;Name=HMS-Beagle{}2330;Alias=HMS-Beagle#100082,TE60391;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tHMS-Beagle\t22415073\t22415352\t.\t-\t.\tID=FBti0060689;Name=invader1{}2628;Alias=invader1#1576,TE60689;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tDoc\t22415470\t22415824\t.\t+\t.\tID=FBti0060570;Name=HMS-Beagle{}2509;Alias=HMS-Beagle#1513,TE60570;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tFlyBase\tS\t22415856\t22420241\t.\t-\t.\tID=FBti0060540;Name=Doc{}2479;Alias=Doc#1502,TE60540;derived_cyto_location=40F7-40F7;derived_comput_cyto_location=40F7\n+chr2L\tDHGP\troo\t22582024\t22583757\t.\t+\t.\tID=RR48839_transposable_element;Name=S{}RR48839;h-band_cyto_range=h35-h36;cyto_range=40D-40F\n+chr2L\tDHGP\tF\t22605666\t22614751\t.\t-\t.\tID=RR49033_transposable_element;Name=roo{}RR49033;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tMax\t22679852\t22684556\t.\t+\t.\tID=RR48902_transposable_element;Name=F{}RR48902;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tS\t22765149\t22773721\t.\t+\t.\tID=RR48810_transposable_element;Name=Max{}RR48810;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tGATE\t22776474\t22778207\t.\t+\t.\tID=RR48497_transposable_element;Name=S{}RR48497;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tinvader3\t22899297\t22907772\t.\t+\t.\tID=RR48945_transposable_element;Name=GATE{}RR48945;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tinvader3\t23057903\t23063349\t.\t-\t.\tID=RR49017_transposable_element;Name=invader3{}RR49017;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tFlyBase\tJuan\t23059027\t23060915\t.\t+\t.\tID=FBti0059748;Name=invader3{}1687;Alias=TE19812,TE19813,FBti0019812,FBti0019813,invader3#864,invader3{}454,invader3{}455,TE59748;derived_cyto_location=38C2-38C2\n+chr2L\tDHGP\tDoc\t23267989\t23272224\t.\t+\t.\tID=RR48345_transposable_element;Name=Juan{}RR48345;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tF\t23288997\t23293720\t.\t-\t.\tID=RR48348_transposable_element;Name=Doc{}RR48348;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tIvk\t23353253\t23357949\t.\t-\t.\tID=RR44129_transposable_element;Name=F{}RR44129;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\troo\t23382539\t23387909\t.\t+\t.\tID=RR48366_transposable_element;Name=Ivk{}RR48366;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tDoc\t23405712\t23414824\t.\t+\t.\tID=RR48370_transposable_element;Name=roo{}RR48370;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tMcClintock\t23467777\t23472472\t.\t+\t.\tID=RR41919_transposable_element;Name=Doc{}RR41919;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n+chr2L\tDHGP\tBari1\t23475714\t23482166\t.\t+\t.\tID=RR48378_transposable_element;Name=McClintock{}RR48378;cyto_range=40D-40F;h-band_cyto_range=h35-h36\n' |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_chromosome.absence.refined.bp.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_chromosome.absence.refined.bp.summary Fri Apr 29 05:47:54 2016 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Chr Start End TransposonName 5'_Junction 3'_Junction Variant Reference Frequency |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_chromosome.insertion.refined.bp.summary --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_chromosome.insertion.refined.bp.summary Fri Apr 29 05:47:54 2016 -0400 |
| b |
| @@ -0,0 +1,8 @@ +Chr Start End TransposonName TransposonDirection Class VariantSupport Frequency Junction1 Junction1Support Junction2 Junction2Support 5'_Support 3'_Support +chr2L 8900590 8900703 FBgn0000481_Doc antisense 1p1 8 0.1667 8900646 0 8900646 0 5 3 +chr2L 8907814 8908314 FBgn0000155_roo antisense singleton 1 0.0179 8908064 0 8908064 0 0 1 +chr2L 8927841 8928341 FBgn0004141_HeT-A sense singleton 1 0.0333 8928091 0 8928091 0 0 1 +chr2L 8959585 8960085 FBgn0000481_Doc sense 2p 3 0.0236 8959835 0 8959835 0 0 3 +chr2L 8988151 8988651 FBgn0000155_roo antisense singleton 1 0.0159 8988401 0 8988401 0 1 0 +chr2L 8989135 8989635 FBgn0004141_HeT-A antisense singleton 0.5 0.0182 8989385 0 8989385 0 0 0.5 +chr2L 8989135 8989635 FBgn0000481_Doc antisense singleton 0.5 0.0182 8989385 0 8989385 0 0 0.5 |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_chromosome.sites --- a/test-data/test_chromosome.sites Thu Apr 28 07:57:12 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -chr2L 2966910 2966911 FBgn0000481_Doc Insertion -chr2L 2965226 2965227 FBgn0001167_gypsy Insertion -chr2L 2933354 2935475 FBgn0003122_pogo Excision -chr2L 2920517 2920518 FBgn0010302_Burdock Insertion -chr2L 2763540 2763541 FBgn0000199_blood Insertion -chr2L 2714436 2714437 FBgn0000349_copia Insertion -chr2L 2661258 2663012 FBgn0001249_I-element Excision -chr2L 2569343 2569344 FBgn0004141_HeT-A Insertion -chr2L 2412907 2412908 FBgn0003055_P-element Insertion -chr2L 2397941 2397942 FBgn0000155_roo Insertion -chr2L 2294097 2299243 FBgn0000349_copia Excision -chr2L 2131306 2131307 FBgn0001283_jockey Insertion -chr2L 2112168 2119772 FBgn0003007_opus Excision -chr2L 2100430 2109522 FBgn0000155_roo Excision -chr2L 2003871 2003872 FBgn0003122_pogo Insertion |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_chromosome.sorted.bam |
| b |
| Binary file test-data/test_chromosome.sorted.bam has changed |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_chromosome.sorted.bam.bai |
| b |
| Binary file test-data/test_chromosome.sorted.bam.bai has changed |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_concensus.fa --- a/test-data/test_concensus.fa Thu Apr 28 07:57:12 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,1143 +0,0 @@\n->FBgn0010302_Burdock\n-AGTTAACACAATCACAAAACACCCGAAATATAGTCGTAAGCCTCAAGTGC\n-TTTTCCCATCTATAGATCGAGCTTTACCTATAAGAAACTGTAACTTGTTA\n-AGCTTTAGAGATAAGAACTCTTGCTATACTTAAGTCAGTCGATTTTGGAA\n-GATTAGAAGCGTCGGTCATCGCCACGTACTTACTATTCGTCTCATTAAGT\n-GCAGACCGCGCAAGCCTATTGTAATTAATAAACTTACGCTAATAAATATA\n-TGGAAAATCTACTAAAATGATAATTGGCGCCCAAACGGATATAAAAACCT\n-ACGATAACTGAATAATTATAAATAAATAACAAAAGGAGGATCCGGAGACA\n-AAACCAGCGGCTTTGGCTAATTAACTCTAACCTAAGAAATAAAAATTTGC\n-TGATTACATAAAATATAATATTAATTACTAAGACCATCTACCTTAAAATT\n-GTTTGTTAATCACTATTATTATATTGTAAGTATAACGCTTATTGAACGAA\n-TTAAAAATATTATTATTATTATTATATTATAACCTATGCAAAGAGTATTG\n-ATAATAAAAATACATGAGTGACAGTGATAACCTTTTAGACAACCTAGTGT\n-CAAGCTTAAATAAATGGTCAGCGCACCAGGCAAGTAGGCAAAACAGTGCA\n-GAAAAAAATAATAAGTCATCAGATAATTGGTGGTCAAAAACAAAGACAAC\n-TAGCGAAATGGAATTTGAAGCTCAGTTAAAAGCGATCGTAGAGAGTGCTG\n-TTGCCGGTGCGCTCGCAGTCCAAAAACAATCATTTGAAAAGCAATTGCAG\n-GAGATGAATGAGCGAATCGGGAAATTAACAGTGAACACCCCAGAGGTGGA\n-AACTTATGTAGATGCTGAAATTAGACCAGGTGTTGTCTGTAGCGAGCCTC\n-TAGATATACTTAAATCTCTGCCAGATTTTGATGGCAAAAGTGAAACATAT\n-GTGTCGTGGAGAAAAGCGGCTCATGTCGCTTTTAAAGTTTTCAAAGATTA\n-CGAGGGAAGTTCAACATTTTACCAAGCTCTTGGTATTATGCGAAATAAAA\n-TAAAAGGTCCAGCGAATACAGTATTGGCTTCTTTTAATACTCCGTTACAT\n-TTCAAAGCAATGATCAGCCGTCTTGATTTCACATATTCTGACAAAAGGCC\n-GATCTATCTAATCGAACAAGAGCTATCAACTTTGCGACAGGGAGACATGA\n-CTCTTACTGAATTCTACGATGAAGTCGAGAAAAAACTGACCCTACTTACC\n-AACAAGACAATAATGACATTTGATAGTGCCTTGGCGATGTCACTGAATGA\n-AAAGTACAGGACGGACGCGTTACGTGTATTTGTAACCGGAGCTAAGAAAT\n-CGTTGAGCGACATTCTTTTTGCAAAAGGTCCAAAAGATTTACCAACTGCT\n-CTCGCTTTAGCGCAAGAGGTCGAGTCGAACCATGAGCGTTACCAATTCGC\n-CCTTATTTATTCTAAAAATATTGGAGACAGGGGTCAGAAAATCGAACAAA\n-GGCACAGCGATAAGGATAGAAACTCAATCATGCCCATGCAAACTAAAAAC\n-CCATATTTTAGCAAGCGTCAGGTGCATACTTATGATAACCAGGAAAGACA\n-AGATCCAGTCCAGTTAACAAATCCTGATGTATCCATGCGATCTAGAAGAA\n-CTGGAAATTTTGGACAAACTCCATTTCCGACTCAGGGAAATATTTGGCCA\n-TCCCAACAGCAAAATTCTTGGCCATCTCAACAACAATATTCTTGGCCATC\n-CCAACAACAAAATTCATTTCGAACACAAAATCAATTCGCATCGCAACCCC\n-AACAGCAAAACACAAGTCAGGCTCAGGGACATTTTGGGTATGCGCAAGCA\n-TCAAAAAGACCAACGAGTGGCAGTGCAAGGTTTACAGGGCCAAAACAGCA\n-GAGGATCAACTACTTACCTCATGAGAAAGGTCAATGTGAGGAAGATACAG\n-ACGGTTATCAAAAGGAGGCAGAAGCGGAGGTTGATGATTATGAGGACGAA\n-CTAGTGAATTACGATCATGTTCATTTTTTAGCCACAAATCCCTGCTACCG\n-TACATAGAAAGAGAGATAGCAGGGAGAACCATAAAACTTTTGATTGACAC\n-CGGGGCTTCGAAAAATTACATACAGCCCCTCCCTGAATTAAAAAACATAA\n-TGCCGGTACAAAATAAATTCACGGTAAAATCGCTTCATGGTTGCAACACC\n-GTCAAACAGAAATGCTTTATTAAGCTATTTAACACATCTGTTCAATTCTT\n-TATTCTTCCAAGTCTCTCTAGTTTTGACGCAATAATAGGACTTGACCTTT\n-TGAAACAGGGAAATGCAACGTTAGATTTTAAGAACAAAACGTTGAATATC\n-AACAATGAAGTGGAATCTATTCAGTTTTTGAGATGTGACAGCGTAAATTT\n-CGCCAACATAGAGAATATTGTGGTTCCAAATCAGATATCTAATAAATTCC\n-ATACAATGCTTCGAAACCGATTGGCCGTCTTTGCGGAACCGGAAGAAGCA\n-CTGCCGTATAATACCAACATTGTTGCCACAATACGTACTGAGGACGACCA\n-ACCCATTTACTCAAAACTCTATCCGTACCCCATGGGCGTATCGGATTTTG\n-TGAATAAGGAGACACATGCTTTGTTAAAGGACGGAATTATCAGGCCCTCG\n-TCGTCACCTTACAACAATCCGGTTTGGGTAGTCGATAAAAAAGGTACAGA\n-TGAAGAGGGAAATACTAAGAAAAGGTTGGTTATAGATTTTAGAAAACTAA\n-ATTTAAAAACAATCGACGACAAGTACCCTATACCAAACGTAGTATGGATC\n-TTGTCAAATTTGGGAAAAGCCAGATTCTTTACAACCCTTGACCTTAAATC\n-GGCGTTTCACCAAATTCTGCTCGCAGAAAAGGATAGAGCGAAAACTGCCT\n-TTTCAGTAGGAAATGGAAAATACGAGTTTTGCCGTTTGCCGTTTGGCTTG\n-AAAAATGCCCCAAGTATTTTTCAACGTGCTATTGATGATGTTGTTAGGGA\n-CCGTATAGGAAAGTCATGTTACGTTTACGTTGACGACGTAATAATATTTT\n-CAAACGGAATTGAGGACCACGTAAACGACGTTGCTTGGGTACTAGACAGA\n-CTGTCTGGGGCAAACATGAGGGTTTCTAAAGAGAAATCGTTTTTCTTCAA\n-GGAAAGCGTCGAGTATCTCGGATTCATGGTGTCAAGTGGAGGTATCACAA\n-CCAGTCCTAGCAAAGTAGAGGCTATTCAGAAATATAATCAACCTACTAAT\n-CTGTTTAGTGTTCGATCGTTTTTAGGGCTAGCAAGTTATTACCGCTGCTT\n-TATTAAGGACTTCGCCTCTATTGCTAGACCACTCACTGACATTCTGAAGG\n-GTGAAAACGGAAAGGTTTCCGCAAGCCAGTCTAAAAAGATACCAATTTCT\n-TTCGATGAAAGACAATGTTCTGCTTTTGAGAAGCTTAAAAATGTTCTTGT\n-CTCCGAAAATGTAATGTTATTGTATCCCGATTATAGAAAAGCCTTTGACT\n-TAACAACAGACGCTTCGGCTTTTGGCCTGGGGGCAGTCTTATCACAGGAT\n-GGCAAGCCTGTTACAATGATTTCGAGAACTTTACAGGATAGAGAACTTAA\n-TTTCGCAACAAATGAACGAGAACTTTTGGCCATCGTTTGGGCTTTAAAGT\n-CTCTTAGGAACTATCTATATGGTGTCAAAAACTTAAACATTTTTACAGAT\n-CACCAGCCGTTAACATACGCCGTGTCAGATAGGAATCCAAATGCAAAAAT\n-CAAGAGATGGAAGGCGTTTATAGACGAACATAATGCTAAAATTTTCTATA\n-AACCT'..b'AAGTAATCAGACAAGTCAAATTACTCACTAACGA\n-AAAAACGGTGGTAGTACCAAATCAGGAGCTGCAACCAGGTATAATAGTAG\n-CAAGCACCATTGCCGATAGCAAAAACGCATTGATTCGCATTATAAATACA\n-AATAATAAAGACGCCATAATAGATAGCGCGAAGATCAAATGCGAATCAAT\n-GAAAGACTATGACATTTTTACAACACCAGTAGAAAAGGAAAATAGAACTG\n-AAGAAATTTTAAAACAATTAAGATTCCCTAAACAATTCAATAATGAACTA\n-ACTAAGTTATGCACCGAGTTTAGCGATATTTTTGGTCTAGAAACAGAACC\n-AATATCGGCTAACAATTTCTACAAACAAAAACTCAGATTAGGGGAAAAAA\n-CACCGGTCTATATAAAAAACTATCGCATGGCAGATAGCCAAAAACCAGAA\n-ATCGCCAGACAGGTAAAAAAATTAATAGATGATGGAATAGTTGAACCATC\n-AATGTCTGAATATAATAGTCCATTACTTTTGGTTCCAAAGAAACCACTTC\n-CGAATTCCACGGAAAAAAGATGGCGATTAGCAGTTGACTATCGTCAAATA\n-AATAAGAAACTATTATCAGACAAATTTCCACTTCCAAGAATAGAAGATAT\n-TCTTGATCAATTAGGAAGAGCAAAGTATTTTTCATGTCTCGACCTAATGT\n-CTGGATTCCACCAGATAGAACTAGAAAAAAGGTATAGAGATATAACGTCA\n-TTTTCAACAGCCAATGGCTCATATCGCTTCACGCGATTACCATACGGACT\n-GAAAGTAGCACCAAACTCCTTCCAACGTAGGATGACACTTGCATTTTCTG\n-GTCTTGAACCATCGCAAGCATTTCTATATATGGATGACTTAGTAGTAATA\n-GGTTGTTCAGAAAAACATATGCTCAAAAATTTGACTAACGTATTCGAGCT\n-ATGTAGACGACATAATTTGAAACTACATCCAGGGAAATGTTCTTTCTTTA\n-TGAAAGAAGTAACATATTTGGGTCACAAATGTACCGATAAAGGTATACTC\n-CCAGATGACACCAAATATGAAGTTATAGAAAAATATCCTATACCAACAGA\n-TGCCGACAGTGCTAGGCGTTTCGTAGCCTTCTGTAATTATTACAGACGTT\n-TCATTAAAAATTTTTCTGATCATTCACGCCACTTAACGAGGCTTTGTAAA\n-AAGAATGTTCAATTCGAATGGACAGCAGAATGCAATGATGCATTCGAATA\n-CCTTAAAACAGAATTAATGAAACCAACATTACTACAGTACCCAGATTTCG\n-GTAAAGAATTTTGCATAACAACCGATGCTAGTAAACAGGCATGCGGAGCG\n-GTACTTACACAAGATCACAATGGTCAACAACTTCCAGTGGCATACGCTTC\n-AAGAATGTTCACTCAAGGTGAAAGTAATAAGTCCACTACAGAACAAGAAT\n-TAACGGCCATTCATTGGGCCATAAATCATTTTCGACCATACATATATGGC\n-AAGCATTTCATGGTAAAAAGCGATCATAGACCATTGTCATACCTATTCTC\n-TATGAAAAATCCAAGTTCAAAACTCACTCGTATGAGGCTGGATTTAGAAG\n-AGTATGACTTTACTGTAGAATATCTTAAGGGGAAAGATAACCATATTGCG\n-GACGCCTTGTCTCGCATAACAATAAAAGATCTGAAAACAATCAACAGAGA\n-AATATTAAAAGTTACCACCAGATCAAAAGCTAAACAGGAAAATTCCTGTA\n-AGGACGAAGCAATAGTCAAAATACAAGAGGAAAAAGAGCAAACAATAGAA\n-AAGCCCAAAGTCTATGAAGTTGTCAATAATAATGACACAAAGAAATATGT\n-TTTAATCAAAATAGATAAACACAAGTGTTTATTAAAACGAGGAAAAACAA\n-TTGTTTCACGCTTTGATGTTGATGACTTGTATTCTAATGAAACATTTGAT\n-CTAAATCAATTCTTTCAAAGGCTTATTTCAAAAGCCGGAATGCATAAAAT\n-AACAAAAATGCGAATATCACCAAGCGAACAGATGTTCCAATTTGTATCAC\n-TAAATGAATTTAAAATAAAGGGCAACCGAGTACTCGAAAAAGTAGAACTA\n-GCTATTCTACAAAAGGTGATAATTATAGACAAAAATGACGAAGCTCAGAT\n-TAAAGAAATTTTGACAAAATTCCATGATGATCCTATAGAAGGAGGCCACA\n-CTGGTATTTCGCGAACCCAGTCAAAAATCAAAAGATTTTATTATTGGCCC\n-CAGATGACCAAGACAATCTCAAAGTATGTAAAGACTTGTTTGAAATGTCA\n-ACAAGCCAAAATTACAACACATACGAAAACTCCATTAACATTGATGCCAA\n-CGCCAGCAACAGCATTTGATACTGTTTTAATTGATACCATTGGTCCACTA\n-CCGAAATCGGAAGACGGAAATGAGTATGCAGTTACAATCATATGCGATCT\n-AACCAAGTTTTTAGTAACTATTCCAACACCAAATAAAAGTGCTAAAACAG\n-TTGCAAAGGCTATATTTGAATTATTTGTACTGAAGTACGGTCCAATGAAG\n-ACGTTCATTACAGATCAAGGTACGGAATACAAAAATTCACTTATGAATGA\n-ATTATGCAAATATATGCATATAGAAAATCTAACATCTAGCGCTCACCATC\n-ATCAAACTTTAGGAACAATAGAAAGAAGCCACCGAACTTTTAATGAATAT\n-ATACGTTCATACATATCGGTTAACAAAAGTGATTGGGACATTTGGTTACC\n-ATATTTCACTTATTGCTTCAATACAACACCCTCAATAGTCCATGACTATT\n-GCCCATACGAACTAGTATTTGGCAGACTACCCAGACAATTCAAAGATTTC\n-AGTAAGATAAACAAAATAGACCCAATATACAACTTAGACGACTACTCTAA\n-AGAGCTTAAATGCAGACTAGAATTGTCGTACAACAGAGCAAGAAGAATGT\n-TAGAAAAAGCAAAAGCGGATAGAAAATTAAGATATGATAGGAATACAAAT\n-AATTTCGAATTAAAAATAGGAGATAAAGTATTACTTAGAAAAGAAACAGG\n-TCATAAGTTAGATAAAAGATATGAAGGTCCTTATGACGTAGTAGATATAG\n-GAATAAATGACAATATAACCATTAAAACAGGAAGTAAGAAACAACAAATA\n-GTACATAAAGATAGGCTAAAAAAGCACAAATAGAATGAAAAAAAAAAAGG\n-GCAATCAATGCCAAACCTTTCATAATAAAACTTAAATAACGGCCTGATCA\n-GCCAAAACAATATAACAAAGACATAGACATAATCGAATTTTTATTAATTC\n-AAAATACATACATATTTTTTCTTTATTCATTTAAAAATTCTATATCATAA\n-ATAATGTTAATTCATTAAAAATAATATTTAAGTAATTTTTATTTTATAAT\n-GGTAATATAGTTGATAGAAAATAACTTCATTTCTTTACGTTATTTTAAAA\n-AAGAGGGGAGGTGTAGTATGTGCATATATCGAGGGTACACTGTACCTATA\n-AGTACACAGCAACACTTAGTTGCATTGCATAAATAAATGTCTCAAGTGAG\n-CGTGATATAAGATCACCCATTTATGCTTTAAGCTAAGTCAGCATCCCCAC\n-GCTGGCCGCTGGCCATATATGCGCATAAGCTCTCTCTCTCTCTCTCTTAT\n-ACATATATATATACGCTGCTCTTCTGCCGCTGTCGACGGCGGCGCAGTCG\n-CAGTATTTAGGTAAGATTAGACACTCTGTAGAGGTTAAGCGGGCAGAACC\n-GTTTCTGCTACTCGAAGAGATAAGAAGAAATAAAAAGGTGGCCTGACGGC\n-TGCACCCAACTGCAAGGAAAACACGTGTTCTCAATTGGTGGCATATATTG\n-GTTTATTACA\n' |
| b |
| diff -r e19d9742c99b -r ca36262102d8 test-data/test_consensus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_consensus.fa Fri Apr 29 05:47:54 2016 -0400 |
| b |
| b'@@ -0,0 +1,1143 @@\n+>FBgn0010302_Burdock\n+AGTTAACACAATCACAAAACACCCGAAATATAGTCGTAAGCCTCAAGTGC\n+TTTTCCCATCTATAGATCGAGCTTTACCTATAAGAAACTGTAACTTGTTA\n+AGCTTTAGAGATAAGAACTCTTGCTATACTTAAGTCAGTCGATTTTGGAA\n+GATTAGAAGCGTCGGTCATCGCCACGTACTTACTATTCGTCTCATTAAGT\n+GCAGACCGCGCAAGCCTATTGTAATTAATAAACTTACGCTAATAAATATA\n+TGGAAAATCTACTAAAATGATAATTGGCGCCCAAACGGATATAAAAACCT\n+ACGATAACTGAATAATTATAAATAAATAACAAAAGGAGGATCCGGAGACA\n+AAACCAGCGGCTTTGGCTAATTAACTCTAACCTAAGAAATAAAAATTTGC\n+TGATTACATAAAATATAATATTAATTACTAAGACCATCTACCTTAAAATT\n+GTTTGTTAATCACTATTATTATATTGTAAGTATAACGCTTATTGAACGAA\n+TTAAAAATATTATTATTATTATTATATTATAACCTATGCAAAGAGTATTG\n+ATAATAAAAATACATGAGTGACAGTGATAACCTTTTAGACAACCTAGTGT\n+CAAGCTTAAATAAATGGTCAGCGCACCAGGCAAGTAGGCAAAACAGTGCA\n+GAAAAAAATAATAAGTCATCAGATAATTGGTGGTCAAAAACAAAGACAAC\n+TAGCGAAATGGAATTTGAAGCTCAGTTAAAAGCGATCGTAGAGAGTGCTG\n+TTGCCGGTGCGCTCGCAGTCCAAAAACAATCATTTGAAAAGCAATTGCAG\n+GAGATGAATGAGCGAATCGGGAAATTAACAGTGAACACCCCAGAGGTGGA\n+AACTTATGTAGATGCTGAAATTAGACCAGGTGTTGTCTGTAGCGAGCCTC\n+TAGATATACTTAAATCTCTGCCAGATTTTGATGGCAAAAGTGAAACATAT\n+GTGTCGTGGAGAAAAGCGGCTCATGTCGCTTTTAAAGTTTTCAAAGATTA\n+CGAGGGAAGTTCAACATTTTACCAAGCTCTTGGTATTATGCGAAATAAAA\n+TAAAAGGTCCAGCGAATACAGTATTGGCTTCTTTTAATACTCCGTTACAT\n+TTCAAAGCAATGATCAGCCGTCTTGATTTCACATATTCTGACAAAAGGCC\n+GATCTATCTAATCGAACAAGAGCTATCAACTTTGCGACAGGGAGACATGA\n+CTCTTACTGAATTCTACGATGAAGTCGAGAAAAAACTGACCCTACTTACC\n+AACAAGACAATAATGACATTTGATAGTGCCTTGGCGATGTCACTGAATGA\n+AAAGTACAGGACGGACGCGTTACGTGTATTTGTAACCGGAGCTAAGAAAT\n+CGTTGAGCGACATTCTTTTTGCAAAAGGTCCAAAAGATTTACCAACTGCT\n+CTCGCTTTAGCGCAAGAGGTCGAGTCGAACCATGAGCGTTACCAATTCGC\n+CCTTATTTATTCTAAAAATATTGGAGACAGGGGTCAGAAAATCGAACAAA\n+GGCACAGCGATAAGGATAGAAACTCAATCATGCCCATGCAAACTAAAAAC\n+CCATATTTTAGCAAGCGTCAGGTGCATACTTATGATAACCAGGAAAGACA\n+AGATCCAGTCCAGTTAACAAATCCTGATGTATCCATGCGATCTAGAAGAA\n+CTGGAAATTTTGGACAAACTCCATTTCCGACTCAGGGAAATATTTGGCCA\n+TCCCAACAGCAAAATTCTTGGCCATCTCAACAACAATATTCTTGGCCATC\n+CCAACAACAAAATTCATTTCGAACACAAAATCAATTCGCATCGCAACCCC\n+AACAGCAAAACACAAGTCAGGCTCAGGGACATTTTGGGTATGCGCAAGCA\n+TCAAAAAGACCAACGAGTGGCAGTGCAAGGTTTACAGGGCCAAAACAGCA\n+GAGGATCAACTACTTACCTCATGAGAAAGGTCAATGTGAGGAAGATACAG\n+ACGGTTATCAAAAGGAGGCAGAAGCGGAGGTTGATGATTATGAGGACGAA\n+CTAGTGAATTACGATCATGTTCATTTTTTAGCCACAAATCCCTGCTACCG\n+TACATAGAAAGAGAGATAGCAGGGAGAACCATAAAACTTTTGATTGACAC\n+CGGGGCTTCGAAAAATTACATACAGCCCCTCCCTGAATTAAAAAACATAA\n+TGCCGGTACAAAATAAATTCACGGTAAAATCGCTTCATGGTTGCAACACC\n+GTCAAACAGAAATGCTTTATTAAGCTATTTAACACATCTGTTCAATTCTT\n+TATTCTTCCAAGTCTCTCTAGTTTTGACGCAATAATAGGACTTGACCTTT\n+TGAAACAGGGAAATGCAACGTTAGATTTTAAGAACAAAACGTTGAATATC\n+AACAATGAAGTGGAATCTATTCAGTTTTTGAGATGTGACAGCGTAAATTT\n+CGCCAACATAGAGAATATTGTGGTTCCAAATCAGATATCTAATAAATTCC\n+ATACAATGCTTCGAAACCGATTGGCCGTCTTTGCGGAACCGGAAGAAGCA\n+CTGCCGTATAATACCAACATTGTTGCCACAATACGTACTGAGGACGACCA\n+ACCCATTTACTCAAAACTCTATCCGTACCCCATGGGCGTATCGGATTTTG\n+TGAATAAGGAGACACATGCTTTGTTAAAGGACGGAATTATCAGGCCCTCG\n+TCGTCACCTTACAACAATCCGGTTTGGGTAGTCGATAAAAAAGGTACAGA\n+TGAAGAGGGAAATACTAAGAAAAGGTTGGTTATAGATTTTAGAAAACTAA\n+ATTTAAAAACAATCGACGACAAGTACCCTATACCAAACGTAGTATGGATC\n+TTGTCAAATTTGGGAAAAGCCAGATTCTTTACAACCCTTGACCTTAAATC\n+GGCGTTTCACCAAATTCTGCTCGCAGAAAAGGATAGAGCGAAAACTGCCT\n+TTTCAGTAGGAAATGGAAAATACGAGTTTTGCCGTTTGCCGTTTGGCTTG\n+AAAAATGCCCCAAGTATTTTTCAACGTGCTATTGATGATGTTGTTAGGGA\n+CCGTATAGGAAAGTCATGTTACGTTTACGTTGACGACGTAATAATATTTT\n+CAAACGGAATTGAGGACCACGTAAACGACGTTGCTTGGGTACTAGACAGA\n+CTGTCTGGGGCAAACATGAGGGTTTCTAAAGAGAAATCGTTTTTCTTCAA\n+GGAAAGCGTCGAGTATCTCGGATTCATGGTGTCAAGTGGAGGTATCACAA\n+CCAGTCCTAGCAAAGTAGAGGCTATTCAGAAATATAATCAACCTACTAAT\n+CTGTTTAGTGTTCGATCGTTTTTAGGGCTAGCAAGTTATTACCGCTGCTT\n+TATTAAGGACTTCGCCTCTATTGCTAGACCACTCACTGACATTCTGAAGG\n+GTGAAAACGGAAAGGTTTCCGCAAGCCAGTCTAAAAAGATACCAATTTCT\n+TTCGATGAAAGACAATGTTCTGCTTTTGAGAAGCTTAAAAATGTTCTTGT\n+CTCCGAAAATGTAATGTTATTGTATCCCGATTATAGAAAAGCCTTTGACT\n+TAACAACAGACGCTTCGGCTTTTGGCCTGGGGGCAGTCTTATCACAGGAT\n+GGCAAGCCTGTTACAATGATTTCGAGAACTTTACAGGATAGAGAACTTAA\n+TTTCGCAACAAATGAACGAGAACTTTTGGCCATCGTTTGGGCTTTAAAGT\n+CTCTTAGGAACTATCTATATGGTGTCAAAAACTTAAACATTTTTACAGAT\n+CACCAGCCGTTAACATACGCCGTGTCAGATAGGAATCCAAATGCAAAAAT\n+CAAGAGATGGAAGGCGTTTATAGACGAACATAATGCTAAAATTTTCTATA\n+AACCT'..b'AAGTAATCAGACAAGTCAAATTACTCACTAACGA\n+AAAAACGGTGGTAGTACCAAATCAGGAGCTGCAACCAGGTATAATAGTAG\n+CAAGCACCATTGCCGATAGCAAAAACGCATTGATTCGCATTATAAATACA\n+AATAATAAAGACGCCATAATAGATAGCGCGAAGATCAAATGCGAATCAAT\n+GAAAGACTATGACATTTTTACAACACCAGTAGAAAAGGAAAATAGAACTG\n+AAGAAATTTTAAAACAATTAAGATTCCCTAAACAATTCAATAATGAACTA\n+ACTAAGTTATGCACCGAGTTTAGCGATATTTTTGGTCTAGAAACAGAACC\n+AATATCGGCTAACAATTTCTACAAACAAAAACTCAGATTAGGGGAAAAAA\n+CACCGGTCTATATAAAAAACTATCGCATGGCAGATAGCCAAAAACCAGAA\n+ATCGCCAGACAGGTAAAAAAATTAATAGATGATGGAATAGTTGAACCATC\n+AATGTCTGAATATAATAGTCCATTACTTTTGGTTCCAAAGAAACCACTTC\n+CGAATTCCACGGAAAAAAGATGGCGATTAGCAGTTGACTATCGTCAAATA\n+AATAAGAAACTATTATCAGACAAATTTCCACTTCCAAGAATAGAAGATAT\n+TCTTGATCAATTAGGAAGAGCAAAGTATTTTTCATGTCTCGACCTAATGT\n+CTGGATTCCACCAGATAGAACTAGAAAAAAGGTATAGAGATATAACGTCA\n+TTTTCAACAGCCAATGGCTCATATCGCTTCACGCGATTACCATACGGACT\n+GAAAGTAGCACCAAACTCCTTCCAACGTAGGATGACACTTGCATTTTCTG\n+GTCTTGAACCATCGCAAGCATTTCTATATATGGATGACTTAGTAGTAATA\n+GGTTGTTCAGAAAAACATATGCTCAAAAATTTGACTAACGTATTCGAGCT\n+ATGTAGACGACATAATTTGAAACTACATCCAGGGAAATGTTCTTTCTTTA\n+TGAAAGAAGTAACATATTTGGGTCACAAATGTACCGATAAAGGTATACTC\n+CCAGATGACACCAAATATGAAGTTATAGAAAAATATCCTATACCAACAGA\n+TGCCGACAGTGCTAGGCGTTTCGTAGCCTTCTGTAATTATTACAGACGTT\n+TCATTAAAAATTTTTCTGATCATTCACGCCACTTAACGAGGCTTTGTAAA\n+AAGAATGTTCAATTCGAATGGACAGCAGAATGCAATGATGCATTCGAATA\n+CCTTAAAACAGAATTAATGAAACCAACATTACTACAGTACCCAGATTTCG\n+GTAAAGAATTTTGCATAACAACCGATGCTAGTAAACAGGCATGCGGAGCG\n+GTACTTACACAAGATCACAATGGTCAACAACTTCCAGTGGCATACGCTTC\n+AAGAATGTTCACTCAAGGTGAAAGTAATAAGTCCACTACAGAACAAGAAT\n+TAACGGCCATTCATTGGGCCATAAATCATTTTCGACCATACATATATGGC\n+AAGCATTTCATGGTAAAAAGCGATCATAGACCATTGTCATACCTATTCTC\n+TATGAAAAATCCAAGTTCAAAACTCACTCGTATGAGGCTGGATTTAGAAG\n+AGTATGACTTTACTGTAGAATATCTTAAGGGGAAAGATAACCATATTGCG\n+GACGCCTTGTCTCGCATAACAATAAAAGATCTGAAAACAATCAACAGAGA\n+AATATTAAAAGTTACCACCAGATCAAAAGCTAAACAGGAAAATTCCTGTA\n+AGGACGAAGCAATAGTCAAAATACAAGAGGAAAAAGAGCAAACAATAGAA\n+AAGCCCAAAGTCTATGAAGTTGTCAATAATAATGACACAAAGAAATATGT\n+TTTAATCAAAATAGATAAACACAAGTGTTTATTAAAACGAGGAAAAACAA\n+TTGTTTCACGCTTTGATGTTGATGACTTGTATTCTAATGAAACATTTGAT\n+CTAAATCAATTCTTTCAAAGGCTTATTTCAAAAGCCGGAATGCATAAAAT\n+AACAAAAATGCGAATATCACCAAGCGAACAGATGTTCCAATTTGTATCAC\n+TAAATGAATTTAAAATAAAGGGCAACCGAGTACTCGAAAAAGTAGAACTA\n+GCTATTCTACAAAAGGTGATAATTATAGACAAAAATGACGAAGCTCAGAT\n+TAAAGAAATTTTGACAAAATTCCATGATGATCCTATAGAAGGAGGCCACA\n+CTGGTATTTCGCGAACCCAGTCAAAAATCAAAAGATTTTATTATTGGCCC\n+CAGATGACCAAGACAATCTCAAAGTATGTAAAGACTTGTTTGAAATGTCA\n+ACAAGCCAAAATTACAACACATACGAAAACTCCATTAACATTGATGCCAA\n+CGCCAGCAACAGCATTTGATACTGTTTTAATTGATACCATTGGTCCACTA\n+CCGAAATCGGAAGACGGAAATGAGTATGCAGTTACAATCATATGCGATCT\n+AACCAAGTTTTTAGTAACTATTCCAACACCAAATAAAAGTGCTAAAACAG\n+TTGCAAAGGCTATATTTGAATTATTTGTACTGAAGTACGGTCCAATGAAG\n+ACGTTCATTACAGATCAAGGTACGGAATACAAAAATTCACTTATGAATGA\n+ATTATGCAAATATATGCATATAGAAAATCTAACATCTAGCGCTCACCATC\n+ATCAAACTTTAGGAACAATAGAAAGAAGCCACCGAACTTTTAATGAATAT\n+ATACGTTCATACATATCGGTTAACAAAAGTGATTGGGACATTTGGTTACC\n+ATATTTCACTTATTGCTTCAATACAACACCCTCAATAGTCCATGACTATT\n+GCCCATACGAACTAGTATTTGGCAGACTACCCAGACAATTCAAAGATTTC\n+AGTAAGATAAACAAAATAGACCCAATATACAACTTAGACGACTACTCTAA\n+AGAGCTTAAATGCAGACTAGAATTGTCGTACAACAGAGCAAGAAGAATGT\n+TAGAAAAAGCAAAAGCGGATAGAAAATTAAGATATGATAGGAATACAAAT\n+AATTTCGAATTAAAAATAGGAGATAAAGTATTACTTAGAAAAGAAACAGG\n+TCATAAGTTAGATAAAAGATATGAAGGTCCTTATGACGTAGTAGATATAG\n+GAATAAATGACAATATAACCATTAAAACAGGAAGTAAGAAACAACAAATA\n+GTACATAAAGATAGGCTAAAAAAGCACAAATAGAATGAAAAAAAAAAAGG\n+GCAATCAATGCCAAACCTTTCATAATAAAACTTAAATAACGGCCTGATCA\n+GCCAAAACAATATAACAAAGACATAGACATAATCGAATTTTTATTAATTC\n+AAAATACATACATATTTTTTCTTTATTCATTTAAAAATTCTATATCATAA\n+ATAATGTTAATTCATTAAAAATAATATTTAAGTAATTTTTATTTTATAAT\n+GGTAATATAGTTGATAGAAAATAACTTCATTTCTTTACGTTATTTTAAAA\n+AAGAGGGGAGGTGTAGTATGTGCATATATCGAGGGTACACTGTACCTATA\n+AGTACACAGCAACACTTAGTTGCATTGCATAAATAAATGTCTCAAGTGAG\n+CGTGATATAAGATCACCCATTTATGCTTTAAGCTAAGTCAGCATCCCCAC\n+GCTGGCCGCTGGCCATATATGCGCATAAGCTCTCTCTCTCTCTCTCTTAT\n+ACATATATATATACGCTGCTCTTCTGCCGCTGTCGACGGCGGCGCAGTCG\n+CAGTATTTAGGTAAGATTAGACACTCTGTAGAGGTTAAGCGGGCAGAACC\n+GTTTCTGCTACTCGAAGAGATAAGAAGAAATAAAAAGGTGGCCTGACGGC\n+TGCACCCAACTGCAAGGAAAACACGTGTTCTCAATTGGTGGCATATATTG\n+GTTTATTACA\n' |