Mercurial > repos > clifinder > clifinder
changeset 14:feecd33c8390 draft
"planemo upload for repository https://github.com/GReD-Clermont/CLIFinder/ commit 96ee8f4901f2938dae7befb1e41c697628c22f54"
| author | pierre.pouchin |
|---|---|
| date | Tue, 11 Feb 2020 09:28:56 -0500 |
| parents | 7978868868de |
| children | 6d7caeea1e74 |
| files | CLIFinder.xml LICENSE LINE_html4.1.pl LINE_html_4_1.xml README.rst script/CLIFinder.pl script/CLIFinder_results.R script/js/jquery.min.js script/static/images/arrows.png script/static/images/header_bkg.png script/static/images/row_bkg.png test-data/TE.fa test-data/est-small.fa.gz test-data/genome.fa test-data/one.fastq test-data/refseq-small.txt test-data/res.html test-data/res_files/final_result_chimerae.txt test-data/res_files/first_results.txt test-data/res_files/results.txt test-data/rmsk-small.txt test-data/rna-small.fa.gz test-data/two.fastq tool-data/blastdb.loc.sample tool-data/bwa_index.loc.sample tool-data/bwa_mem_index.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
| diffstat | 28 files changed, 3462 insertions(+), 1254 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CLIFinder.xml Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,306 @@ +<tool name="CLIFinder" id="CLIFinder" version="0.5.0" profile="16.01"> + <description>Find chimerics transcripts containing LINEs sequences</description> + <macros> + <xml name="source_bwa" token_arg="Argument" token_build="Build argument" token_ref=""> + <conditional name="source"> + <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param name="indices" argument="@ARG@" type="select" label="Select @REF@"> + <options from_data_table="bwa_mem_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="file" argument="@ARG@" type="data" format="fasta" label="Select @REF@ from history" help="We will also use @BUILD@"/> + </when> + </conditional> + </xml> + <xml name="source_blast" token_arg="Argument" token_build="Build argument" token_ref=""> + <conditional name="source"> + <param name="source" type="select" label="Will you select the reference database from your history or use a built-in index?"> + <option value="indexed">Use a built-in index</option> + <option value="history">Generate one from the history</option> + <option value="url">Download one from some URL</option> + </param> + <when value="indexed"> + <param name="indices" argument="@ARG@" type="select" label="Select @REF@"> + <options from_data_table="blastdb"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + </param> + </when> + <when value="history"> + <param name="file" argument="@ARG@" type="data" format="fasta" label="Select @REF@ from history" help="We will also use @BUILD@"/> + </when> + <when value="url"> + <param name="file" argument="@ARG@" type="text" label="Download @REF@ from URL" help="We will not use @BUILD@: please provide link to tar.gz"/> + </when> + </conditional> + </xml> + </macros> + <requirements> + <requirement type="package" version="1.9">samtools</requirement> + <requirement type="package" version="2.26.0gx">bedtools</requirement> + <requirement type="package" version="4.0.9_p2">repeatmasker</requirement> + <requirement type="package" version="0.7.17">bwa</requirement> + <requirement type="package" version="0.0.14">fastx_toolkit</requirement> + <requirement type="package" version="1.20.1">wget</requirement> + <requirement type="package" version="5.26.2">perl</requirement> + <requirement type="package" version="2.50">perl-getopt-long</requirement> + <requirement type="package" version="0.45">perl-file-copy-recursive</requirement> + <requirement type="package" version="2.02">perl-parallel-forkmanager</requirement> + <requirement type="package" version="0.34">perl-statistics-r</requirement> + <requirement type="package" version="3.5.1">r-base</requirement> + <requirement type="package" version="1.8.5">r-plyr</requirement> + <requirement type="package" version="1.34.0">bioconductor-genomicranges</requirement> + </requirements> + <version_command>perl '$__tool_directory__/script/CLIFinder.pl' --version | head -n 1 | grep 'version' | cut -d ' ' -f 3</version_command> + <command detect_errors="aggressive"><![CDATA[ +perl '$__tool_directory__/script/CLIFinder.pl' + + #if str($inputs.custom) == 'true' + #for $x in $inputs.fastq + --first '$x.first' + --name '$x.name' + --second '$x.second' + #end for + #else + #for $x in $inputs.fastq + --first '$x.first' + --name '$x.first.name' + --second '$x.second' + #end for + #end if + + #if $genome.source.source == "history" + --ref '$genome.source.file' + --build_ref + #else + --ref '$genome.source.indices.fields.path' + #end if + + #if $te.source.source == "history" + --TE '$te.source.file' + --build_TE + #else + --TE '$te.source.indices.fields.path' + #end if + + #if str($rnadb.blast.run) == 'true' + #if $rnadb.blast.source.source == "indexed" + --rnadb '$rnadb.blast.source.indices.fields.path' + #else + --rnadb '$rnadb.blast.source.file' + #end if + #if $rnadb.blast.source.source == "history" + --build_rnadb + #end if + #end if + + #if str($estdb.blast.run) == 'true' + #if $estdb.blast.source.source == "indexed" + --estdb '$estdb.blast.source.indices.fields.path' + #else + --estdb '$estdb.blast.source.file' + #end if + #if $estdb.blast.source.source == "history" + --build_estdb + #end if + #end if + + --rmsk '$rmsk' + --refseq '$refseq' + --html '$chimerae' + --html_path '${chimerae.files_path}' + --size_insert '$size_insert' + --size_read '$size' + --min_unique '$min_unique' + --BDir '$BDir' + --min_L1 '$min_L1' + --mis_L1 '$mis_L1' + --threads "\${GALAXY_SLOTS:-4}" + ]]> + </command> + <inputs> + <conditional name="inputs"> + <param name="custom" type="select" label="Use custom name for the input sequence files?"> + <option value="true">Yes</option> + <option value="false" selected="true">No: the names will be extracted automatically</option> + </param> + <when value="true"> + <repeat name="fastq" title="Input sequences" min="1"> + <param argument="--first" type="data" format="fastqsanger" label="First set of paired-end reads"/> + <param argument="--name" type="text" value="" label="Label for the input sequences"/> + <param argument="--second" type="data" format="fastqsanger" label="Second set of paired-end reads"/> + </repeat> + </when> + <when value="false"> + <repeat name="fastq" title="Input sequences" min="1"> + <param argument="--first" type="data" format="fastqsanger" label="First set of paired-end reads"/> + <param argument="--second" type="data" format="fastqsanger" label="Second set of paired-end reads"/> + </repeat> + </when> + </conditional> + <section name="genome" title="Reference genome" expanded="true"> + <expand macro="source_bwa" arg="--ref" build="--build_ref" ref="a reference genome"/> + </section> + <section name="te" title="Transposable Elements" expanded="true"> + <expand macro="source_bwa" arg="--TE" build="--build_TE" ref="reference TE sequences"/> + </section> + <section name="rnadb" title="RNA Blast database" expanded="true"> + <conditional name="blast"> + <param name="run" type="select" label="Should blast be ran?"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <expand macro="source_blast" arg="--rnadb" build="--build_rnadb" ref="reference RNA sequences"/> + </when> + <when value="false" /> + </conditional> + </section> + <section name="estdb" title="EST Blast database" expanded="true"> + <conditional name="blast"> + <param name="run" type="select" label="Should blast be ran?"> + <option value="true">Yes</option> + <option value="false">No</option> + </param> + <when value="true"> + <expand macro="source_blast" arg="--estdb" build="--build_estdb" ref="reference EST sequences"/> + </when> + <when value="false" /> + </conditional> + </section> + <param argument="--rmsk" name="rmsk" type="data" format="tabular" label="Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC)"/> + <param argument="--refseq" name="refseq" type="data" format="tabular" label="Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC)"/> + <param name="BDir" type="select" > + <option value="0">Undirectional libraries</option> + <option value="1">TEs sequences in first read in pair</option> + <option value="2">TEs sequences in second read in pair</option> + </param> + <param argument="--size_read" name="size" type="integer" value="100" label="Reads size"/> + <param argument="--size_insert" name="size_insert" type="integer" value="250" label="Maximum insert size (bp)"/> + <param argument="--min_L1" name="min_L1" type="integer" value="50" label="Minimun bp mapping on selected TEs database"/> + <param argument="--mis_L1" name="mis_L1" type="integer" value="2" label="Number of mismatches tolerated in TEs mapping sequences"/> + <param argument="--min_unique" name="min_unique" type="integer" value="33" label="minimum consecutive bp corresponding to a unique sequence"/> + </inputs> + <outputs> + <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/> + </outputs> + <tests> + <test> + <conditional name="inputs"> + <param name="custom" value="true"/> + <repeat name="fastq"> + <param name="first" value="one.fastq" ftype="fastqsanger" /> + <param name="name" value="test"/> + <param name="second" value="two.fastq" ftype="fastqsanger" /> + </repeat> + </conditional> + <section name="genome"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="genome.fa" /> + </conditional> + </section> + <section name="te"> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="TE.fa" /> + </conditional> + </section> + <section name="rnadb"> + <conditional name="blast"> + <param name="run" value="true" /> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="rna-small.fa.gz" /> + </conditional> + </conditional> + </section> + <section name="estdb"> + <conditional name="blast"> + <param name="run" value="true" /> + <conditional name="source"> + <param name="source" value="history" /> + <param name="file" value ="est-small.fa.gz" /> + </conditional> + </conditional> + </section> + <param name="rmsk" value="rmsk-small.txt" /> + <param name="refseq" value="refseq-small.txt" /> + <param name="BDir" value="0" /> + <param name="size" value="100" /> + <param name="size_insert" value="500" /> + <param name="min_L1" value="30" /> + <param name="mis_L1" value="6" /> + <param name="min_unique" value="30" /> + <output name="chimerae" file="res.html" compare="diff" lines_diff="0"> + <extra_files type="file" name="results.txt" value="res_files/results.txt" compare="diff" /> + <extra_files type="file" name="first_results.txt" value="res_files/first_results.txt" compare="diff" /> + <extra_files type="file" name="final_result_chimerae.txt" value="res_files/final_result_chimerae.txt" compare="diff" /> + </output> + </test> + </tests> + <help> + <![CDATA[ +**CLIFinder version 0.5.0** + +**Usage:** + + CLIFinder.pl --first [first fastq of paired-end set 1] --name [name 1] --second [second fastq of paired-end set 1] [--first [first fastq of paired-end set 2] --name [name 2] --second [second fastq of paired-end set 2] ...] --ref [reference genome] [--build_ref] --TE [transposable elements] [--build_TE] --html [results.html] --html-path [results directory][options] + +**Arguments:** + --first [fastq] First fastq file to process from paired-end set + + --name [name] Name of the content to process + + --second [fastq] Second fastq file to process from paired-end set + + --ref [reference] Fasta file containing the reference genome + + --TE [TE] Fasta file containing the transposable elements + + --rmsk [txt file] Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC) + + --refseq [txt file] Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC) + + --html [file] Main HTML file where results will be displayed + + --html-path [path] Folder where results will be stored + +For any fasta file, if a bwa index is not provided, you should build it through the corresponding *--build_[element]* argument + +**Options:** + --rnadb [RNA db] Blast database with RNA sequences (optional) + + --estdb [EST db] Blast database with RNA sequences (optional) + + --size_read [INT] Size of reads + + --BDir [0|1|2] Orientation of reads (0: undirectional libraries, 1: TEs sequences in first read in pair, 2: TEs sequences in second read in pair) + + --size_insert [INT] Maximum size of insert tolerated between R1 and R2 for alignment on the reference genome + + --min_L1 [INT] Minimum number of bp matching for L1 mapping + + --mis_L1 [INT] Maximum number of mismatches tolerated for L1 mapping + + --min_unique [INT] Number of consecutive bp not annotated by RepeatMasker + + --threads [INT] Number of threads (default: 1) + +For Blast database files, if a fasta is provided, the database can be built with '--build_[db]'. Otherwise, provide a path or URL. "tar(.gz)" files are acceptable, as well as wild card (rna*) URLs. + + ]]> + </help> + <citations> + <citation type="doi">10.1093/bioinformatics/btx671</citation> + </citations> +</tool>
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--- a/LINE_html4.1.pl Wed Jan 31 09:59:07 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1101 +0,0 @@ - #/usr/bin/perl - -################################################ -#Declaration of necessary libraries############# -################################################ - -use strict; -use warnings; -use Sys::CPU; -use Parallel::ForkManager; -use POSIX; -use Statistics::R ; -use Getopt::Long; -use File::Basename; - -################################################ -#Declaration of necessary global variables###### -################################################ - -my (@fastq1, @fastq2, @name, $html, $size_reads, $ref, $TE, $build_index, $build_TE, $html_repertory, $maxInsertSize, $prct, $help, $image, $Bdir, $minL1, $mis_L1); - -##################################################################### -#Definition options of execution according to the previous variables# -##################################################################### - -GetOptions ( -"first:s" => \@fastq1, -"second:s" => \@fastq2, -"name:s" => \@name, -"html:s" => \$html, -"TE:s" => \$TE, -"ref:s" => \$ref, -"build_TE" => \$build_TE, -"build_index" => \$build_index, -"pourcentage:i" => \$prct, -"size_insert:i" => \$maxInsertSize, -"size_read:i" => \$size_reads, -"html_path:s" => \$html_repertory, -"image:s" => \$image, -"BDir:i" => \$Bdir, -"minL1:i" => \$minL1, -"mis_L1:i" => \$mis_L1, -); -my $iprct = 100 - (($prct / $size_reads)*100) ; -my $mis_auth = $size_reads - $minL1 + $mis_L1 ; -my $eprct = ($iprct * $size_reads) /100; -my $dprct = ((100-$iprct) * $size_reads) / 100; - -################################################ -#Construct index of ref and TE if doesn't exist# -################################################ - -`(bwa index $ref) 2> /dev/null ` if ($build_index); -`(bwa index $TE) 2> /dev/null ` if ($build_TE); - -############################################ -#Create repository to store resulting files# -############################################ - -mkdir $html_repertory; - -###################################################### -#Define number of Cpu process we can use = total /5 # -###################################################### - -my $cpu = int(Sys::CPU::cpu_count() /5) ; - -########################################## -#Define hash # -########################################## - -my %frag_exp_id; - -########################## -#Data file we have to use# -########################## - -my $NCBI_est = $html_repertory.'/est_human'; # NCBI Human est -my $NCBI_rna = $html_repertory.'/rna'; # NCBI Human rna -my $rmsk = $html_repertory.'/rmsk.bed'; # UCSC repeat sequences -#################################### -# Redirection standart error output# -#################################### - -my $file = $html_repertory.'/report.txt'; -open STDERR, '>', $file or die "Can't redirect STDERR: $!"; - -############################## -# Analyse of each fastq file # -############################## - - -my @garbage; my $num = 0; -foreach my $tabR (0..$#fastq1) -{ - ################################################### - # Paired end mapping against L1 promoter sequences# - ################################################### - - print STDERR "alignement of $name[$tabR] to L1\n"; - my $sam = $html_repertory.'/'.$name[$tabR]."_L1.sam"; push(@garbage, $sam); - align_paired( $TE, $fastq1[$tabR], $fastq2[$tabR], $sam, $cpu, $mis_auth); - print STDERR "alignement done\n"; - - ################################################## - # Creation of two fastq for paired halfed mapped:# - # - _1 correspond to sequences mapped to L1 # - # - _2 correspond to sequences unmapped to L1 # - ################################################## - print STDERR "getting pairs with one mate matched to L1 and the other mate undetected by repeatmasker as a repeat sequence\n"; - - my $out_ASP_1 = $html_repertory.'/'.$name[$tabR]."_1.fastq"; push(@garbage, $out_ASP_1); - my $out_ASP_2 = $html_repertory.'/'.$name[$tabR]."_2.fastq"; push(@garbage, $out_ASP_2); - - ##split mate that matched to L1 and others## - my ($ASP_readsHashR, $half_num_out) = get_half($sam); - # $ASP_reads{$line[0]}[0] mapped - $ASP_reads{$line[0]}[1] unmapped - - ##pairs obtained after repeatmasker on the other mate## - my $left = sort_out($cpu, $out_ASP_1, $out_ASP_2, $ASP_readsHashR); - - print STDERR "number of half mapped pairs : $half_num_out\n"; - print STDERR "number of pairs after repeatmasker: $left\n"; - - ################################################## - # Alignment of halfed mapped pairs on genome # - ################################################## - print STDERR "alignement of potential chimeric sequences to the genome\n"; - $sam = $html_repertory.'/'.$name[$tabR]."_genome.sam"; - push(@garbage, $sam); - align_genome( $ref, $out_ASP_1, $out_ASP_2, $sam, $cpu); - print STDERR "alignement done\n"; - - ##compute the number of sequences obtained after alignement ## - - $left = `samtools view -Shc $sam 2> /dev/null`; - chomp $left; $left = $left/2; - print STDERR "number of sequences....: $left\n"; - - ################################################## - # Create bedfiles of potential chimerae # - # and Know repeat sequences removed # - ################################################## - - print STDERR "looking for chimerae\n"; - results($html_repertory, $sam, $name[$tabR], \%frag_exp_id, $num); - $num++; - -} - - - -##define files variables ## - -my $repfirst = $html_repertory.'/first.bed'; push(@garbage,$repfirst); -my $repsecond = $html_repertory.'/second.bed'; push(@garbage,$repsecond); -my $repMfirst = $html_repertory.'/firstM.bed'; push(@garbage,$repMfirst); -my $repMsecond = $html_repertory.'/secondM.bed'; push(@garbage,$repMsecond); -#my $covRepMsecond = $html_repertory.'/covSecondM.bed'; push(@garbage,$covRepMsecond); - - -##Concate all files for first and second mate results ## - -`cat $html_repertory/*-first.bed > $repfirst`; #*/ -`cat $html_repertory/*-second.bed > $repsecond`; #*/ - -## Sort Files and generate files that merge reads in the same locus ## -`bedtools sort -i $repfirst 2> /dev/null | bedtools merge -scores max -d 100 -s -nms -i /dev/stdin > $repMfirst 2> /dev/null`; -`bedtools sort -i $repsecond 2> /dev/null | bedtools merge -scores max -d 100 -s -nms -i /dev/stdin > $repMsecond 2> /dev/null`; - -my (%Gviz, %frag_uni, @second_R, @second_exp, @results); -my $merge_target = $html_repertory.'/target_merged.bed'; push(@garbage, $merge_target); -my $merge = $html_repertory.'/merged.bed'; push(@garbage, $merge); - -open (my $mT, ">".$merge_target) || die "cannot open $merge_target\n"; -open (my $m, ">".$merge) || die "cannot open $merge\n"; -open (my $in, $repMsecond) || die "cannot open secondM\n"; -my $cmp = 0; -while (<$in>) -{ - chomp $_; - my @tmp = (0) x scalar(@fastq1); - my @line = split /\t/, $_; - my @names =split /;/, $line[3]; - foreach my $n (@names){$n =~/(.*?)\/[12]/; $frag_uni{$1} = $cmp; $tmp[$frag_exp_id{$1}]++; } - $second_exp[$cmp] = \@tmp; - $cmp++; - push @second_R, [$line[0],$line[1],$line[2],$line[5]]; -} - -$cmp = 0; -open ($in, $repMfirst) || die "cannot open firstM\n"; -while (<$in>) -{ - chomp $_; - my %sec; - my @line = split /\t/, $_; - my @names =split /;/, $line[3]; - my @tmp = (0) x scalar(@fastq1); - foreach my $n (@names){$n =~/(.*?)\/[12]/; $tmp[$frag_exp_id{$1}]++; } - foreach my $n (@names) - { - $n =~/(.*?)\/[12]/; - unless (exists ($sec{$frag_uni{$1}}) ) - { - my @lmp = ($line[0], $line[1], $line[2], $line[5]); - foreach my $exp_N (@tmp){ push @lmp, $exp_N;} - push (@lmp, $second_R[$frag_uni{$1}]->[0], $second_R[$frag_uni{$1}]->[1], $second_R[$frag_uni{$1}]->[2], $second_R[$frag_uni{$1}]->[3]); - foreach my $exp_N (@{$second_exp[$frag_uni{$1}]}){ push @lmp, $exp_N;} - - my $name = $cmp.'-'.$second_R[$frag_uni{$1}]->[0].'-'.$second_R[$frag_uni{$1}]->[1].'-'.$second_R[$frag_uni{$1}]->[2]; - print $mT $second_R[$frag_uni{$1}]->[0]."\t".$second_R[$frag_uni{$1}]->[1]."\t".$second_R[$frag_uni{$1}]->[2]."\t$name\t29\t".$second_R[$frag_uni{$1}]->[3]."\n"; - - my ($b, $e) = (0,0); - if ($line[1] < $second_R[$frag_uni{$1}]->[1]) - { - $b = $line[1] - 1000; $e = $second_R[$frag_uni{$1}]->[2] + 1000; - $name = $cmp.'-'.$line[0].'-'.$b.'-'.$e; - print $m $line[0]."\t".$b."\t".$e."\t$name\t29\t".$second_R[$frag_uni{$1}]->[3]."\n"; - } - else - { - $b = $second_R[$frag_uni{$1}]->[1] - 1000; $e = $line[2] + 1000; - $name = $cmp.'-'.$line[0].'-'.$b.'-'.$e; - print $m $line[0]."\t".$b."\t".$e."\t$name\t29\t".$second_R[$frag_uni{$1}]->[3]."\n"; - } - $results[$cmp] = \@lmp; - $cmp++; - } - $sec{$frag_uni{$1}} = undef; - } -} -close $mT; close $m; - -my $fasta = $html_repertory.'/target_merged.fasta'; push(@garbage, $fasta); -my $extend = $html_repertory.'/extend.fasta'; push(@garbage, $extend); - -`bedtools getfasta -name -fi $ref -bed $merge -fo $extend`; -`bedtools getfasta -name -fi $ref -bed $merge_target -fo $fasta`; - -################################################ -#Blast against human rna and est # -################################################ - -##get databases for est and rna -`wget -r -nH -nd -np --accept=est* https://galaxy.gred-clermont.fr/clifinder/ -P $html_repertory `; -`wget -r -nH -nd -np --accept=rna* https://galaxy.gred-clermont.fr/clifinder/ -P $html_repertory `; - - -print STDERR "blast against human rna\n"; -my $tabular = $html_repertory."/chimerae_rna.tab"; push(@garbage, $tabular); -blast($NCBI_rna, $fasta, $tabular, $cpu); -my $rna = extract_blast($tabular); - -print STDERR "blast against human est\n"; -my $tabular2 = $html_repertory."/chimerae_est.tab";push(@garbage, $tabular2); -blast($NCBI_est, $fasta, $tabular, $cpu); -my $est = extract_blast($tabular); - -################################################ -#Create Results html file # -################################################ -print STDERR "save result in file\n"; -save_csv(); -print STDERR "create HTML\n"; -html_tab($rna,$est,$html_repertory); -$extend = $extend.'*'; -push(@garbage,glob($extend)); -unlink @garbage; -my $toErase = $html_repertory.'\rna*'; -unlink glob "$toErase"; -$toErase = $html_repertory.'\est*'; -unlink glob "$toErase"; - - -print STDERR "Job done!\n"; - -########################################### END MAIN ########################################################## - - -############################################################################################################## -############################################ FUNCTIONS ################################################# -############################################################################################################## - - - -############################################################ -##Function that aligned paired-end reads on a genome######## -############################################################ -## @param: # -## $index: referential genome # -## $fasq1: first paired end file # -## $fasq2: second paired end file # -## $sam: Alignment output file # -## $number_of_cpus: Number of Cpu used # -############################################################ - -sub align_genome -{ - my ($index, $fastq1, $fastq2, $sam, $number_of_cpus) = @_ ; - my @L_garbage =(); - my $sai1 = $sam."_temporary.sai1"; push @L_garbage,$sai1; - my $sai2 = $sam."_temporary.sai2"; push @L_garbage,$sai2; - `bwa aln -o4 -e1000 -t $number_of_cpus $index $fastq1 > $sai1 2> /dev/null`; - `bwa aln -o4 -e1000 -t $number_of_cpus $index $fastq2 > $sai2 2> /dev/null`; - ## -A force the insertion size - `bwa sampe -s -A -a $maxInsertSize $index $sai1 $sai2 $fastq1 $fastq2 2> /dev/null | samtools view -F4 -f 2 -Sh /dev/stdin > $sam`; - unlink @L_garbage; -} - - -############################################################ -##Function get_half get alignement on TE ### -############################################################ -## @param: # -## $sam: Name of alignement file # -## # -## @return: # -## $ASP_readsHashR: table to store sequences # -## $half_num_out: number of alignment saved # -############################################################ - -sub get_half -{ - ## store name of file - my $sam = shift; - open(my $fic, $sam) || die "cannot open sam file! $!\n"; ## Open file - my (%ASP_reads); my $cmp = 0; ## Declare variables for - my $sequence = ''; - - ##read file## - while(<$fic>) - { - chomp $_; - ##We don't consider lines of sam files that are in header## - next if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ); - ##We split line in several part## - my @line = split (/\t/,$_); - - ##Find if alignemets have min_L1 consecutives bases mapped on R1 ## - ##Corriger enlever la condition mis_L1 = 0 ## -# if ($mis_L1 != 0) -# { - if ($_ =~/NM:i:(\d+)\t.*MD:Z:(.*)/) - { - my $misT = $1; my $MD = $2; my $maxT = 0; - $MD = $1 if ($MD =~ /(.*)\t/); - $MD =~ s/\^//g; - my @tab = split /[ATCG]/,$MD; - my $tot = 0; - my $accept = 0; - if ($misT <= $mis_L1){$accept = 1;} - else - { - if ( $mis_L1 > scalar(@tab) ) { $maxT = scalar(@tab); } - else{ $maxT = $mis_L1; } - for (my $t = 0; $t < $maxT ; $t++) - { - $tot += $tab[$t] if $tab[$t] ne ''; - } - $accept = 1 if $tot >= $minL1; - } - ## if sequence is not accepted we go to the next sequence ## - next if $accept == 0; - } -# } - - ##looking for flag of the alignment and keep only good reads## - ##Find if it aligns on R1 or on R2## - - if ($line[1] == 73 || $line[1] == 89 || $line[1] == 117 || $line[1] == 69 || $line[1] == 133 || $line[1] == 181 || $line[1] == 153|| $line[1] == 137) - { - if ( $Bdir == 0 || ($Bdir == 1 && $line[1] & 64) || ($Bdir = 2 && $line[1] & 128)) - { - $cmp++; - $sequence = $line[9]; - ## if sequence is reversed aligned then reverse sequence ## - if ($line[1] & 16) - { - $sequence =reverse($sequence); - $sequence =~ tr/atgcuATGCU/tacgaTACGA/; - } - ## define table contains ## - $ASP_reads{$line[0]} = [undef,undef] unless exists( $ASP_reads{$line[0]} ); - - ##split if first mate (R1) is mapped on L1 or not (R2) ## - if ($line[1] & 8) - { - $ASP_reads{$line[0]}[0] = "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; - } - else - { - $ASP_reads{$line[0]}[1] = "\@".$line[0]."\n".$sequence."\n+\n".$line[10]."\n"; - } - } - } - } - close $fic; - return ( \%ASP_reads, $cmp); -} - -############################################################ -##Function sort_out: extract paired end reads ### -############################################################ -## @param: # -## $cpus: number of Cpu used # -## $out1: output file accepted 1 # -## $out2: output file accepted 2 # -## $readsHashTabR: reads to consider # -############################################################ - -sub sort_out -{ - my ($cpus, $out1, $out2, $readsHashTabR) = @_; - my ($name,$path) = fileparse($out2,'.fastq'); - my %repeat; - my @garbage = (); my $cmp = 0; - my $repout = $html_repertory.'/'.$name."_repout/"; - my $fa = $html_repertory.'/'.$name.".fa"; push (@garbage,$fa ); - my $second = $html_repertory.'/'.$name."_temporary.fastq"; push (@garbage,$second); - mkdir $repout; - my %notLine; - - ##Write on file containing of readssHashTabR - - open(my $tmp, ">".$second) || die "cannot open temp file $second\n"; - while ( my ($k,$v) = each %{$readsHashTabR} ) - { - print $tmp ${$v}[1] if defined(${$v}[1]); - } - close $tmp; - - ## Transform fastq file to fasta - - `fastq_to_fasta -i $second -o $fa -Q33`; - - ##Launch RepeatMasker on fasta file - - `RepeatMasker -s -pa $cpus -dir $repout -species human $fa`; - my $repfile = $repout.$name.".fa.out"; - open (my $rep, $repfile) || die "cannot open $repfile $!\n"; - while(<$rep>) - { - chomp; - ## test the percent of repeats ## - my $string = $_; - $string =~ s/^\s+//; - next unless ($string =~ /^\d/); - $string =~ s/\s+/ /g; - my @line = split (' ',$string); - if ( exists($repeat{$line[4]}) ) - { - $repeat{$line[4]}->[0] = $line[5] if $repeat{$line[4]}->[0] > $line[5]; - $repeat{$line[4]}->[1] = $line[6] if $repeat{$line[4]}->[1] < $line[6]; - } - else{ $repeat{$line[4]} = [$line[5],$line[6]];} - } - close $rep; - - ## store in table if pair passed the repeat test ## - while (my ($k, $v) = each %repeat) - { - $notLine{$k} = 1 unless ($v->[0] > $dprct || $v->[1] < $eprct); - } - - ##write resulting reads in both files for paired ## - open(my $accepted_1, ">".$out1 ) || die "cannot open $out1 file $!\n"; - open(my $accepted_2, ">".$out2 ) || die "cannot open $out2 file $!\n"; - while ( my ($k,$v) = each %{$readsHashTabR} ) - { - if ( defined (${$v}[0]) && defined (${$v}[1]) ) - { - unless (defined ($notLine{$k}) && $notLine{$k} == 1) - { - $cmp++; - print $accepted_1 ${$v}[0]; - print $accepted_2 ${$v}[1]; - } - } - } - close $accepted_1; close $accepted_2; - - ##drop files and directories generated by repeatmasker## - my $toErase = $repout.'*'; - unlink glob "$toErase"; - unlink @garbage; rmdir $repout; - return $cmp; -} - -############################################################ -##Function that aligned paired-end reads on a referential### -############################################################ -## @param: # -## $index: referential file # -## $fasq1: first file paired end reads # -## $fasq2: second file paired end reads # -## $sam: output alignment file # -## $number_of_cpus: number of CPU used # -## $mis: tolerated mismatches # -############################################################ -sub align_paired -{ - my ($index, $fastq1, $fastq2, $sam, $number_of_cpus, $mis) = @_ ; - my @garbage = (); - my $sai1 = $sam."_temporary.sai1"; push @garbage,$sai1; - my $sai2 = $sam."_temporary.sai2"; push @garbage,$sai2; - - ##alignement with bwa - - `bwa aln -n $mis -t $number_of_cpus $index $fastq1 > $sai1 2> /dev/null`; - `bwa aln -n $mis -t $number_of_cpus $index $fastq2 > $sai2 2> /dev/null`; - `bwa sampe $index $sai1 $sai2 $fastq1 $fastq2 > $sam 2> /dev/null`; - - ## delete temporary single aligned files - unlink @garbage; -} - -############################################################ -##Function that aligned reads on a referential ### -############################################################ -## @param: # -## $index: referential file # -## $fasq: reads file # -## $sam: output alignment file # -## $number_of_cpus: number of CPU used # -############################################################ - -sub align -{ - my ($index, $fastq, $sam, $number_of_cpus ) = @_ ; - `bwa aln -o4 -e$maxInsertSize -t $number_of_cpus $index $fastq 2> /dev/null | bwa samse $index /dev/stdin $fastq > $sam 2> /dev/null`; -} - -############################################################ -##Function results computes bed files for result ### -############################################################ -## @param: # -## $out_repository: repository to store results # -## $file: sam file resulting of alignement # -## $name: name of paireds end reads file # -## $hashRef: store number for each first read value # -## $ps: number of the paired end file # -############################################################ - -sub results -{ - my ($out_repertory, $file, $name, $hashRef,$ps) = @_; - my $namefirst = $out_repertory.'/'.$name.'-first.bed'; push(@garbage, $namefirst); - my $namesecond = $out_repertory.'/'.$name.'-second.bed'; push(@garbage, $namesecond); - - ##get database forrepeatmasker - `wget https://galaxy.gred-clermont.fr/clifinder/rmsk.bed -P $out_repository `; push(@garbage, $rmsk); - - ## store reads mapped in proper pair respectively first and second in pair in bam files and transform in bed files## - `samtools view -Sb -f66 $file 2> /dev/null | bedtools bamtobed -i /dev/stdin > temp_name_first 2> /dev/null`; - `samtools view -Sb -f130 $file 2> /dev/null | bedtools bamtobed -i /dev/stdin > temp_name_second 2> /dev/null`; - - ##compute converage of second mate on rmsk## - my $baseCov = 0; - my %IdCov = (); - my @coverage = `bedtools coverage -b temp_name_second -a $rmsk`; - - - ## store coverage fraction ## - foreach my $covRmsk (@coverage) - { - chomp $covRmsk; - my @split_cov = split /\t/, $covRmsk; - ##generate identifier for IdCov ## - $split_cov[3] =~ /(.*?)\/[12]/; - ##store value in IdCov ## - if (!exists($IdCov{$1})) - { - $IdCov{$1} = $split_cov[-1]; - } - else - { - IdCov{$1} = $split_cov[-1] if $split_cov[-1] > IdCov{$1}; - } - } - - ## get only first mate that have less tant $iprct repeats ## - open (my $tmp_fi, 'temp_name_first') || die "cannot open $namefirst!\n"; - open (my $nam_fi, ">".$namefirst) || die "cannot open $namefirst!\n"; - while (<$tmp_fi>) - { - my @line = split /\t/, $_; - $line[3] =~ /(.*?)\/[12]/; - - if ($IdCov{$1} <= $iprct/100) - { - print $nam_fi $_; - - ${$hashRef}{$1}= $ps; - } - } - close $tmp_fi; close $nam_fi; - - - ## get only second mate that have less than $iprct repeats ## - - open (my $tmp_sec, 'temp_name_second') || die "cannot open $namesecond!\n"; - open (my $nam_sec, ">".$namesecond) || die "cannot open $namesecond!\n"; - while (<$tmp_sec>) - { - my @line = split /\t/, $_; - $line[3] =~ /(.*?)\/[12]/; - if ($IdCov{$1} <= $iprct/100) - { - print $nam_sec $_; - } - } - close $tmp_sec; close $nam_sec; -} - -#sub results -#{ -# my ($out_repertory, $file, $name, $hashRef,$ps) = @_; -# my $namefirst = $out_repertory.'/'.$name.'-first.bed'; push(@garbage, $namefirst); -# my $namesecond = $out_repertory.'/'.$name.'-second.bed'; push(@garbage, $namesecond); -# `samtools view -Sb -f66 $file 2> /dev/null | bedtools bamtobed -i /dev/stdin > $namefirst 2> /dev/null`; -# `samtools view -Sb -f130 $file 2> /dev/null | bedtools bamtobed -i /dev/stdin > $namesecond 2> /dev/null`; -# open( my $in, $out_repertory.'/'.$name.'-first.bed') || die "cannot open first read bed\n"; -# while (<$in>) -# { -# my @line = split /\t/, $_; -# $line[3] =~ /(.*?)\/1/; -# ${$hashRef}{$1}= $ps; -# } -#} - - -############################################################ -##Function blast: blast nucleotide sequences on ref ### -############################################################ -## @param: # -## $db:database where to search # -## $fasta: file containing nucleotide sequences # -## $tabular: out file name # -## $cpu: Number of Cpu used # -############################################################ - - - -sub blast -{ - my ($db, $fasta, $tabular, $cpus) = @_; - `blastn -db $db -query $fasta -num_threads $cpus -out $tabular -outfmt 6 -evalue 10e-10`; -} - -############################################################ -##Function extract_blast: extract result from blast ### -############################################################ -## @param: # -## $file: Name of sequences file # -## @return: hash that contains sequences # -############################################################ - - -sub extract_blast -{ - my $file = shift; - my %hash = (); - open (my $f, $file) || die "cannot open $file\n"; - while (<$f>) - { - chomp $_; - my ($seq,$id) = split /\t/,$_; - $seq = $1 if ($seq =~ /(\d+)-(.*?)-(\d+)-(\d+)/); - $hash{$seq} = [] unless exists $hash{$seq}; - push @{$hash{$seq}}, $id; - } - close $f; - return \%hash; -} - -############################################################ -##Function print_header: header of html file ### -############################################################ -## @param: # -############################################################ - - - -sub print_header -{ - my $fileR = shift; my $title = shift; - print $fileR "<!DOCTYPE html> <html> <head> <title>$title</title>"; - print $fileR "<style type=\"text/css\"> - body { font-family:Arial, Helvetica, Sans-Serif; font-size:0.8em;} - #report { border-collapse:collapse;} - #report h4 { margin:0px; padding:0px;} - #report img { float:right;} - #report ul { margin:10px 0 10px 40px; padding:0px;} - #report th { background:#7CB8E2 url(header_bkg.png) repeat-x scroll center left; color:#fff; padding:7px 15px; text-align:left;} - #report td { background:#C7DDEE none repeat-x scroll center left; color:#000; padding:7px 15px; } - #report tr.odd td { background:#fff url(row_bkg.png) repeat-x scroll center left; cursor:pointer; } - #report div.arrow { background:transparent url(arrows.png) no-repeat scroll 0px -16px; width:16px; height:16px; display:block;} - #report div.up { background-position:0px 0px;} - </style>\n"; - print $fileR " <script src=\"./jquery.min.js\" type=\"text/javascript\"></script>\n"; - print $fileR "<script type=\"text/javascript\"> - \$(document).ready(function(){ - \$(\"#report tr:odd\").addClass(\"odd\"); - \$(\"#report tr:not(.odd)\").hide(); - \$(\"#report tr:first-child\").show(); - - \$(\"#report tr.odd\").click(function(){ - \$(this).next(\"tr\").toggle(); - \$(this).find(\".arrow\").toggleClass(\"up\"); - }); - //\$(\"#report\").jExpand(); -}); -</script>"; -print $fileR "</head> <body> <table id=\"report\" >\n"; -} - -############################################################ -##Function html_tab: definition of html file ### -############################################################ -## @param: # -## $html_repository: repository to store results # -## $rna: results for know RNA # -## $est: results for known EST # -############################################################ - -sub html_tab -{ - my ($rna,$est) = @_; - my $out = $html_repertory; - - `wget https://galaxy.gred-clermont.fr/clifinder/arrows.png -P $out && wget https://galaxy.gred-clermont.fr/clifinder/row_bkg.png -P $out && wget https://galaxy.gred-clermont.fr/clifinder/jquery.min.js -P $out`; - my $chimOut = $html; - - open(my $tab, ">".$chimOut) || die "cannot open $chimOut"; - print_header($tab,"Chimerae"); - print $tab "<tr> - <th>L1 chromosome</th> - <th>L1 start</th> - <th>L1 end</th> - <th>L1 strand</th>"; - for my $i (0..$#fastq1) - { - print $tab "\t<th>$name[$i] read #</th>\n"; - } - print $tab " - <th>Chimera chromosome</th> - <th>Chimera start</th> - <th>Chimera end</th> - <th>Chimera strand</th>"; - for my $i (0..$#fastq1) - { - print $tab " <th>$name[$i] read #</th>\n"; - } - print $tab "\t<th>Known RNA</th> - \t<th>Known EST</th>\n\t<th></th>\n</tr>"; - - for my $i (0..$#results) - { - print $tab "<tr>"; - foreach my $j (@{$results[$i]}) - { - print $tab " <td>$j</td>"; - } - my ($Hrna, $Hest) = ('',''); - $Hrna = ${$rna}{$i}[0] if exists(${$rna}{$i}); - $Hest = ${$est}{$i}[0] if exists(${$est}{$i}); - my $Lrna ='link break'; my $Lest = 'link break'; - chomp $Hrna; chomp $Hest; - $Lrna = $3 if $Hrna =~/gi\|(.*?)\|(.*?)\|(.*)\|$/; - $Lest = $3 if $Hest =~/gi\|(.*?)\|(.*?)\|(.*)\|$/; - print $tab "\t<td><A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/$Lrna\">$Hrna</A></td>\n"; - print $tab "\t<td><A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/$Lest\">$Hest</A></td>\n"; - print $tab "\t<td><div class=\"arrow\"></div></td>\n</tr>\n"; - my $img = 'link break'; - $img = $i.'.svg'; - my $colspan = scalar(@fastq1) * 2 + 8 ; - print $tab "<tr>\n\t<td valign=top colspan = $colspan><img src=\"$img\"/></td>\n\t<td valign=top>"; - if (exists(${$rna}{$i})) - { - for (my $w = 1; $w <= $#{${$rna}{$i}}; $w++) - { - $Hrna = ''; - $Hrna = ${$rna}{$i}[$w]; - $Lrna ='link break'; - chomp $Hrna; - $Lrna = $3 if $Hrna =~/gi\|(.*?)\|(.*?)\|(.*)\|$/; - print $tab "<A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/$Lrna\">$Hrna</A><br>\n"; - } - delete ${$rna}{$i}; - } - print $tab "</td>\n\t<td valign=top>"; - if (exists (${$est}{$i})) - { - for (my $w = 1; $w <= $#{${$est}{$i}}; $w++) - { - $Hest = ''; - $Hest = ${$est}{$i}[$w]; - chomp $Hest; - $Lest ='link break'; - $Lest = $3 if $Hest =~/gi\|(.*?)\|(.*?)\|(.*)\|$/; - print $tab "\t<A HREF=\"http://www.ncbi.nlm.nih.gov/nuccore/$Lest\">$Hest</A><br>\n"; - } - delete ${$est}{$i}; - } - print $tab "</td>\n\t<td></td>\n</tr>\n"; - } - print $tab qw{ - </table> - }; - print $tab "<a href=\"report.txt\">Report</a>"; - print $tab qw{ - </body> - </html> - }; - close $tab; -} - -############################################################ -##Function save_csv: save results in different formats ### -############################################################ -## @param: # -############################################################ -sub save_csv{ - - my $out = $html_repertory; - my $Line_only=$html_repertory.'/'.'Line_only_hg19.txt.gz'; push(@garbage, $Line_only); #Line Only H19 database - my $Hg19_refseq=$html_repertory.'/'.'hg19_refseq.bed'; push(@garbage, $Hg19_refseq);#h19 refseq bed file - my $out1= $html_repertory.'/results.txt'; - my $out2= $html_repertory.'/first_results.txt'; - my $out3 =$html_repertory.'/final_result_chimerae.txt'; - - #load databases needed - - `wget https://galaxy.gred-clermont.fr/clifinder/Line_only_hg19.txt.gz -P $out`; - `wget https://galaxy.gred-clermont.fr/clifinder/hg19_refseq.bed -P $out `; - - - # save result in csv file ## - - my $filed = $out1; - open(my $tab, ">".$filed) || die "cannot open $file"; - print $tab "L1 chromosome \t L1 start \t L1 end \t L1 strand";; - for my $i (0..$#fastq1) - { - print $tab "\t $name[$i] read #"; - } - print $tab "\t Chimera chromosome\t Chimera start \t Chimera end \t Chimera strand"; - for my $i (0..$#fastq1) - { - print $tab "\t $name[$i] read #"; - } - print $tab "\n"; - for my $i ( 0 .. $#results ) - { - my $rowref = $results[$i]; - my $n = @$rowref - 1; - for my $j ( 0 .. $n-1 ) - { - print $tab "$results[$i][$j]\t"; - } - print $tab "$results[$i][$n]\n"; - } - close $tab; - - ##Add some information via R Scripts## - - use Statistics::R; - # Create bridge between Perl and R - my $R = Statistics::R->new(); - $R->startR; - eval{ - $R->send( - qq ' - rm(list=ls()) - library(GenomicRanges) - library(plyr) - chim<-read.delim("$out1") - - chim<-chim[order(chim[,$#fastq1+7],decreasing=F),] - chim<-chim[order(chim[,2],decreasing=F),] - chr<-sub("chr","",as.character(chim[,1])) - chim<-chim[order(as.numeric(chr)),] - - grchim <- GRanges(seqnames = chim[,1], - IRanges(start = chim[,2], - end = chim[,3]),strand=chim[,4]) - - - grchim\$ID<-paste("Id_",1:length(chim[,1]),sep="") - - mcols(grchim)<-cbind(mcols(grchim),chim[,5:($#fastq1+9)]) - - - grfusR<- union(grchim,grchim) - - position<-as.data.frame(findOverlaps(grfusR,grchim)) - - grfusR\$dup<- table(position[,1]) - - position2<-as.data.frame(findOverlaps(grfusR[grfusR\$dup>1],grchim)) - - - grfusR2<-grfusR - strand(grfusR2)<- "+" - gr3<-union(grfusR2,grfusR2) - position3<- as.data.frame(findOverlaps(gr3,grfusR2)) - gr3\$dup<-table(position3[,1]) - - position3<-as.data.frame(findOverlaps(gr3[gr3\$dup>1],grfusR2)) - grfusR\$info<-"no" - grfusR\$info [position3[,2]]<-"overlap sens opposé" - - - - grfusR\$ID<-"Id" - grfusR\$ID[position[!duplicated(position[,1]),1]]<-grchim\$ID[position[!duplicated(position[,1]),2]] - - if(nrow(position2)!=0) - { - result <- aggregate(position2[,2] ~ position2[,1], data = position2, paste, collapse = "_") - grfusR\$ID[grfusR\$dup>1]<-paste("ID",result[,2],sep="_") - } - - mcols(grfusR)<-cbind(mcols(grfusR), mcols(grchim[position[!duplicated(position[,1]),2]])) - - - - min<-ddply(as.data.frame(grchim), .(seqnames,end,strand), function(x)x[x\$Chimera.start==min(x\$Chimera.start),]) - min<-ddply(as.data.frame(min), .(seqnames,start,strand), function(x)x[x\$Chimera.start==min(x\$Chimera.start),]) - max<-ddply(as.data.frame(grchim), .(seqnames,end,strand), function(x)x[x\$Chimera.end==max(x\$Chimera.end),]) - max<-ddply(as.data.frame(max), .(seqnames,start,strand), function(x)x[x\$Chimera.end==max(x\$Chimera.end),]) - - grfusR<-as.data.frame(grfusR) - grfusR<-grfusR[order(grfusR[,1],grfusR[,2],grfusR[,3],grfusR[,4],decreasing=F),] - - grfusR\$Chimera.start<- min\$Chimera.start - grfusR\$Chimera.end<-max\$Chimera.end - - - datax<-as.data.frame(grfusR) - colnames(datax)[1:3]<-colnames(chim)[1:3] - colnames(datax)[5]<-colnames(chim)[4] - - - grchim2 <- GRanges(seqnames = datax[,$#fastq1+12], - IRanges(start = datax[,$#fastq1+13], - end = datax[,$#fastq1+14]),strand=datax[,$#fastq1+15]) - mcols(grchim2)<-datax[,-c(4,$#fastq1+12:$#fastq1+15)] - - - - grfus<- union(grchim2,grchim2) - - position<-as.data.frame(findOverlaps(grfus,grchim2)) - - grfus\$dup<- table(position[,1]) - - position2<-as.data.frame(findOverlaps(grfus[grfus\$dup>1],grchim2)) - - grchim2[ position2[,2] ] - - - - - grfus\$ID_final<-"Id" - grfus\$ID_final[position[!duplicated(position[,1]),1]]<-grchim2\$ID[position[!duplicated(position[,1]),2]] - - if(nrow(position2)!=0) - { - result <- aggregate(position2[,2] ~ position2[,1], data = position2, paste, collapse = "_") - grfus\$ID_final[grfus\$dup>1]<-paste("Id",result[,2],sep="_") - } - - - - mcols(grfus)<-cbind(mcols(grfus), mcols(grchim2[position[!duplicated(position[,1]),2]])) - - for (i in 0:$#fastq1) - { - mcols(grfus)[grfus\$dup>1,12+i] <- mcols(grfus)[grfus\$dup>1,12+i] + mcols(grchim2)[position[duplicated(position[,1]),2],10+i] - } - - - grfus2<-grfus - strand(grfus2)<-"+" - gr3<-union(grfus2,grfus2) - - position3<- as.data.frame(findOverlaps(gr3,grfus2)) - gr3\$dup<-table(position3[,1]) - - position3<-as.data.frame(findOverlaps(gr3[gr3\$dup>1],grfus2)) - - grfus\$info [position3[,2]]<-"overlap sens opposé" - - min<-ddply(as.data.frame(grchim2), .(seqnames,end,strand), function(x)x[x\$L1.start==min(x\$L1.start),]) - min<-ddply(data.frame(min), .(seqnames,start,strand), function(x)x[x\$L1.start==min(x\$L1.start),]) - max<-ddply(as.data.frame(grchim2), .(seqnames,end,strand), function(x)x[x\$L1.end==max(x\$L1.end),]) - max<-ddply(data.frame(max), .(seqnames,start,strand), function(x)x[x\$L1.end==max(x\$L1.end),]) - - grfus1<-as.data.frame(grfus) - grfus1<-grfus1[order(grfus1[,1],grfus1[,2],grfus1[,3],grfus1[,4],decreasing=F),] - - grfus1\$L1.start<- min\$L1.start - grfus1\$L1.end<-max\$L1.end - - dataf<-as.data.frame(grfus1) - - result<-( data.frame("Chimera.Chr"= dataf\$L1.chromosome, "Chimera.Start"=apply(data.frame( dataf\$start,dataf\$end,dataf\$L1.start,dataf\$L1.end ),1,min) , "Chimera.End"= apply(data.frame( dataf\$start,dataf\$end,dataf\$L1.start,dataf\$L1.end ),1,max) ,"Chimera.Strand"=dataf\$L1.strand ,"L1.Chr"= dataf\$L1.chromosome, "L1.Start"=dataf\$L1.start ,"L1.End"= dataf\$L1.end , "L1.Strand"=dataf\$L1.strand , "Unique.Chr"= dataf\$seqnames, "Unique.Start"=dataf\$start , "Unique.End"= dataf\$end , "Unique.Strand"=dataf\$strand , "ID_final"=dataf\$ID_final,"info"=dataf\$info, dataf[,18:($#fastq1+18)] ) ) - - result<-result[order(result[,2],decreasing=F),] - chr<-sub("chr","",as.character(result[,1])) - result<-result[order(as.numeric(chr)),] - options(scipen=10) - write.table(result,"$out2",sep="\t",row.names = F,quote = F) - grchim <- GRanges(seqnames = result\$L1.Chr, - IRanges(start = result\$L1.Start, - end = result\$L1.End),strand=result\$L1.Strand) - mcols(grchim)<-result - - Rep<-read.delim("$Line_only",skip=1) - - Gene<-read.delim("$Hg19_refseq") - grLINE <- GRanges(seqnames = Rep\$genoName, - IRanges(start = Rep\$genoStart, - end = Rep\$genoEnd), - repStrand=as.character(Rep\$strand), - repName =as.character(Rep\$repName)) - - grGene <- GRanges(seqnames = Gene\$chrom, - IRanges(start = Gene\$txStart, - end = Gene\$txEnd), - geneStrand=as.character(Gene\$strand), - geneName = as.character(Gene\$name2)) - - position<-as.data.frame(findOverlaps(grchim,grLINE)) - - position2<-as.data.frame(findOverlaps(grchim,grGene)) - - table(grLINE\$repName[position[,2]]) - write.table(table(grLINE\$repName[position[,2]])) - - grchim\$GeneName<-"no_gene" - - grchim\$GeneName[position2[,1]]<- grGene\$geneName[position2[,2]] - - grchim\$GeneStrand<-"*" - - grchim\$GeneStrand[position2[,1]]<- grLINE\$geneStrand[position2[,2]] - - grchim\$repName<-"no" - - grchim\$repName[position[,1]]<- grLINE\$repName[position[,2]] - - grchim\$repStart<-0 - - grchim\$repStart[position[,1]]<-start(grLINE[position[,2]]) - - grchim\$repEnd<-0 - - grchim\$repEnd[position[,1]]<-end(grLINE[position[,2]]) - - grchim\$repWidth<-0 - - grchim\$repWidth[position[,1]]<-width(grLINE[position[,2]]) - - grchim\$repStrand<-"*" - - grchim\$repStrand[position[,1]]<- grLINE\$repStrand[position[,2]] - - dup<-position[duplicated(position[,1]),1] - if(length(dup != 0)) - { - for (i in 1:length(dup)) - { - - grchim\$repName[dup[i]] <-paste(grLINE\$repName[position[position[,1]==dup[i],2]],collapse="/") - grchim\$repStart[dup[i]] <-paste(start(grLINE[position[position[,1]==dup[i],2]]),collapse="/") - grchim\$repEnd[dup[i]] <-paste(end(grLINE[position[position[,1]==dup[i],2]]),collapse="/") - grchim\$repWidth[dup[i]] <-paste(width(grLINE[position[position[,1]==dup[i],2]]),collapse="/") - grchim\$repStrand[dup[i]] <-paste(grLINE\$repStrand[position[position[,1]==dup[i],2]],collapse="/") - - } - } - - final_result<-as.data.frame(grchim) - options(scipen=10) - write.table(final_result[,-c(1:5)],"$out3",sep="\t",row.names = F,quote = F) - ' - ); - }; - - $R->stop(); - unlink @garbage; - - - - -} - -
--- a/LINE_html_4_1.xml Wed Jan 31 09:59:07 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,111 +0,0 @@ -<tool name="chimericLineFinder4" id="LINE mosaic transcripts finder4" version="0.4.1"> - <description>Find chimerics transcripts containing LINEs sequences</description> - <command interpreter="perl"> - - LINE_html4.1.pl - - --first ${first} - --name ${first.name} - --second ${second} - - - #if $Genome.refGenomeSource == "history": - --ref "${Genome.ownFile}" - --build_index - #else: - --ref "${Genome.indices.fields.path}" - #end if - - #if $TE.refGenomeSource == "history": - --TE "${TE.ownFile}" - --build_TE - #else: - --TE "${TE.indices.fields.path}" - #end if - - - #for $input_file in $input_files: - --first ${input_file.first} - --name ${input_file.first.name} - --second ${input_file.second} - #end for - --html $chimerae - --html_path ${chimerae.files_path} - --size_insert $size_insert - --size_read $size - --pourcentage $prct - --image $image - --BDir $BDir - --minL1 $minL1 - --mis_L1 $mis_L1 - - - </command> - - <requirements> - <requirement type="package" version="3.1.0">R</requirement> - <requirement type="package" version="0.7.12">bwa</requirement> - <requirement type="package" version="2.17.0">bedTools</requirement> - </requirements> - - <inputs> - <param format="fastqsanger" name="first" type="data" label="first set of paired-end reads" help=""/> - <param format="fastqsanger" name="second" type="data" label="second set of paired-end reads" help=""/> - <repeat name="input_files" title="Additional Fastq Files"> - <param name="first" type="data" format="fastqsanger" label="FASTQ file" help="first set of paired-end reads" /> - <param name="second" type="data" format="fastqsanger" label="FASTQ file" help="second set of paired-end reads" /> - </repeat> - - <conditional name="Genome"> - <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a reference genome"> - <options from_data_table="bwa_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - - - <conditional name="TE"> - <param name="refGenomeSource" type="select" label="Will you select TE database from your history or use a built-in index?"> - <option value="indexed">Use a built-in index</option> - <option value="history">Use one from the history</option> - </param> - <when value="indexed"> - <param name="indices" type="select" label="Select a TE reference"> - <options from_data_table="bwa_indexes"> - <filter type="sort_by" column="2" /> - <validator type="no_options" message="No indexes are available" /> - </options> - </param> - </when> - <when value="history"> - <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference from history" /> - </when> - </conditional> - - <param name="BDir" type="select" > - <option value="0">Undirectional libraries</option> - <option value="1">TEs sequences in first read in pair</option> - <option value="2">TEs sequences in second read in pair</option> - </param> - - <param name="size" type="integer" value="100" label="reads size"/> - <param name="size_insert" type="integer" value="250" label="maximum insert size (bp)"/> - <param name ="minL1" type="integer" value="50" label="minimun bp mapping on selected TEs database"/> - <param name ="mis_L1" type="integer" value="2" label="number of mismatches tolerated in TEs mapping sequences"/> - <param name="prct" type="integer" value="33" label="minimum consecutive bp corresponding to a unique sequence"/> - </inputs> - <outputs> - <data format="html" name="chimerae" label="${tool.name}_on_${on_string}"/> - </outputs> -</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,69 @@ +.. image:: https://travis-ci.org/GReD-Clermont/CLIFinder.svg?branch=master + :target: https://travis-ci.org/GReD-Clermont/CLIFinder + +CLIFinder v0.5.0 +================ + + +Description +----------- + +L1 Chimeric Transcripts (LCTs) are transcribed from LINE 1 antisense promoter and include the L1 5’UTR sequence in antisense orientation followed by the adjacent genomic region. +CLIFinder v0.4.1 is a Galaxy tool, specifically designed to identify potential LCTs from one or several oriented RNA-seq paired-end reads in the human genome. +CLIFinder v0.4.1 is customizable to detect transcripts initiated by different types of repeat elements. + + + +Installation +------------ + +Some tools are used by CLIFinder that must be installed and added to the PATH (listed in CLIFinder.xml). This is easily done through conda with the command: +:: + + conda create -n clifinder samtools=1.9 bedtools=2.26.0gx repeatmasker=4.0.9_p2 bwa=0.7.17 fastx_toolkit=0.0.14 perl=5.26.2 perl-getopt-long=2.50 perl-file-copy-recursive=0.45 perl-parallel-forkmanager=2.02 perl-statistics-r=0.34 r-base=3.5.1 r-plyr=1.8.5 bioconductor-genomicranges=1.34.0 wget=1.20.1 + +You should then be able to use CLIFinder by activating the conda environment and running the script with: +:: + + conda activate clifinder + perl script/CLIFinder.pl + +Galaxy uses conda to solve tool requirements starting with Galaxy release 16.01 so that is the minimum version required to install this tool (which can be done through the toolshed: https://toolshed.g2.bx.psu.edu/repository?repository_id=5c73d1cf20ab37c3). + + + +Usage +----- + +The command you need to use to run the script is as follows: +:: + + CLIFinder.pl --first <first fastq of paired-end set 1> --name <name 1> --second <second fastq of paired-end set 1> [--first <first fastq of paired-end set 2> --name <name 2> --second <second fastq of paired-end set 2> ...] --ref <reference genome> [--build_ref] --TE <transposable elements> [--build_TE] --html <results.html> --html-path <results directory> [options] + + + Arguments: + --first <fastq file> First fastq file to process from paired-end set + --name <name> Name of the content to process + --second <fastq file> Second fastq file to process from paired-end set + --ref <reference> Fasta file containing the reference genome + --TE <TE> Fasta file containing the transposable elements + --rmsk <text file> Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC) + --refseq <text file> Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC) + --html Main HTML file where results will be displayed + --html-path Folder where results will be stored + + For any fasta file, if a bwa index is not provided, you should build it through the corresponding '--build_[element]' argument + + Options: + --rnadb <RNA db> Blast database containing RNA sequences (default: empty) + --estdb <EST db> Blast database containing EST sequences (default: empty) + --size_read <INT> Size of reads (default: 100) + --BDir <0|1|2> Orientation of reads (0: undirectional libraries, 1: TEs sequences in first read in pair, 2: TEs sequences in second read in pair) (default: 0) + --size_insert <INT> Maximum size of insert tolerated between R1 and R2 for alignment on the reference genome (default: 250) + --min_L1 <INT> Minimum number of bp matching for L1 mapping (default: 50) + --mis_L1 <INT> Maximum number of mismatches tolerated for L1 mapping (default: 2) + --min_unique <INT> Minimum number of consecutive bp not annotated by RepeatMasker (default: 33) + --threads <INT> Number of threads (default: 1) + + For Blast database files, if a fasta is provided, the database can be built with '--build_[db]'. Otherwise, provide a path or URL. "tar(.gz)" files are acceptable, as well as wild card (rna*) URLs. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/script/CLIFinder.pl Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,1100 @@ +#!/usr/bin/env perl + +################################################ +#Declaration of necessary libraries############# +################################################ + +use strict; +use warnings; +use Parallel::ForkManager; +use POSIX; +use Statistics::R; +use Getopt::Long qw(HelpMessage VersionMessage); +use File::Basename; +use File::Copy::Recursive; +use FindBin qw($Bin); +use Archive::Tar; + +our $VERSION = '0.5.0'; + + +##################################################################### +#Definition options of execution according to the previous variables# +##################################################################### + +GetOptions( + "first|1=s" => \my @fastq1, + "second|2=s" => \my @fastq2, + "name=s" => \my @name, + "html=s" => \my $html, + "html_path=s" => \my $html_repertory, + "TE=s" => \my $TE, + "ref=s" => \my $ref, + "rnadb:s" => \my $rna_source, + "estdb:s" => \my $est_source, + "build_TE" => \my $build_TE, + "build_ref" => \my $build_ref, + "build_rnadb" => \my $build_rnadb, + "build_estdb" => \my $build_estdb, + "rmsk=s" => \my $rmsk_source, + "refseq=s" => \my $refseq, + "min_unique:i" => \(my $prct = 33), + "size_insert:i" => \(my $maxInsertSize = 250), + "size_read:i" => \(my $size_reads = 100), + "BDir:i" => \(my $Bdir = 0), + "min_L1:i" => \(my $min_L1 = 50), + "mis_L1:i" => \(my $mis_L1 = 2), + "threads:i" => \(my $threads = 1), + 'help' => sub { HelpMessage(0); }, + 'version' => sub { VersionMessage(0); }, +) or HelpMessage(1); + +HelpMessage(1) unless @fastq1 && @fastq2 && @name && defined($TE) && defined($ref) && defined($rmsk_source) && defined($refseq) && defined($html) && defined($html_repertory); + +my $iprct = 100 - (($prct / $size_reads)*100) ; +my $mis_auth = $size_reads - $min_L1 + $mis_L1 ; +my $eprct = ($iprct * $size_reads) /100; +my $dprct = ((100-$iprct) * $size_reads) / 100; + +################################################ +#Construct index of ref and TE if doesn't exist# +################################################ + +`(bwa index $ref)` if ($build_ref); +`(bwa index $TE)` if ($build_TE); + +############################################ +#Create repository to store resulting files# +############################################ + +mkdir $html_repertory; + +########################################## +#Define hash # +########################################## + +my %frag_exp_id; + +########################## +#Data file we have to use# +########################## + +print STDOUT "Extracting data from rmsk file\n"; +my $line_only=$html_repertory.'/'.'line_only.txt'; +my $rmsk = $html_repertory.'/rmsk.bed'; +filter_convert_rmsk($rmsk_source, $rmsk, $line_only); + +############################## +# Analyse of each fastq file # +############################## + +my @garbage; my $num = 0; +foreach my $tabR (0..$#fastq1) +{ + ################################################### + # Paired end mapping against L1 promoter sequences# + ################################################### + + print STDOUT "Alignement of $name[$tabR] to L1\n"; + my $sam = $html_repertory.'/'.$name[$tabR]."_L1.sam"; push(@garbage, $sam); + align_paired( $TE, $fastq1[$tabR], $fastq2[$tabR], $sam, $threads, $mis_auth); + print STDOUT "Alignement done\n"; + + ################################################## + # Creation of two fastq for paired halfed mapped:# + # - _1 correspond to sequences mapped to L1 # + # - _2 correspond to sequences unmapped to L1 # + ################################################## + + print STDOUT "Getting pairs with one mate matched to L1 and the other mate undetected by repeatmasker as a repeat sequence\n"; + + my $out_ASP_1 = $html_repertory.'/'.$name[$tabR]."_1.fastq"; push(@garbage, $out_ASP_1); + my $out_ASP_2 = $html_repertory.'/'.$name[$tabR]."_2.fastq"; push(@garbage, $out_ASP_2); + + ##split mate that matched to L1 and others## + my ($ASP_readsHashR, $half_num_out) = get_half($sam, $mis_L1, $min_L1, $Bdir); + # $ASP_reads{$line[0]}[0] mapped - $ASP_reads{$line[0]}[1] unmapped + + ##pairs obtained after repeatmasker on the other mate## + my $left = sort_out($threads, $out_ASP_1, $out_ASP_2, $dprct, $eprct, $ASP_readsHashR, $html_repertory); + + print STDOUT "Number of half mapped pairs : $half_num_out\n"; + print STDOUT "Number of pairs after repeatmasker: $left\n"; + + ################################################## + # Alignment of halfed mapped pairs on genome # + ################################################## + print STDOUT "Alignment of potential chimeric sequences to the genome\n"; + $sam = $html_repertory.'/'.$name[$tabR]."_genome.sam"; + push(@garbage, $sam); + align_genome($ref, $out_ASP_1, $out_ASP_2, $sam, $maxInsertSize, $threads); + print STDOUT "Alignment done\n"; + + ##compute the number of sequences obtained after alignment ## + + $left = `samtools view -@ $threads -Shc $sam`; + chomp $left; $left = $left/2; + print STDOUT "Number of sequences: $left\n"; + + ################################################## + # Create bedfiles of potential chimerae # + # and Know repeat sequences removed # + ################################################## + + print STDOUT "Looking for chimerae\n"; + results($html_repertory, $sam, $name[$tabR], $iprct, \%frag_exp_id, $rmsk, $num, \@garbage); + $num++; +} + +##define files variables ## + +my $repfirst = $html_repertory.'/first.bed'; push(@garbage,$repfirst); +my $repsecond = $html_repertory.'/second.bed'; push(@garbage,$repsecond); +my $repMfirst = $html_repertory.'/firstM.bed'; push(@garbage,$repMfirst); +my $repMsecond = $html_repertory.'/secondM.bed'; push(@garbage,$repMsecond); +#my $covRepMsecond = $html_repertory.'/covSecondM.bed'; push(@garbage,$covRepMsecond); + +##Concate all files for first and second mate results ## + +`cat $html_repertory/*-first.bed > $repfirst`; #*/ +`cat $html_repertory/*-second.bed > $repsecond`; #*/ + +## Sort Files and generate files that merge reads in the same locus ## +print STDOUT "Sort files and merge reads in the same locus\n"; +`bedtools sort -i $repfirst | bedtools merge -c 4,5 -o collapse,max -d 100 -s > $repMfirst `; +`bedtools sort -i $repsecond | bedtools merge -c 4,5 -o collapse,max -d 100 -s > $repMsecond `; + +my (%frag_uni, @second_R, @second_exp, @results); +my $merge_target = $html_repertory.'/target_merged.bed'; push(@garbage, $merge_target); +my $merge = $html_repertory.'/merged.bed'; push(@garbage, $merge); + +open (my $mT, ">".$merge_target) || die "cannot open $merge_target\n"; +open (my $m, ">".$merge) || die "cannot open $merge\n"; +open (my $in, $repMsecond) || die "cannot open secondM\n"; +my $cmp = 0; +while (<$in>) +{ + chomp $_; + my @tmp = (0) x scalar(@fastq1); + my @line = split /\t/, $_; + my @names =split /,/, $line[4]; + foreach my $n (@names){$n =~/(.*?)\/[12]/; $frag_uni{$1} = $cmp; $tmp[$frag_exp_id{$1}]++; } + $second_exp[$cmp] = \@tmp; + $cmp++; + push @second_R, [$line[0],$line[1],$line[2],$line[3]]; +} + +$cmp = 0; +open ($in, $repMfirst) || die "cannot open firstM\n"; +while (<$in>) +{ + chomp $_; + my %sec; + my @line = split /\t/, $_; + my @names =split /,/, $line[4]; + my @tmp = (0) x scalar(@fastq1); + foreach my $n (@names){$n =~/(.*?)\/[12]/; $tmp[$frag_exp_id{$1}]++; } + foreach my $n (@names) + { + $n =~/(.*?)\/[12]/; + unless (exists ($sec{$frag_uni{$1}}) ) + { + my @lmp = ($line[0], $line[1], $line[2], $line[3]); + foreach my $exp_N (@tmp){ push @lmp, $exp_N;} + push (@lmp, $second_R[$frag_uni{$1}]->[0], $second_R[$frag_uni{$1}]->[1], $second_R[$frag_uni{$1}]->[2], $second_R[$frag_uni{$1}]->[3]); + foreach my $exp_N (@{$second_exp[$frag_uni{$1}]}){ push @lmp, $exp_N;} + + my $name = $cmp.'-'.$second_R[$frag_uni{$1}]->[0].'-'.$second_R[$frag_uni{$1}]->[1].'-'.$second_R[$frag_uni{$1}]->[2]; + print $mT $second_R[$frag_uni{$1}]->[0]."\t".$second_R[$frag_uni{$1}]->[1]."\t".$second_R[$frag_uni{$1}]->[2]."\t$name\t29\t".$second_R[$frag_uni{$1}]->[3]."\n"; + + my ($b, $e) = (0,0); + if ($line[1] < $second_R[$frag_uni{$1}]->[1]) + { + $b = $line[1] - 1000; $e = $second_R[$frag_uni{$1}]->[2] + 1000; + $name = $cmp.'-'.$line[0].'-'.$b.'-'.$e; + print $m $line[0]."\t".$b."\t".$e."\t$name\t29\t".$second_R[$frag_uni{$1}]->[3]."\n"; + } + else + { + $b = $second_R[$frag_uni{$1}]->[1] - 1000; $e = $line[2] + 1000; + $name = $cmp.'-'.$line[0].'-'.$b.'-'.$e; + print $m $line[0]."\t".$b."\t".$e."\t$name\t29\t".$second_R[$frag_uni{$1}]->[3]."\n"; + } + $results[$cmp] = \@lmp; + $cmp++; + } + $sec{$frag_uni{$1}} = undef; + } +} +close $mT; close $m; + +my $fasta = $html_repertory.'/target_merged.fasta'; push(@garbage, $fasta); +my $extend = $html_repertory.'/extend.fasta'; push(@garbage, $extend); + +`bedtools getfasta -name -fi $ref -bed $merge -fo $extend`; +`bedtools getfasta -name -fi $ref -bed $merge_target -fo $fasta`; + +################################################ +#Blast against human rna and est, if provided # +################################################ + +my $rna; +my $est; +if(defined($rna_source)) +{ + ##get databases for est and rna + print STDOUT "Getting blast databases for rna\n"; + my $rna_db = get_blastdb_from_source($rna_source, $build_rnadb, 'rna', $html_repertory); + + print STDOUT "Blast against human rna\n"; + my $tabular = $html_repertory."/chimerae_rna.tab"; push(@garbage, $tabular); + blast($rna_db, $fasta, $tabular, $threads); + $rna = extract_blast($tabular); + + # Clean RNA blast database if in html dir + if(rindex($rna_db, $html_repertory, 0) == 0) + { + my $toErase = $rna_db.'.*'; + unlink glob "$toErase"; + } +} +if(defined($est_source)) +{ + print STDOUT "Getting blast databases for est\n"; + my $est_db = get_blastdb_from_source($est_source, $build_estdb, 'est', $html_repertory); + + print STDOUT "Blast against human est\n"; + my $tabular2 = $html_repertory."/chimerae_est.tab"; push(@garbage, $tabular2); + blast($est_db, $fasta, $tabular2, $threads); + $est = extract_blast($tabular2); + + # Clean EST blast database if in html dir + if(rindex($est_db, $html_repertory, 0) == 0) + { + my $toErase = $est_db.'.*'; + unlink glob "$toErase"; + } +} + +################################################ +#Create Results html file # +################################################ +print STDOUT "Save results in file\n"; +save_csv(\@fastq1, \@name, \@results, $line_only, $refseq, $html_repertory); + +print STDOUT "Create HTML\n"; +html_tab(\@fastq1, \@name, \@results, $rna, $est, $html, $html_repertory); + +$extend = $extend.'*'; +push(@garbage, glob($extend)); +push(@garbage, $line_only); +push(@garbage, $rmsk); +unlink @garbage; + +print STDOUT "Job done!\n"; + +########################################### END MAIN ########################################################## + + +############################################################################################################## +############################################ FUNCTIONS ################################################# +############################################################################################################## + + +############################################################ +## Function to convert rmsk table to bed and line_only ##### +############################################################ +## @param: # +## $source: rmsk table file # +## $bed: rmsk bed file # +## $line_only: rmsk table file with only LINE # +############################################################ + +sub filter_convert_rmsk +{ + my ($source, $bed, $line_only) = @_; + open(my $input, $source) || die "cannot open rmsk file! $!\n"; ## Open source file + open(my $bedfile, ">".$bed) || die "cannot open output bed file for rmsk! $!\n"; ## Open bed file + open(my $linefile, ">".$line_only) || die "cannot open output LINE-only file for rmsk! $!\n"; ## Open line_only file + my @headers; + my %indices; + + print $linefile "#filter: rmsk.repClass = 'LINE'\n"; + + while(<$input>) + { + chomp $_; + if($. == 1) + { + if(substr($_, 0, 1) ne "#") + { + die "rmsk file does not have header starting with #\n"; + } + else + { + print $linefile "$_\n"; + my $firstline = substr($_, 1); + @headers = split(/\t/, $firstline); + @indices{@headers} = 0..$#headers; + } + } + else + { + my @line = split(/\t/,$_); + if($line[$indices{"repClass"}] eq "LINE") + { + print $linefile "$_\n"; + } + print $bedfile "$line[$indices{'genoName'}]\t$line[$indices{'genoStart'}]\t$line[$indices{'genoEnd'}]\t$line[$indices{'repName'}]\t$line[$indices{'swScore'}]\t$line[$indices{'strand'}]\n"; + } + } + close $input; + close $bedfile; + close $linefile; +} + + +############################################################ +## Function to get blast db from the specified source ###### +############################################################ +## @param: # +## $source: db source (URL or path) # +## $build_db: whether the db should be created # +## $name: name of the db that could be created # +## $dest_dir: where the data can be placed # +## @return: # +## $path: blast db path # +############################################################ + +sub get_blastdb_from_source +{ + my ($source, $build_db, $name, $dest_dir) = @_; + # Assume source is just db path + my $path = $source; + my ($file) = $path =~ m~([^/\\]*)$~; + my $dbname = $file; + my @garbage; + + if($build_db) + { + $dbname = $name; + $path = $dest_dir.'/'.$name; + print STDOUT "Making $dbname blast database\n"; + `makeblastdb -in $source -dbtype nucl -out $path`; + } + else + { + # Check if source is URL + if(index($source, ":/") != -1) + { + my $url = $source; + if($file =~ /\*/) + { + $url =~ s/\Q$file//; + print STDOUT "Downloading blast database from $url\n"; + `wget -q -N -r -nH -nd -np --accept=$file $url -P $dest_dir`; + + # Assume regexp matches db name + $dbname =~ s/\*$//; + } + else + { + print STDOUT "Downloading blast database from $url\n"; + `wget -q -N $source -P $dest_dir`; + push(@garbage, $dest_dir.'/'.$file); + } + if($? == 0) + { + print "Downloaded database\n"; + } + else + { + print "Error while downloading database\n"; + } + $path = $dest_dir.'/'.$dbname; + } + if(index($file, ".") != -1) + { + if(index($file, ".tar") != -1) + { + ## Extract tar files + print STDOUT "Extracting blast database from $file\n"; + my @properties = ('name'); + my $tar=Archive::Tar->new(); + $tar->setcwd($dest_dir); + $tar->read($path); + my @files = $tar->list_files(\@properties); + $tar->extract(); + $tar->clear(); + unlink @garbage; + + ## Get dbname from filenames + my @parts = split(/\./, $files[0]); + $dbname = $parts[0]; + $path = $dest_dir.'/'.$dbname; + print STDOUT "Extracted database\n"; + } + else + { + print STDOUT "Unexpected file format for database" + } + } + } + print "Using $dbname database\n"; + return $path; +} + +############################################################ +##Function that aligned paired-end reads on a genome######## +############################################################ +## @param: # +## $index: referential genome # +## $fasq1: first paired end file # +## $fasq2: second paired end file # +## $sam: alignment output file # +## $maxInsertSize: maximum size of insert # +## $threads: number of threads used # +############################################################ + +sub align_genome +{ + my ($index, $fastq1, $fastq2, $sam, $maxInsertSize, $threads) = @_ ; + my @L_garbage =(); + my $sai1 = $sam."_temporary.sai1"; push @L_garbage,$sai1; + my $sai2 = $sam."_temporary.sai2"; push @L_garbage,$sai2; + `bwa aln -o4 -e1000 -t $threads $index $fastq1 > $sai1`; + `bwa aln -o4 -e1000 -t $threads $index $fastq2 > $sai2`; + ## -A force the insertion size + `bwa sampe -s -A -a $maxInsertSize $index $sai1 $sai2 $fastq1 $fastq2 | samtools view -@ $threads -F4 -f 2 -Sh /dev/stdin -o $sam`; + unlink @L_garbage; +} + + +############################################################ +##Function get_half get alignement on TE ### +############################################################ +## @param: # +## $sam: name of alignement file # +## $mis_L1: maximum number of mismatches # +## $min_L1: minimum number of bp matching # +## $Bdir: reads orientation # +## # +## @return: # +## $ASP_readsHashR: table to store sequences # +## $half_num_out: number of alignment saved # +############################################################ + +sub get_half +{ + ## store name of file + my $sam = shift; + my $mis_L1 = shift; + my $min_L1 = shift; + my $Bdir = shift; + open(my $fic, $sam) || die "cannot open sam file! $!\n"; ## Open file + my (%ASP_reads); my $cmp = 0; ## Declare variables for + my $sequence = ''; + my $score = ''; + + ##read file## + while(<$fic>) + { + chomp $_; + ##We don't consider lines of sam files that are in header## + next if ($_ =~ /^\@[A-Za-z][A-Za-z](\t[A-Za-z][A-Za-z0-9]:[ -~]+)+$/ || $_ =~ /^\@CO\t.*/ ); + ##We split line in several part## + my @line = split (/\t/,$_); + + ##Find if alignemets have min_L1 consecutives bases mapped on R1 ## + if ($_ =~/NM:i:(\d+)\t.*MD:Z:(.*)/) + { + my $misT = $1; my $MD = $2; my $maxT = 0; + $MD = $1 if ($MD =~ /(.*)\t/); + $MD =~ s/\^//g; + my @tab = split /[ATCG]/,$MD; + my $tot = 0; + my $accept = 0; + if ($misT <= $mis_L1){$accept = 1;} + else + { + if ( $mis_L1 > scalar(@tab) ) { $maxT = scalar(@tab); } + else{ $maxT = $mis_L1; } + for (my $t = 0; $t < $maxT ; $t++) + { + $tot += $tab[$t] if $tab[$t] ne ''; + } + $accept = 1 if $tot >= $min_L1; + } + ## if sequence is not accepted we go to the next sequence ## + next if $accept == 0; + } + + ##looking for flag of the alignment and keep only good reads## + ##Find if it aligns on R1 or on R2## + + if ($line[1] == 73 || $line[1] == 89 || $line[1] == 117 || $line[1] == 69 || $line[1] == 133 || $line[1] == 181 || $line[1] == 153|| $line[1] == 137) + { + if ( $Bdir == 0 + || ($Bdir == 1 && (($line[1] & 064 && $line[1] & 8) || ($line[1] & 128 && $line[1] & 4))) + || ($Bdir == 2 && (($line[1] & 128 && $line[1] & 8) || ($line[1] & 064 && $line[1] & 4))) ) + { + $cmp++; + $sequence = $line[9]; + $score = $line[10]; + ## if sequence is reversed aligned then reverse complement sequence and reverse score ## + if ($line[1] & 16) + { + $sequence = reverse($sequence); + $score = reverse($score); + $sequence =~ tr/atgcuATGCU/tacgaTACGA/; + } + ## define table contains ## + $ASP_reads{$line[0]} = [undef,undef] unless exists( $ASP_reads{$line[0]} ); + + ##split if first mate (R1) is mapped on L1 or not (R2) ## + if ($line[1] & 8) + { + $ASP_reads{$line[0]}[0] = "\@".$line[0]."\n".$sequence."\n+\n".$score."\n"; + } + else + { + $ASP_reads{$line[0]}[1] = "\@".$line[0]."\n".$sequence."\n+\n".$score."\n"; + } + } + } + } + close $fic; + return ( \%ASP_reads, $cmp); +} + +############################################################ +##Function sort_out: extract paired end reads ### +############################################################ +## @param: # +## $threads: number of threads used # +## $out1: output file accepted 1 # +## $out2: output file accepted 2 # +## $dprct: number of bp not annotated by RepeatMasker# +## $eprct: number of repeated bases tolerated # +## $readsHashTabR: reads to consider # +## $html_repertory: folder for html files # +############################################################ + +sub sort_out +{ + my ($threads, $out1, $out2, $dprct, $eprct, $readsHashTabR, $html_repertory) = @_; + my ($name,$path) = fileparse($out2,'.fastq'); + my %repeat; + my @garbage = (); my $cmp = 0; + my $repout = $html_repertory.'/'.$name."_repout/"; + my $fa = $html_repertory.'/'.$name.".fa"; push (@garbage,$fa ); + my $second = $html_repertory.'/'.$name."_temporary.fastq"; push (@garbage,$second); + mkdir $repout; + my %notLine; + + ##Write on file containing of readssHashTabR + + open(my $tmp, ">".$second) || die "cannot open temp file $second\n"; + while ( my ($k,$v) = each %{$readsHashTabR} ) + { + print $tmp ${$v}[1] if defined(${$v}[1]); + } + close $tmp; + + ## Transform fastq file to fasta + + `fastq_to_fasta -i $second -o $fa -Q33`; + + ##Launch RepeatMasker on fasta file + + `RepeatMasker -s -pa $threads -dir $repout -engine hmmer -species human $fa`; + my $repfile = $repout.$name.".fa.out"; + open (my $rep, $repfile) || die "cannot open $repfile $!\n"; + while(<$rep>) + { + chomp; + ## test the percent of repeats ## + my $string = $_; + $string =~ s/^\s+//; + next unless ($string =~ /^\d/); + $string =~ s/\s+/ /g; + my @line = split (' ',$string); + if ( exists($repeat{$line[4]}) ) + { + $repeat{$line[4]}->[0] = $line[5] if $repeat{$line[4]}->[0] > $line[5]; + $repeat{$line[4]}->[1] = $line[6] if $repeat{$line[4]}->[1] < $line[6]; + } + else{ $repeat{$line[4]} = [$line[5],$line[6]];} + } + close $rep; + + ## store in table if pair passed the repeat test ## + while (my ($k, $v) = each %repeat) + { + $notLine{$k} = 1 unless ($v->[0] > $dprct || $v->[1] < $eprct); + } + + ##write resulting reads in both files for paired ## + open(my $accepted_1, ">".$out1 ) || die "cannot open $out1 file $!\n"; + open(my $accepted_2, ">".$out2 ) || die "cannot open $out2 file $!\n"; + while ( my ($k,$v) = each %{$readsHashTabR} ) + { + if ( defined (${$v}[0]) && defined (${$v}[1]) ) + { + unless (defined ($notLine{$k}) && $notLine{$k} == 1) + { + $cmp++; + print $accepted_1 ${$v}[0]; + print $accepted_2 ${$v}[1]; + } + } + } + close $accepted_1; close $accepted_2; + + ##drop files and directories generated by repeatmasker## + my $toErase = $repout.'*'; + unlink glob "$toErase"; + unlink @garbage; rmdir $repout; + return $cmp; +} + +############################################################ +##Function that aligned paired-end reads on a referential### +############################################################ +## @param: # +## $index: referential file # +## $fasq1: first file paired end reads # +## $fasq2: second file paired end reads # +## $sam: output alignment file # +## $threads: number of threads used # +## $mis: tolerated mismatches # +############################################################ +sub align_paired +{ + my ($index, $fastq1, $fastq2, $sam, $threads, $mis) = @_ ; + my @garbage = (); + my $sai1 = $sam."_temporary.sai1"; push @garbage,$sai1; + my $sai2 = $sam."_temporary.sai2"; push @garbage,$sai2; + + ##alignement with bwa + + `bwa aln -n $mis -t $threads $index $fastq1 > $sai1`; + `bwa aln -n $mis -t $threads $index $fastq2 > $sai2`; + `bwa sampe $index $sai1 $sai2 $fastq1 $fastq2 > $sam`; + + ## delete temporary single aligned files + unlink @garbage; +} + +############################################################ +##Function that aligned reads on a referential ### +############################################################ +## @param: # +## $index: referential file # +## $fasq: reads file # +## $sam: output alignment file # +## $maxInsertSize: maximum size of insert # +## $threads: number of threads used # +############################################################ + +sub align +{ + my ($index, $fastq, $sam, $maxInsertSize, $threads ) = @_ ; + `bwa aln -o4 -e$maxInsertSize -t $threads $index $fastq | bwa samse $index /dev/stdin $fastq > $sam `; +} + +############################################################ +##Function results computes bed files for result ### +############################################################ +## @param: # +## $out_repository: repository to store results # +## $file: sam file resulting of alignement # +## $name: name of paireds end reads file # +## $iprct: percentage of repeats tolerated # +## $hashRef: store number for each first read value # +## $rmsk: UCSC repeat sequences # +## $ps: number of the paired end file # +## $garbage_ref: reference to garbage array # +############################################################ + +sub results +{ + my ($out_repertory, $file, $name, $iprct, $hashRef, $rmsk, $ps, $garbage_ref) = @_; + my $namefirst = $out_repertory.'/'.$name.'-first.bed'; push(@$garbage_ref, $namefirst); + my $namesecond = $out_repertory.'/'.$name.'-second.bed'; push(@$garbage_ref, $namesecond); + + ## store reads mapped in proper pair respectively first and second in pair in bam files and transform in bed files## + `samtools view -Sb -f66 $file | bedtools bamtobed -i /dev/stdin > temp_name_first`; + `samtools view -Sb -f130 $file | bedtools bamtobed -i /dev/stdin > temp_name_second`; + + ##compute converage of second mate on rmsk## + my $baseCov = 0; + my %IdCov = (); + my @coverage = `bedtools coverage -a temp_name_second -b $rmsk`; + + + ## store coverage fraction ## + foreach my $covRmsk (@coverage) + { + chomp $covRmsk; + my @split_cov = split /\t/, $covRmsk; + ##generate identifier for IdCov ## + $split_cov[3] =~ /(.*?)\/[12]/; + ##store value in IdCov ## + if (!exists($IdCov{$1})) + { + $IdCov{$1} = $split_cov[-1]; + } + else + { + $IdCov{$1} = $split_cov[-1] if $split_cov[-1] > $IdCov{$1}; + } + } + + ## get only first mate that have less tant $iprct repeats ## + open (my $tmp_fi, 'temp_name_first') || die "cannot open $namefirst!\n"; + open (my $nam_fi, ">".$namefirst) || die "cannot open $namefirst!\n"; + while (<$tmp_fi>) + { + my @line = split /\t/, $_; + $line[3] =~ /(.*?)\/[12]/; + + if ($IdCov{$1} <= $iprct/100) + { + print $nam_fi $_; + + ${$hashRef}{$1}= $ps; + } + } + close $tmp_fi; close $nam_fi; + + + ## get only second mate that have less than $iprct repeats ## + + open (my $tmp_sec, 'temp_name_second') || die "cannot open $namesecond!\n"; + open (my $nam_sec, ">".$namesecond) || die "cannot open $namesecond!\n"; + while (<$tmp_sec>) + { + my @line = split /\t/, $_; + $line[3] =~ /(.*?)\/[12]/; + if ($IdCov{$1} <= $iprct/100) + { + print $nam_sec $_; + } + } + close $tmp_sec; close $nam_sec; +} + +#sub results +#{ +# my ($out_repertory, $file, $name, $hashRef,$ps) = @_; +# my $namefirst = $out_repertory.'/'.$name.'-first.bed'; push(@garbage, $namefirst); +# my $namesecond = $out_repertory.'/'.$name.'-second.bed'; push(@garbage, $namesecond); +# `samtools view -Sb -f66 $file | bedtools bamtobed -i /dev/stdin > $namefirst`; +# `samtools view -Sb -f130 $file | bedtools bamtobed -i /dev/stdin > $namesecond`; +# open( my $in, $out_repertory.'/'.$name.'-first.bed') || die "cannot open first read bed\n"; +# while (<$in>) +# { +# my @line = split /\t/, $_; +# $line[3] =~ /(.*?)\/1/; +# ${$hashRef}{$1}= $ps; +# } +#} + + +############################################################ +##Function blast: blast nucleotide sequences on ref ### +############################################################ +## @param: # +## $db: database where to search # +## $fasta: file containing nucleotide sequences # +## $tabular: out file name # +## $threads: number of threads used # +############################################################ + + + +sub blast +{ + my ($db, $fasta, $tabular, $threads) = @_; + `blastn -db $db -query $fasta -num_threads $threads -out $tabular -outfmt 6 -evalue 10e-10`; +} + +############################################################ +##Function extract_blast: extract result from blast ### +############################################################ +## @param: # +## $file: name of sequences file # +## @return: hash that contains sequences # +############################################################ + + +sub extract_blast +{ + my $file = shift; + my %hash = (); + open (my $f, $file) || die "cannot open $file\n"; + while (<$f>) + { + chomp $_; + my ($seq,$id) = split /\t/,$_; + $seq = $1 if ($seq =~ /(\d+)-(.*?)-(\d+)-(\d+)/); + $hash{$seq} = [] unless exists $hash{$seq}; + push @{$hash{$seq}}, $id; + } + close $f; + return \%hash; +} + +############################################################ +##Function print_header: header of html file ### +############################################################ +## @param: # +############################################################ + +sub print_header +{ + my $fileR = shift; my $title = shift; + print $fileR "<!DOCTYPE html>\n<html>\n<head>\n\t<title>$title</title>\n"; + print $fileR "\t<style type=\"text/css\">\n"; + print $fileR "\t\tbody { font-family:Arial, Helvetica, Sans-Serif; font-size:0.8em;}\n"; + print $fileR "\t\t#report { border-collapse:collapse;}\n"; + print $fileR "\t\t#report h4 { margin:0px; padding:0px;}\n"; + print $fileR "\t\t#report img { float:right;}\n"; + print $fileR "\t\t#report ul { margin:10px 0 10px 40px; padding:0px;}\n"; + print $fileR "\t\t#report th { background:#7CB8E2 url(static/images/header_bkg.png) repeat-x scroll center left; color:#fff; padding:7px 15px; text-align:left;}\n"; + print $fileR "\t\t#report td { background:#C7DDEE none repeat-x scroll center left; color:#000; padding:7px 15px; }\n"; + print $fileR "\t\t#report tr.odd td { background:#fff url(static/images/row_bkg.png) repeat-x scroll center left; cursor:pointer; }\n"; + print $fileR "\t\t#report div.arrow { background:transparent url(static/images/arrows.png) no-repeat scroll 0px -16px; width:16px; height:16px; display:block;}\n"; + print $fileR "\t\t#report div.up { background-position:0px 0px;}\n"; + print $fileR "\t</style>\n"; + print $fileR "\t<script src=\"./js/jquery.min.js\" type=\"text/javascript\"></script>\n"; + print $fileR "\t<script type=\"text/javascript\">\n"; + print $fileR "\t\t\$(document).ready(function(){\n"; + print $fileR "\t\t\t\$(\"#report tr:odd\").addClass(\"odd\");\n"; + print $fileR "\t\t\t\$(\"#report tr:not(.odd)\").hide();\n"; + print $fileR "\t\t\t\$(\"#report tr:first-child\").show();\n"; + print $fileR "\t\t\t\$(\"#report tr.odd\").click(function(){\n"; + print $fileR "\t\t\t\t\$(this).next(\"tr\").toggle();\n"; + print $fileR "\t\t\t\t\$(this).find(\".arrow\").toggleClass(\"up\");\n"; + print $fileR "\t\t\t});\n"; + print $fileR "\t\t\t//\$(\"#report\").jExpand();\n"; + print $fileR "\t\t});\n\t</script>\n"; + print $fileR "</head>\n<body>\n\t<table id=\"report\">\n"; +} + +############################################################ +##Function html_tab: definition of html file ### +############################################################ +## @param: # +## $fastq1_ref: reference to first paired end files # +## $name_ref: reference to names of reads files # +## $results_ref: reference to results files # +## $rna: results for known RNA # +## $est: results for known EST # +## $html: html results file # +## $html_repertory: repository to store results # +############################################################ + +sub html_tab +{ + my ($fastq1_ref, $name_ref, $results_ref, $rna, $est, $html, $html_repertory) = @_; + my $out = $html_repertory; + my @fastq1 = @{$fastq1_ref}; + my @name = @{$name_ref}; + my @results = @{$results_ref}; + + # Copy HTML resources to results folder + File::Copy::Recursive::dircopy "$Bin/js/", "$out/js" or die "Copy failed: $!"; + File::Copy::Recursive::dircopy "$Bin/static/", "$out/static" or die "Copy failed: $!"; + + my $chimOut = $html; + + open(my $tab, ">".$chimOut) || die "cannot open $chimOut"; + print_header($tab,"Chimerae"); + print $tab "\t\t<tr>\n\t\t\t<th>L1 chromosome</th>\n\t\t\t<th>L1 start</th>\n\t\t\t<th>L1 end</th>\n\t\t\t<th>L1 strand</th>\n"; + for my $i (0..$#fastq1) + { + print $tab "\t\t\t<th>$name[$i] read #</th>\n"; + } + print $tab "\t\t\t<th>Chimera chromosome</th>\n\t\t\t<th>Chimera start</th>\n\t\t\t<th>Chimera end</th>\n\t\t\t<th>Chimera strand</th>\n"; + for my $i (0..$#fastq1) + { + print $tab "\t\t\t<th>$name[$i] read #</th>\n"; + } + if(defined($rna)) + { + print $tab "\t\t\t<th>Known RNA</th>\n"; + } + else + { + print $tab "\t\t\t<th></th>\n"; + } + if(defined($est)) + { + print $tab "\t\t\t<th>Known EST</th>\n"; + } + else + { + print $tab "\t\t\t<th></th>\n"; + } + print $tab "\t\t\t<th></th>\n\t\t</tr>\n"; + + for my $i (0..$#results) + { + print $tab "\t\t<tr>\n"; + foreach my $j (@{$results[$i]}) + { + print $tab "\t\t\t<td>$j</td>\n"; + } + my ($Hrna, $Hest) = ('',''); + $Hrna = ${$rna}{$i}[0] if exists(${$rna}{$i}); + $Hest = ${$est}{$i}[0] if exists(${$est}{$i}); + chomp $Hrna; chomp $Hest; + if($Hrna) + { + print $tab "\t\t\t<td><a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/nuccore/$Hrna\">$Hrna</a></td>\n"; + } + else + { + print $tab "\t\t\t<td></td>\n"; + } + if($Hest) + { + print $tab "\t\t\t<td><a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/nuccore/$Hest\">$Hest</a></td>\n"; + } + else + { + print $tab "\t\t\t<td></td>\n"; + } + print $tab "\t\t\t<td><div class=\"arrow\"></div></td>\n\t\t</tr>\n"; + my $colspan = scalar(@fastq1) * 2 + 8 ; + print $tab "\t\t<tr>\n\t\t\t<td valign=top colspan=$colspan></td>\n\t\t\t<td valign=top>\n"; + if (exists(${$rna}{$i})) + { + for (my $w = 1; $w <= $#{${$rna}{$i}}; $w++) + { + $Hrna = ''; + $Hrna = ${$rna}{$i}[$w]; + chomp $Hrna; + print $tab "\t\t\t\t<a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/nuccore/$Hrna\">$Hrna</a><br>\n"; + } + delete ${$rna}{$i}; + } + print $tab "\t\t\t</td>\n\t\t\t<td valign=top>\n"; + if (exists (${$est}{$i})) + { + for (my $w = 1; $w <= $#{${$est}{$i}}; $w++) + { + $Hest = ''; + $Hest = ${$est}{$i}[$w]; + chomp $Hest; + print $tab "\t\t\t\t<a target=\"_blank\" rel=\"noopener noreferrer\" href=\"https://www.ncbi.nlm.nih.gov/nuccore/$Hest\">$Hest</a><br>\n"; + } + delete ${$est}{$i}; + } + print $tab "\t\t\t</td>\n\t\t\t<td></td>\n\t\t</tr>\n"; + } + print $tab "\t</table>\n</body>\n</html>\n"; + close $tab; +} + +############################################################ +##Function save_csv: save results in different formats ### +############################################################ +## @param: # +## $fastq1_ref: reference to first paired end files # +## $name_ref: reference to names of reads files # +## $results_ref: reference to results files # +## $line_only: Line only database # +## $refseq: refseq text file # +## $out: repository to store results # +############################################################ +sub save_csv{ + my ($fastq1_ref, $name_ref, $results_ref, $line_only, $refseq, $out) = @_; + my @fastq1 = @{$fastq1_ref}; + my @name = @{$name_ref}; + my @results = @{$results_ref}; + my $out1= $out.'/results.txt'; + my $out2= $out.'/first_results.txt'; + my $out3= $out.'/final_result_chimerae.txt'; + + # save result in csv file ## + + my $filed = $out1; + open(my $tab, ">".$filed) || die "cannot open $filed"; + print $tab "L1 chromosome \t L1 start \t L1 end \t L1 strand";; + for my $i (0..$#fastq1) + { + print $tab "\t $name[$i] read #"; + } + print $tab "\t Chimera chromosome\t Chimera start \t Chimera end \t Chimera strand"; + for my $i (0..$#fastq1) + { + print $tab "\t $name[$i] read #"; + } + print $tab "\n"; + for my $i ( 0 .. $#results ) + { + my $rowref = $results[$i]; + my $n = @$rowref - 1; + for my $j ( 0 .. $n-1 ) + { + print $tab "$results[$i][$j]\t"; + } + print $tab "$results[$i][$n]\n"; + } + close $tab; + + ##Add some information via R Scripts## + + # Create bridge between Perl and R + my $R = Statistics::R->new(); + $R->start(); + $R->set('out1', $out1); + $R->set('out2', $out2); + $R->set('out3', $out3); + $R->set('nfastq', $#fastq1); + $R->set('line_only', $line_only); + $R->set('refseq', $refseq); + my $R_out = $R->run_from_file("$Bin/CLIFinder_results.R"); + $R->stop(); + print STDOUT "$R_out\n"; +} + +__END__ + +=head1 NAME + + CLIFinder - Identification of L1 Chimeric Transcripts in RNA-seq data + +=head1 SYNOPSIS + + CLIFinder.pl --first <first fastq of paired-end set 1> --name <name 1> --second <second fastq of paired-end set 1> [--first <first fastq of paired-end set 2> --name <name 2> --second <second fastq of paired-end set 2> ...] --ref <reference genome> [--build_ref] --TE <transposable elements> [--build_TE] --html <results.html> --html-path <results directory> [options] + + Arguments: + --first <fastq file> First fastq file to process from paired-end set + --name <name> Name of the content to process + --second <fastq file> Second fastq file to process from paired-end set + --ref <reference> Fasta file containing the reference genome + --TE <TE> Fasta file containing the transposable elements + --rmsk <text file> Tab-delimited text file (with headers) containing reference repeat sequences (e.g. rmsk track from UCSC) + --refseq <text file> Tab-delimited file (with headers) containing reference genes (e.g. RefGene.txt from UCSC) + --html <html file> Main HTML file where results will be displayed + --html_path <dir> Folder where results will be stored + + For any fasta file, if a bwa index is not provided, you should build it through the corresponding '--build_[element]' argument + + Options: + --rnadb <RNA db> Blast database containing RNA sequences (default: empty) + --estdb <EST db> Blast database containing EST sequences (default: empty) + --size_read <INT> Size of reads (default: 100) + --BDir <0|1|2> Orientation of reads (0: undirectional libraries, 1: TEs sequences in first read in pair, 2: TEs sequences in second read in pair) (default: 0) + --size_insert <INT> Maximum size of insert tolerated between R1 and R2 for alignment on the reference genome (default: 250) + --min_L1 <INT> Minimum number of bp matching for L1 mapping (default: 50) + --mis_L1 <INT> Maximum number of mismatches tolerated for L1 mapping (default: 2) + --min_unique <INT> Minimum number of consecutive bp not annotated by RepeatMasker (default: 33) + --threads <INT> Number of threads (default: 1) + + For Blast database files, if a fasta is provided, the database can be built with '--build_[db]'. Otherwise, provide a path or URL. \"tar(.gz)\" files are acceptable, as well as wild card (rna*) URLs. +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/script/CLIFinder_results.R Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,224 @@ +#!/usr/bin/env Rscript + +args = commandArgs(trailingOnly = TRUE) +missing_args = TRUE + +if (length(args) == 0 && exists("out1") && exists("out2") && exists("out3") && exists("nfastq") && exists("line_only") && exists("refseq")) +{ + missing_args = FALSE +} else if(length(args) == 6) +{ + missing_args = FALSE + out1 = args[1] + out2 = args[2] + out3 = args[3] + nfastq = as.numeric(args[4]) + line_only = args[5] + refseq = args[6] +} + +if(missing_args) +{ + stop("6 arguments must be supplied or the variables must be set before calling the script.", call. = FALSE) +} else { + suppressPackageStartupMessages(library(GenomicRanges)) + suppressPackageStartupMessages(library(plyr)) + + chim <- read.delim(out1) + + chim <- chim[order(chim[, nfastq+7], decreasing = F), ] + chim <- chim[order(chim[, 2], decreasing = F), ] + chr <- sub("chr", "", as.character(chim[, 1])) + suppressWarnings(chim <- chim[order(as.numeric(chr)), ]) + + grchim <- GRanges(seqnames = chim[, 1], + IRanges(start = chim[, 2], + end = chim[, 3]), strand = chim[, 4]) + + grchim$ID <- paste("Id_", 1:length(chim[, 1]), sep = "") + + mcols(grchim) <- cbind(mcols(grchim), chim[, 5:(nfastq+9)]) + + grfusR <- union(grchim, grchim) + + suppressWarnings(position <- as.data.frame(findOverlaps(grfusR, grchim))) + + grfusR$dup <- as.vector(table(position[, 1])) + + suppressWarnings(position2 <- as.data.frame(findOverlaps(grfusR[grfusR$dup>1], grchim))) + + grfusR2 <- grfusR + strand(grfusR2) <- "+" + gr3 <- union(grfusR2, grfusR2) + suppressWarnings(position3 <- as.data.frame(findOverlaps(gr3, grfusR2))) + gr3$dup <- as.vector(table(position3[, 1])) + + suppressWarnings(position3 <- as.data.frame(findOverlaps(gr3[gr3$dup>1], grfusR2))) + grfusR$info <- "no" + grfusR$info [position3[, 2]] <- "overlap sens opposé" + + grfusR$ID <- "Id" + grfusR$ID[position[!duplicated(position[, 1]), 1]] <- grchim$ID[position[!duplicated(position[, 1]), 2]] + + if(nrow(position2) != 0) + { + result <- aggregate(position2[, 2] ~ position2[, 1], data = position2, paste, collapse = "_") + grfusR$ID[grfusR$dup>1] <- paste("ID", result[, 2], sep = "_") + } + + mcols(grfusR) <- cbind(mcols(grfusR), mcols(grchim[position[!duplicated(position[, 1]), 2]])) + + min <- ddply(as.data.frame(grchim), .(seqnames, end, strand), function(x)x[x$Chimera.start == min(x$Chimera.start), ]) + min <- ddply(as.data.frame(min), .(seqnames, start, strand), function(x)x[x$Chimera.start == min(x$Chimera.start), ]) + max <- ddply(as.data.frame(grchim), .(seqnames, end, strand), function(x)x[x$Chimera.end == max(x$Chimera.end), ]) + max <- ddply(as.data.frame(max), .(seqnames, start, strand), function(x)x[x$Chimera.end == max(x$Chimera.end), ]) + + grfusR <- as.data.frame(grfusR) + grfusR <- grfusR[order(grfusR[, 1], grfusR[, 2], grfusR[, 3], grfusR[, 4], decreasing = F), ] + + grfusR$Chimera.start <- min$Chimera.start + grfusR$Chimera.end <- max$Chimera.end + + datax <- as.data.frame(grfusR) + colnames(datax)[1:3] <- colnames(chim)[1:3] + colnames(datax)[5] <- colnames(chim)[4] + + grchim2 <- GRanges(seqnames = datax[, nfastq+11], + IRanges(start = datax[, nfastq+12], + end = datax[, nfastq+13]), strand = datax[, nfastq+14]) + + mcols(grchim2) <- datax[, -c(4, nfastq+11:nfastq+14)] + + grfus <- union(grchim2, grchim2) + + suppressWarnings(position <- as.data.frame(findOverlaps(grfus, grchim2))) + + grfus$dup <- as.vector(table(position[, 1])) + + suppressWarnings(position2 <- as.data.frame(findOverlaps(grfus[grfus$dup>1], grchim2))) + + grfus$ID_final <- "Id" + grfus$ID_final[position[!duplicated(position[, 1]), 1]] <- grchim2$ID[position[!duplicated(position[, 1]), 2]] + + if(nrow(position2) != 0) + { + result <- aggregate(position2[, 2] ~ position2[, 1], data = position2, paste, collapse = "_") + grfus$ID_final[grfus$dup>1] <- paste("Id", result[, 2], sep = "_") + } + + mcols(grfus) <- cbind(mcols(grfus), mcols(grchim2[position[!duplicated(position[, 1]), 2]])) + + for (i in 0:nfastq) + { + mcols(grfus)[grfus$dup>1, 11+i] <- mcols(grfus)[grfus$dup>1, 11+i] + mcols(grchim2)[position[duplicated(position[, 1]), 2], 9+i] + } + + grfus2 <- grfus + strand(grfus2) <- "+" + gr3 <- union(grfus2, grfus2) + + suppressWarnings(position3 <- as.data.frame(findOverlaps(gr3, grfus2))) + gr3$dup <- as.vector(table(position3[, 1])) + + suppressWarnings(position3 <- as.data.frame(findOverlaps(gr3[gr3$dup>1], grfus2))) + grfus$info [position3[, 2]] <- "overlap sens opposé" + + min <- ddply(as.data.frame(grchim2), .(seqnames, end, strand), function(x)x[x$L1.start == min(x$L1.start), ]) + min <- ddply(data.frame(min), .(seqnames, start, strand), function(x)x[x$L1.start == min(x$L1.start), ]) + max <- ddply(as.data.frame(grchim2), .(seqnames, end, strand), function(x)x[x$L1.end == max(x$L1.end), ]) + max <- ddply(data.frame(max), .(seqnames, start, strand), function(x)x[x$L1.end == max(x$L1.end), ]) + + grfus1 <- as.data.frame(grfus) + grfus1 <- grfus1[order(grfus1[, 1], grfus1[, 2], grfus1[, 3], grfus1[, 4], decreasing = F), ] + + grfus1$L1.start <- min$L1.start + grfus1$L1.end <- max$L1.end + + dataf <- as.data.frame(grfus1) + + result <- (data.frame("Chimera.Chr" = dataf$L1.chromosome, + "Chimera.Start" = apply(data.frame(dataf$start, + dataf$end, + dataf$L1.start, + dataf$L1.end), 1, min), + "Chimera.End" = apply(data.frame(dataf$start, dataf$end, dataf$L1.start, dataf$L1.end), 1, max), + "Chimera.Strand" = dataf$L1.strand, + "L1.Chr" = dataf$L1.chromosome, + "L1.Start" = dataf$L1.start, + "L1.End" = dataf$L1.end, + "L1.Strand" = dataf$L1.strand, + "Unique.Chr" = dataf$seqnames, + "Unique.Start" = dataf$start, + "Unique.End" = dataf$end, + "Unique.Strand" = dataf$strand, + "ID_final" = dataf$ID_final, + "info" = dataf$info, + dataf[, 16:(nfastq+16)])) + + result <- result[order(result[, 2], decreasing = F), ] + chr <- sub("chr", "", as.character(result[, 1])) + suppressWarnings(result <- result[order(as.numeric(chr)), ]) + options(scipen = 10) + write.table(result, out2, sep = "\t", row.names = F, quote = F) + grchim <- GRanges(seqnames = result$L1.Chr, + IRanges(start = result$L1.Start, + end = result$L1.End), strand = result$L1.Strand) + mcols(grchim) <- result + + Rep <- read.delim(line_only, skip = 1) + grLINE <- GRanges(seqnames = Rep$genoName, + IRanges(start = Rep$genoStart, + end = Rep$genoEnd), + repStrand = as.character(Rep$strand), + repName = as.character(Rep$repName)) + + Gene <- read.delim(refseq) + grGene <- GRanges(seqnames = Gene$chrom, + IRanges(start = Gene$txStart, + end = Gene$txEnd), + geneStrand = as.character(Gene$strand), + geneName = as.character(Gene$name2)) + + suppressWarnings(position <- as.data.frame(findOverlaps(grchim, grLINE))) + suppressWarnings(position2 <- as.data.frame(findOverlaps(grchim, grGene))) + + grchim$GeneName <- "no_gene" + grchim$GeneName[position2[, 1]] <- grGene$geneName[position2[, 2]] + + grchim$GeneStrand <- "*" + grchim$GeneStrand[position2[, 1]] <- grLINE$repStrand[position2[, 2]] + + grchim$repName <- "no" + grchim$repName[position[, 1]] <- grLINE$repName[position[, 2]] + + grchim$repStart <- 0 + grchim$repStart[position[, 1]] <- start(grLINE[position[, 2]]) + + grchim$repEnd <- 0 + grchim$repEnd[position[, 1]] <- end(grLINE[position[, 2]]) + + grchim$repWidth <- 0 + grchim$repWidth[position[, 1]] <- width(grLINE[position[, 2]]) + + grchim$repStrand <- "*" + grchim$repStrand[position[, 1]] <- grLINE$repStrand[position[, 2]] + + dup <- position[duplicated(position[, 1]), 1] + if(length(dup != 0)) + { + for (i in 1:length(dup)) + { + grchim$repName[dup[i]] <- paste(grLINE$repName[position[position[, 1] == dup[i], 2]], collapse = "/") + grchim$repStart[dup[i]] <- paste(start(grLINE[position[position[, 1] == dup[i], 2]]), collapse = "/") + grchim$repEnd[dup[i]] <- paste(end(grLINE[position[position[, 1] == dup[i], 2]]), collapse = "/") + grchim$repWidth[dup[i]] <- paste(width(grLINE[position[position[, 1] == dup[i], 2]]), collapse = "/") + grchim$repStrand[dup[i]] <- paste(grLINE$repStrand[position[position[, 1] == dup[i], 2]], collapse = "/") + } + } + + final_result <- as.data.frame(grchim) + options(scipen = 10) + write.table(final_result[, -c(1:5)], out3, sep = "\t", row.names = F, quote = F) + print("Executed R script") +} +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/TE.fa Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,180 @@ +>L1PA1 +GGGGGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAG +CGACGCAGAAGACGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAGG +GAGTGCCAGACAGTGGGCGCAGGCCAGTGTGTGTGCGCACCGTGCGCGAGCCGAAGCAGG +GCGAGGCATTGCCTCACCTGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCGAGTCAAA +GAAAGGGGTGACGGACGCACCTGGAAAATCGGGTCACTCCCACCCGAATATTGCGCTTTT +CAGACCGGCTTAAGAAACGGCGCACCACGAGACTATATCCCACACCTGGCTCGGAGGGTC +CTACGCCCACGGAATCTCGCTGATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAGGCG +GCAACGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGCTTAGGTAAACAAAGCA +GCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTGT +>L1PA2 +GGGGGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAG +CGACGCAGAAGACGGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAG +GGAGTGCCAGACAGTGGGCGCAGGTCAGTGGGTGCGCGCACCGTGCGCGAGCCGAAGCAG +GGCGAGGCATTGCCTCACTTGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCGAGTCAA +AGAAAGGGGTGACGGACGCACCTGGAAAATCGGGTCACTCCCACCCGAATATTGCGCTTT +TCCGACGGGCTTAAAAAACGGCGCACCACGAGATTATATCCCGCACCTGGCTCGGAGGGT +CCTACGCCCACGGAGTCTCGCTGATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAGGC +GGCAGCGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGCTTAGGTAAACAAAGC +AGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTCTG +>L1PA3 +GGGGGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAG +CGACGCAGAAGACGGGTGATTTCTGCATTTCCATCTGAGGTACCGGGTTCATCTCACTAG +GGAGTGCCAGACAGTGGGCGCAGGACAGTGGGTGCAGCGCACCGTGCGCGAGCCGAAGCA +GGGCGAGGCATTGCCTCACTCGGGAAGCGCAAGGGGTCAGGGAGTTCCCTTTCCTAGTCA +AAGAAAGGGGTGACAGACGGCACCTGGAAAATCGGGTCACTCCCACCCTAATACTGCGCT +TTTCCGACGGGCTTAAAAAACGGCACACCAGGAGATTATATCCCGCACCTGGCTCGGAGG +GTCCTACGCCCACGGAGTCTCGCTGATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAG +GCGGCAGCGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGCTTAGGTAAACAAA +GCAGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTC +>L1PA4 +GGGGGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAG +CGACGCAGAAGACGGGTGATTTCTGCATTTCCAACTGAGGTACCGGGTTCATCTCACTGG +GGAGTGCCAGACAGTGGGTGCAGGACAGTGGGTGCAGCGCACCGTGCGTGAGCCGAAGCA +GGGCGAGGCATTGCCTCACCCGGGAAGCGCAAGGGGTCAGGGAATTCCCTTTCCTAGTCA +AAGAAAGGGGTGACAGACGGCACCTGGAAAATCGGGTCACTCCCACCCTAATACTGCGCT +TTTCCAACGGGCTTAACAAACGGCACACCAGGAGATTATATCCCGCACCTGGCTCGGAGG +GTCCTACGCCCACGGAGCCTCGCTCATTGCTAGCACAGCAGTCTGAGATCAAACTGCAAG +GCGGCAGCGAGGCTGGGGGAGGGGCGCCCGCCATTGCCCAGGCTTGAGTAGGTAAACAAA +GCAGCCGGGAAGCTCGAACTGGGTGGAGCCCACCACAGCTCAAGGAGGCCTGCCTGCCTC +>L1PA5 +GGGGGGAGGAGCCAAGATGGCCGAATAGGAACAGCTCCGGTCTACAGCTCCCAGCGTGAG +CGACGCAGAAGACGGGTGATTTCTGCATTTCCAACTGAGGTACCGGGTTCATCTCACTGG +GGCTTGTCAGACAGTGGGTGCAGGACAGTGGGTGCAGCCCACCGAGCGTGAGCCAAAGCA +GGGCGAGGCATTGCCTCACCCGGGAAGCGCAAGGGGTCAGGGAATTCCCTTTCCTAGCCA +AGGGAAGCTGTGACAGACGGCACCTGGAAAATCGGGTCACTCCCACCCTAATACTGCGCT +TTTCCAATGGTCTTAGCAAACGGCACACCAGGAGATTATATCCCGCGCCTGGCTCGGAGG +GTCCCACGCCCACGGAGCCTCGCTCATTGCTAGCACAGCAGTCTGAGATCGAACTGCAAG +GCGGCAGCGAGGCTGGGGGAGGGGCGCCCGCCATTGCTGAGGCTTGAGTAGGTAAACAAA +GTAGCCGGGAAGCTCGAACTGGGTGGAGCCCACCGCAGCTCAAGGAGGCCTGCCTGCCTC +>L1PA6 +CCAAGATGGCCGAATAGGAACAGCTCCGGTCTGCAGCTCCCAGCGTGATCGACGCAGAAG +ACGGGTGATTTCTGCATTTCCAACTGAGGTACCTGGTTCATCTCATTGGGACTGGTTGGA +CAGTGGGTGCAGCCCACGGAGGGTGAGCCGAAGCAGGGCGGGGCATCGCCTCACCTGGGA +AGCGCAAGGGGTCGGGGATTTCCCTTTCCTAGCCAAGGGAAGCCGTGACAGACTGTACCT +GGAAAAACGGGACACTCCCGCCCAAATACTGCGCTTTTCCAATGGTCTTAGCAAACGGCA +GACCAGGAGATTATATCCCGTGCCTGGCTCGGCGGGTCCCACGCCCATGGAGCCTTGCTC +ACTGCTAGCGCAGCAGTCTGAGATCCACCTGCAAGGCAGCAGCCTGGCAGGGGGAGGGGC +GTCCACCATTGCTGAGGCTTGAGTAGGTAAACAAAGTGGCCAGGAAGCTCGAACTGGGTG +GAGCCCACCGCAGCTCAGCAAGGCCTGCTGCCTCTGTAGACTCCACCTCTGGGGGCAGGG +>L1PA7 +GGTGGCTGGCAAGATGGCCGAATAGGAACAGCTCCGGTCTGCAGCTCCCAGCGAGATCAA +CGCAGAAGGCGGGTGATTTCTGCATTTCCAACTGAGGTACCCGGTTCATCTCATTGGGAC +TGGTTAGACAGTGGGTGCAGCCCACGGAGGGCGAGCCAAAGCAGGGTGGGGCGTCGCCTC +ACCCGGGAAGCACAAGGGGTTGGGGAACTCCCTCCCCTAGCCAAGGGAAGCCATGAGGGA +CTGTGCCATGAGGAATGGTGCACTCCGGCCCAGATACTACGCTTTTCCCACGGTCTTCAC +AACCCGCAGACCAGGAGATTCCCTCGGGTGCCTACACCACCAGGGCCCTGGGTTTCAAGC +ACAAAACTGGGCGGCCATTTGGGCAGACACCGAGCTAGCTGCAGGAGTTTTTTTTTTCAT +ACCCCAGTGGCGCCTGGAATGCCAGCGAGACAGAACCGTTCACTCCCCTGGAAAGGGGGC +TGAAGCCAGGGAGCCAAGTGGTCTAGCTCAGTGGATCCCACCCCCACGGAGCCCAGCAAG +>L1PA8 +TGGCTGGCAAGATGGCCGAATAGGAACAGCTCCGGTCTGCAGCTCCCAGCGAGACCAATG +CAGAAGGCAGGTGATTTCTGCATTTCCAACTGAGGTACCCAGTTCATCTCATTGGGACTG +GTTAGGCAGTGGGTGCAACCCACAGAGGGCAAGCAGAAGCAGGGTGGGGCGTCGCTTCAC +CCAGGAAGTGCAAGGAGCTGGGGGACCTCCCTCCCCCAGCCAAGGGAAGCAGTGAGGGAC +TGTGCTACCCGGCCCGGATACTACGCTTTTCCCACGGTTTTTGCAATCCGCAGATCAGGA +GATTCCCTTGTGTGCCTACACCACCAGGGCCCTGGGTTTCAAGCACAAAACTGGGCAGCT +GTTTGGGCAGACACCGAGCTAGCTGCAGGAGTTTTTTTTCATACCCCAGTGGCACCTGGA +ACCCCAGCGAGACAGAACCTTTCACTCCCCTGGAAAGGGGGCTGAAGCCAGGGAGCCAAG +TGGTCTCGCTCAGCAGGTCCCACTCCCACGGAGCCCAGCAAGCTAAGAACCACTGGCTTG +>L1PA8A +GGGGTGGGGCCAAGATGGCCGACTAGAAGCAGTGGTGTTCGGAGGCTCCCATCGAAAAGA +ACCATAATAAGCATGTGAATCCTTCACCGGCAACCAAGGTATCCAGGTTCTCTCATCAAA +ATTGACTAGAAGGCTGGCGTGACCCACGGAGAGAAGGAAGAGCAGTGTGGTGCGGTGGCC +CACCTGAGAGCCACACGGGGAAGGGGAGCCCCCTCCCCCCAGCCAAGGGAGGCGGTGAGT +GAGCGTGCTACCCAGCCGGGGAAACCGTGCTTTTTCCACGGAACTGTGCAACCCATGGAT +CGGAAGATCCCACTCGTGAACCCATGCCACCGGGGCCTAGGGTCCCAACCCCAGAACGCG +CAGATTCTTACAGCCTCTCAGCTGGAATCTGCTTAAGCCTACCGAACTCCCGGGGGGAGG +GGCGACCAGCACCAGCTGCAGCTGCCTGCTGTCTAAGCCATTTGAGCTCCTTGGGGGAGA +GGCAGCAGCCAGCACTGGGACTCACAACTGCCTAACACACTAAGCTCCCTGGGCGGGGGA +>L1PA10 +GGGGGGAGGGGCCAAGATGGCCAACTAGAAACAGCTGTCGTCGGAGGCTCCCACCGAGAA +GAATGAAAACAGCAAGTGAATCCTGCACCGGCAACTGAGGTATCCAGGTTCTCTCATTGG +GACTGACTAGGCGGTTGGCGCGACCCACGGAGAGCGAGGAAAAGCGGGGTGGTGTGACGG +CCCACCTGGGAGCCACACGGGGCAAGGGGAGCTCCCACCCCCAGCCAAGGGAGGCAGTGA +GTGATCGTGCTACCCTGCCTAGGAAACCACACTTTTTCCACGGATCTGTGCAACCCACGG +ATCAGGAGATCCCCCTCGTGAGCCCACGCCACCAGGGCCTTGGGTCCCAAGCACAGAGCT +GTGCAGATTCTCAGCAGCCACTCGCTGGAGACTGCCTAAGACTACCGAGTTCCTGGGGGG +AGGGGTGGCCATCATCACTCCGGCTGCCTTCTGCCTAAGAAGACTGAGCTCCCTGGGGGA +GGGGAGGCAGCCATCACTGCAGCTCCAGTGTGCCACTTTTCTCCTGCCGGTGCCAGGGAG +>L1PA11 +GGAGGGGGCCAAGATGGCCGATTAGAAGCAGCTGCAGTCTGCAGCACTCACAGAGAGGAA +TGAAAAGGGCAAGTGAATTCAGCACCTTCAACTGAAATATCCAGGTTCTCACATTGGGAC +TGACTAGGCAAACAACTCAACCCATGGAGAATGAAGAAAAGCAGGGTGGGGCGATGGCCC +ACCCAGGAGCGGCACAGAGCCAAGGGAACCCCCACCCCCAGCCAAGGGAAGCGGTGAGTG +ATTGTGCGACCCTGCCTGGGAAACCACGCTTCTCCCATGGATCTTTGCAACCCATGGATC +AGGAGATCCCCTCGTGAGCCCATACCACCAGGGCCTTGGGTCCGATACACAGAGCTGTGT +GGAGTCTCGGCAGAGCAGCTGCTCAGGCACACACAGAGACCCAGGAGTTTTACATACTCC +GGCCCCGGGATTCCCAGCAAGGCAGGAGATCCATCCATACATACCCCTAGGAAGGGGGCT +GAATCCAGGGAGCCAAGCAGCATCATTCTGTGGGCCCCACTTCCACGGCACCTCACAAGT +>L1PA12 +GGAGGTGGCCAAGATGGCCGACTAGAAGCAGCTAGTGTGTGTGGCTCTCACGGAGAGGAA +CGGAAGGGGCGAGTAAATACAGCACCTTCAACTGAAACATCCAGGTACTCGCATTGGGAC +TAATCAAGGAAACAACTCGACCCACGGAGAATGGAGAAAAGCAAGGCAGGACGACGGCCC +ACCCGGGAGCGACACGGAGCCAGGGGAACCTCCCCTGCCCAGGGAAGCGGTGAGTGAATG +TGCGACCCCGGGAAACCACGCTTCTCCCATGGATCTTTGCAACCCTCGGGTCAGGAGATC +CCCTCGTGAACCCACTCCACCAGGGCCTTCAGTCTGACACACAGAGCTACGTGGAGTCTC +GGCAGAGCAGCCGCTCAGGCACGCGCGGAGACCCNGGAGCCTTAGATACCCGGGCTTTCT +GGGCTTCCCGGCAAAAGTAGCTGCAACTCCGGCAAAGTGGGAGGTTAGACCCCCGTACAT +ACCCCTAGGAAAGAGGCTGAATCCAGGGGGCTGAGCAGCGACAGCCTGCAGGCCCCACTT +>L1PA13B +GGGAGTGGCCAAGATGGCCGACTAGAAGCAGCTAGGGTGTGTGGCTCTCATGGAGAGGAA +TGAAAGAGGCAAGTAAATACAGCACCTTCAACTGAAACATCCAGGTACTCACATTGGGAC +TAATCAAGGAAACAACTTAACCCACAGAGAATGGAGAAAAGCAAGGCAGGACGACAGCCC +ACCTGGGAGTAACACGGAGCCAAGGGAACCTCCCCTGCCCAGGGAAGCAGTGAGTGAATG +TGCAACCCCAGGAAACCACGCTTCTCCCATGGATCTTTGCAACCCTCGGGTCAGGAGATC +CCCTCGTGAACCCACTCCACCAGGGCCTTCAGTCTGACACACAGAGCTACGTGGAGTCTT +GGCAGAGCAGCCACTCAGGCATGCGTGGAGACCTAGGAGCTTTACATACTCCGGCTCTGG +GCTTCCTGGCAAAAGTAACTGCAACTCCGGCAAAGTGGGAGGTTAGACCCCCATACATAC +CCCTAGGAAAGAGGCTGAATCCAGGGGGCTAAGCAGCAATGGTCTGCAGGCCCCACTTCC +>L1PA13A +GCAAGATGGCTAACTAGACACAGCCAGGTGGAACAGCTGCCACCGAGGGACCAAGATGAC +TGGCGCACTCCTAACAGATCTTCAGAGGGAAGGCACTGAGAGTGGACAGAGGGAAGACAC +AGAAGCTGGGCTGAAGGGGGAGGAAGCTGGGAACCCTGCATGGGGCTACTATACACCAGG +ACTCATTCCTGGCCCCCAATGACTCCGGGGGAATGGGTGAGTTGAACTGGCAAGGAGCAA +CCTGCTCTCGCCATAGGCCTCTGGAATCCTGGCAGGAGGAGACCCCTTGACCACCACAGA +CACTTGAGTTGGCAGGGAGAGCTGCTTAGAGAAGTGGTAGGGGCAGCACTCCAGCTGATG +TAGAGCCCAGAGGGTTTGGTGCAGGAGCATCTGTAGTGGAGCATGGCCAGGGATGCCCAT +CCCCCTAGGCTCAACTTGCTCCCATAGGAGACTTTAGCCCTAGGGGAACTGTCAGACCTG +AACTCTGCAGGGCAGTCTTGCCCATCAGACGGGGCCAGTCTGACCTGAGCACCCCTTGGT +>L1PA14 +GGGAGTGGCCAAGATGGCCGACTAGAAGCAGCTAGTGTGTGTGGCTCTCACGGAGAGGAA +CAGAAGGGGTGAGTAAATACAACACCTTCAACTGAAACATCCAGGTACTCGCATTGGGAC +TAATCAAGGAAACAACTTGACCCACAGAGAATGAAGAAAAGCAAGGCAGGATAACAGCCC +ACCTGGGAGCAACACGGAGCCAGGGGAACCTCCCCTACCCAGGGAAGTAGTGAGTGAATG +AGTGACCCCGGGAAACCATGCTTCTCCCACAGATCTTTGCAACCCTCAGGTCAGGAGATC +CCCTTGTGAACCCACTCCACCAGGGCCTTCAGTCTGACACACAGAGCTATGTGGAGTCTC +GGCAGAGCAGCTGCTCAGGCATGTGTGGAGACCTTGGAGCCTTAGATACTTGGGCTTCCT +GGCAAAAGTAGCTGCAACTCCAGCAAAGTGGGAGGTTAGACTCCTGTACATACCCCTAGG +AAAGAGGCTGAATCCAGGGGGCTGAGCAGCAACAGTCTGCAGGCCCCACTTCCACGGCAC +>L1PA15A +CAAGATGACTGACTAGGCACACCCAGGAAGAGCTTCTCCCACTAAGACAGACCATCAAGA +AGATTGGCACACTCTGAGCAGATCTTCAGAAGGAAGGCATTGAGAGTGGATGGAGGGAGG +ATACAGAACCTGGGCTGAAGGGGGAGGAAGCTGGGAACCCTGCACAGGGTTGCCGAGCAC +CAGGACTTGTTCCTGGCCCTAAGTGGCTCCTGAGGAAGGGATGAGTAAAATAGGCATGGA +GTGGCCCACTCTCATCATGGACCTCTAGAATCCTAGCTGCAGGAGACTCCACAACCCACA +TGGACATTTGAGCTGGCAGAGAGAGCTACCTGGAGAGTTGGCAGGGACAGGACTCCAGCC +TGCATGGAGCCCAGAGGGTTTGGTATGGGAACAGCTGCAGTGGAGCATGACCAGGGATAC +CCATTCCCCAAGGCTTACCATACTCCTCTAGGTGGCTTTAGCCTTTGTTAACTGTCAGAC +CTGGACAGAACAGGGCTATCTTGCCTATGGGATGGGGCCAGTCTAATCTGAGCACCCCCC +>L1PA15B +CAAGATGGCCAACTAGATACAGCCAGGAGGAACATCTCCCACCAAGAGACCGGGACATCA +AGAAGACTGGCACACTCCAAGCAGATCTTCAGAGAAAAGGCATTGAGAGTGGATAGAGGG +AGGACACAGATGCTGAGCTGAAGGGGAAGGAAGCTGGGAACCCTGCACAGGGCTACAAAA +CACCGGGACTCATTCCTGGCCCCCAGTGACTCCTGGGGAAAGGGTGAGTTGAACAGGTAA +GGAGCAGCCCACTCTCACCATGGACCTCTGGAATCCTGGCAGCAGGAGACCCCACAACCC +CCATGGACACTTGAGCTGGCAGGGAGAGCTGCTTAGAGAGGTGGTAGGAGCAGGACTCCA +GCCTGTGTGGAGCCCAGAGGGTTTGGTGTGGGAACATCTGCAGTGGAGCACGGCCAGGGA +CACCCATCCCCCAAGGCTCGCCATGCTCCTCTAGGAGACTTTAGCCTTGAGGAACTGTCA +GACCTGGACACAGCAGGATGATCTTGCCTATGAAATGGGGCCAGTCCGACCTGAGCACCC +>L1PA16 +TTTTTTCCAAGATGGCAGATTAGAGGCTTTTAGCATGCCTCAGCCACTTGGAAATAGCAA +GATAGTACATAAAGATCAACTCTGTGAGCTTTAATTCAAGAAGGAAAATGGGAATCCACT +AGAATCATGAAGGACACCCCAGATCCTAGGGAGGAGAATGTGGGCAAACAGCCCCCGTGA +TGGTGTCTAGCTGATAAAAGTGAGTGAAGCCCCAGTACATGAGAGAGGCAGAGAGCCTCC +CTCTGTGACTCACCTTTCCACTGGGGATCTGAGCAACCCAGGCCAAGGGAGAGCACTTTG +TTTCTCCCAAGCCCTGGAGCTAACTTGGGGAGAGGCTTGGAGATGCTGTGAGGGAAAGAC +ACCAGGAAAAGCTGCAGGCATTTTCCCAGACCCAGGACTGAGAGCAGGATGCCATTTTTA +ATCTAGGCACATACAAAGTCAGCCATTCTTTGGTAACCCAGCAGCATGGCCATGCAGGCA +TTTTAGTCTTGGGCCAAAGATTGGAGGACCTGCTCTGGAGTGGGGTAGGGGCCTCCACAA
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/genome.fa Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,336 @@ +>chr17:13850000-13860000 +TGCTAAAGCTTCAATGCAGTAGACCAGAGTAGAAAGCTGTAGATGAGGTGATAGTAAATT +CATTTGAGTCAACTCTCCTGACTTCTCTTTCATAATATAAACACATAATTTTCCCTTGTA +TCCTTACAAAAGAGAGACTTCAATATCCATAAACATGTATTTCTATTTTGAGGTTACAGA +CATAAAATTTAAAAATTCAACAGTTCTCAACCATTTCCTTTAGCAATCGCCCATACATAG +ACTATGATGGAAATTAACTAGCAATGCATGAAATTTCTAAAGGAGCTCCTTATGATATCT +CTCTAAAAAAATTTTAAAAGGAGCTATAAAGTTGTTAAACAGATTTATGGTAGTTTTAAT +GTATCTACTAAAATGTTGGATTCATGTCGGCTTTTGTATTAAGGAAAAATGATTTCCTAA +TAACCCCTTATAAAAGTAATTGCTGATTCTAAAGCCGTTATCTTTAAAAATGCTAATATA +GTTTTCTTAGTAAAGCTTCTAAGCAATACTCAGTATGCCTTTCTCATTTTACATATATTC +CTGACACTGATAAATATCAACATATTTTATTTTTGTTTTGCAATTTCtttttataaagac +aatttttaacgagcagtttcaggttcatagcaacattgagtggaaggtacggagatagcc +catatgctcacttcctcaacacatacgcagctcctccagtaaggacataccccatcagag +tggtacattctatacaattgatggacttaacattgatacgtcattgtcacccagagtcca +taatttacattaaggttgcctcttggtattgtatattctgtgggtttggacaaataaata +atggcatcaaccaatcattgtacaaagtagtttcTTTTTCTTTTACATAATTTGTAATAT +TTATTAATAAATAAGGAGTTATATATAATCAATTCACcgatggcacttttatcacagact +aaattcttattaagttgttctgcctcgggcctttctgttttgttgcattaatgggtctaa +cgatccataaaacagtaccacactttgaattcttaaaatttaaaatatatctttaaatct +gCCCAAGAAAATGCTTCTTCCTTTCTGTGCTCCACACCTGCTCTACTGCTGGAGTCATTG +CTGCCACCGTTACctgattctcctctctttgagaaagaagtaagattcacaaccaaatcc +ctttggttggggagtgccatatgacttgttctggccatacctcatgaactcagtgacgtg +ctatttccaggccacagtacttaatgatcagtttgagaccctctaaagatctcttttatc +tgctgcagtacctgccaacctctgagctggaggctgctacttcagctcgaattcatagta +aggaaacaaaaagacatcaacctgcaatgaacacagcatcagaaataaagctttgttatt +ttaagtcattgagctgggcagagaaggaaagcgttgttactgcgtcctaactgagttgat +tccgactaatacaCAGCAAAATAATTGATGTTTTCAAAAACTGCCCCaaatctcattagg +attttgattagaattgtattaatcctgaagattcattttggaggagctagcattttcaca +atattgaatcttcccgtgtccaagaatgtgatatgactcctcactcatgtctcttattct +gaataaggttgtatatatttcataaagTTTACACTAAGAGCTAGGCATGTATTGCTATTT +CTTATTTATGTTTGTTCCCATACTATAAGGATTTTTAATtattctgcaactggacatgct +ggtgaattttcttaatagttctaatagctttggattgagcttgttgttccctaagtcaaa +agtaaatggtgctgaataatggtaattttatgtatttctttctgctaatgaatgcctcat +ttctatttcatatcttactgttttagatggaaattccagaataaggttgaTAATATCTTT +GAATAAGGATATTTTTCTCTCCTTTATcagaggtcagaaagctttttctgtaaaaagtca +gattgtaaatatttttagctttgagaaccagaccatctgtcacagctactcaatactgcc +atggtagcataaaagcagccacaaccaacaaataaaaaaatgaacgtagctgGATTTGAC +TGATAAACATGGTTTACTGAACCTTTTTCTACTTTAATGGCAAGGCTTTTAATGTTTTGC +CATTACTATGATTTTAGTTACTAATTTATTATTTTAAGAAATTATTCCTCCAATTCTACA +TTGCAAAATTTTTCTCTTTTTTGATAATTCATTTTTGACTTCAATCAAGATCATTGTTTT +AAAAATCTGTTACATAGTAATTAAATTAATAGATGCTAAATTTCTCTAGAATGTTCTACA +AATTTTCTAGTATTAAACCACTCTTACATCCCTATATGAGTTTTACTTAGttttattttt +gtttttgttttgtttgagatggagtctcactctgcagcccaggctggagtgcagtggcac +aaccttggctcactgcaacctccgcctcccaggttcaagcgattctcttgcttcagcctc +ctgagtagctgggattgcaggcacctgccacgacactcagctaatttttttgtattttta +gtagggatggggtttcaccatgttggccaggctggtcacgaactcctgacctcaggtgat +ccacccgccttggcctcccagagtgctgggattacaggtgtgaaccactgcacccagccA +GCCATTTTTATTTATTCCTGGATtttattaaacaaaccttaattggatgctcatgatgta +tcaggcacacttgtagaagtaatggatgcagcagtcaacaaaatagaaaaaagttcctgc +tctcatggagctgacattctagtgggaggacaaagataataataaattcacttaaatatg +tcaggtgaaggataagaaagcaaagacaaagagtgtcagggtagggtgccattttagaaa +tgaggttcaggaaggcctttctgatcaggtgacatttgagcagaaacttgaaggaagtga +gggcacagtctaataaattaaataagcaactggaagtagtacactaaattgccaggatag +agaataagcaggatgctagaggggcacatggcaggatcgcctaatgtggtcacagacgtg +gggtgaggagggcttctgggaggaagcaacgtttattctgagaccttgaagaaAAGTTAC +ACCTGtgtgatggttaattttatgtgtcaacttgaccaggccatggggtgcccagacatt +tggtcaaacattattctgggtgtatctgtgaaggtgtttctggatgagatgaatatttgc +attcataggttgagtaaagcaggttgccctttcttacatgggtgtgcctcatccaatcca +ctgacgatctgaatagaacaaaaagactgagtaagagggaattcttcttgcctgactgct +tgagctggggtatcagtcttttcctgtctttgaatttgaactgaaactttggttctcctg +gttctcaggcctttgaactggtcctacaactacaacatcagctttcctgggcctctacct +tgccaactacagattttgggacttctcagcatctatgatcgtatgacctgatttcttata +aatctctttatatgtatacacatgcacacacacacacacacacacacacaaccctattgg +ttctattgctctaaagaaccctgactaattcaATGAGCAGGAGAAAAAATAATATTCTAT +AATAGCATAATTTATAGTCCCCAAATTAGAGGAAAAGAACAGTTTCAAGCAAATGAAAGT +TCAATATAGAGGAAGAGAAGAAATGAGGTAAAGAGTGGGGCTGAACAGATGGGAAGAAAT +CGGGTTGTTCACGATCCTGAAAACCTTCCTGAGCATGCGCTGTGTCCTGTGAGCAGTGGG +AAGCCATTGTGTGTTTTAAGTAGCAAAGTTAAGTAACCAGTGGGGCCACCAGGTATCACA +GCCCCAGTGGTCACCACCCCATTATATCCACCCATAGAATACATGGGCTAGTGCCCATGG +AGTTCAGTCGTATAGAGACATTGAACTGTGTTTTATCATATACTGGGCCACAAGGAAAAT +TTAGATGGACTTTATAAATAAGAAATTGTTCATGCTACATTCTCTGGATTAAAGCAAAAA +GAAATTATAATATAATAAAAGGGTAGTCAAAATATATATATAAAGCCACtgtagagtagg +aaagatactgttctacccatcatgatcaaggaccctataacaaaagacagattaacagag +agaagcataaaaaagatatttaatatagatttaacatgacatagaagtcttcacaagaaa +atgaagatccaaagaaacaggtacacttgagtagctttgtgctggttttgatgaagactt +gagagtggaggggaaacgtaataaagcagaaagggtgtgatctaatggtaataaactgag +ggaacttagcagggcctatttgttcagattcttctctgtgaccctgtgtcctcagggata +aggatgctcatccattcagaggtatagggagggcacctctcacatgagggttttgtgacc +tggttcaggggaaggtcagaaaatccttcccggttgtatgacctgcttccggggagaatg +atgtgggaaggtcagtgagaccttcctgattctgccgttattataaattccttcagcttg +atatattcaataggccaaaatgccctattttggggtagtgtgtcctgaacACATATAGGA +AAATTTTTAAATTCTTCTGTAAAATAAGTCTTGGGCCAATAAGTACATGAAACCTGCAGC +TATCAACTTTATGGACATTAAAAACAAATTAAAAACTTGGAGAGAAAATGATCACAGCAA +TTCAAAGACCAAAAAAATCATAGGCTTGAGGCTTAAATGAGAAAGACTGGCTTAAATGAG +AAAAGTCAAGGAGAAAAATGACCCAAAGGATAAagggcctctgtgtttgttgtgctctcc +acccatctttatgcctgttgccctcactttcttcaagtccctgcccaaattccacctgat +cagagaggctttccctttagcccctttctaagatagcatcctttccctctgctatccgtc +actctctacctctgctttattatccttcccctggcacattctgtgtgtctttgctatcat +ctgagtcctccccctggaataaagctgtgagcgcagggacctctgtctattttgtcccct +gcggcatcccctacttctagaacagtgcctggtacTGGGgctccatgtggcaggtctgtg +actggcctgttcaaacttcatcccctacccaggccaggcatttgccagatgcttaataaa +tactttttgagttaatgCTACAATGCATCACTGGACATCTTTTAAAAGTAATATTCTTTT +GGAGGTATCAAATCTATCTAAAAATATATAGGGATCgttccaagatggccgaataggaag +agcttcattctgcagctcccagcatgatcgatgcagaagacaggtgatttctgcatttcc +aactgaggtgcctggttcatctcactgggactggttggacagtgggtagcccatggaggg +tgagctgaagcagggtggggtgttgcctcgcccaggaagtgcaaggggttggggggtttc +cctttcctagccaagggaagccatgacagactgtacctggaaaatcgggacactcccacc +ctaatactgcatttttccagtggtcgtagcaaatggctcacctggagattatatcccatg +cctggctcagtgggtcccatgcccacagatccttgctcactgctagcacagcagtctgag +atcaaactgcaatgtggcagcctgggctggaggaggggcatccaccattgctgaggcttg +agtatgtaaacaaagcagccaggaagctcgaactgggtggagcccactacagctcaatga +ggcctgcctgcctaccactgtagattccacctctgggagcagggcatagctgaacaaaag +gcagcagaaatttctgcagacttaaacgtccctgtctgacagctctgaagagagaagtgg +ttctcccagcatggggtttgagctctgagaacagacagactgcctcctcaagtgggtccc +tgacccccgtgtagcctaactgggagacacctcccagtaggggccgactgacacctcata +cagccaggtgcccctctgagacgaagcttccagaggaaggatcaggcagcaatatttgct +gttctgcagcctccgtgggtgatacccaggcaaacagggtctggagtggacctccagcaa +actccaacagacctgcagctgagggtcctgactattagaaagaaaactaacaaacagaaa +ggaatagcatcaacatcaacaaaaaggacatccacaccaaaaccccatctgtaggtcacc +atcatcaaagaccaaaggtagataaaaccacaaagatgagaagaaacctgagcagaaaag +ctgaaaattctaaaaaccagagcacctcttctcctacaaaggatcacagctcctcgccag +caatggaacaaagctggatggagagtgactttcacaagttgacagaagtaggcttcagaa +ggtcagtaataacaaacttctccgagctaaaggaggatgttcgaacccatcgcaaagaag +ctaaaaaccttgaaaaaagattagatgaatggctaactagaataaacagtgtagagaaga +ccttaaatgacctgatggagctgaaaaccatggcacaagaactacgtgacgcatgcacaa +gcttcagtagccgattcgatcaagtggaagaaagggtatcagtgattgaagatccaatga +acgaaataaagcaagaagagaaatttagagaaaaaagagtagaaagaaatgaactaagcc +tccaagaaatatgggactatgtgaaaagaccatctatgtttgattggtgtacctgaaagc +gacggggaaaatggaaccaagttggaaaacactcttcaggatattatccaggagaacttc +cccaacctagcaaggcaggcagacattcaaattcaggaaatacagagaacaccacaaaga +tactccttgagaagatcaacctcaagacacataattgtcagattcaccaaggttgaaatg +aaggaagaaattttaagggcagccagaaagaaaggtcgggttacccacaaagggaagccc +atcagactaacagtggatctcttggcagaaaccctacaagccagaagagagtgggggcca +atattcaacattcttaaagaaaagaattttcaacccagaatttcatatccagctaaacta +agcttcataagtgaaggaaaaataaaatcctttacagacaagcaaatgctgagagatttt +gtcaccaccaggcctgccttacaagagttcctgaaggaagcactgaacatggaaaggaac +aactggtaccagccactgcaaaaacatgccaaattgtaaagaccatcaatgctaggaaga +aactgcatcaactaacgagcacaataaccagctgacatcataatgacaggatcaaattca +cacataacaatatctaccttaaatgtaaatgagctaaatgccccaattaaaagacacaga +ctggcaaattggataaagagtcgagacacatcagtgtgctgtattcaggagacccatctc +acatgcagagacacacataagctcaaaataaagggatggaggaagatctaccaagcaaat +ggaaaacaaaaaaaaagcaagggttgcaatcctagtctctgataaaacagactttaaaca +aacaaatatgaaaagagacaaagaaggccattacataatggtaaagggatcaattcaaca +agaagacctaactatcctaaatatatatgcatccaatacaagagcacccagattcataag +gcaagtcctgagagacctacaaagagacttagactcccacacaataataatgggatactt +taacacccccctgtcaatattagacagatcaatgagacagatggttaataaggatatcca +ggacttgaactcagctctgcacgaagcagacctaatagacatctacagaactctcccccc +caaatcaacaaaatacacatttttctcagcaccacatcgcacttattccaaaattgacca +catagttggaagtaaagcactcctcagcaaatgtaaaagaacagaaatcacaacaaactg +tctctcagaccacagtgcaatcaaattagaactcaggattaagaaactcactcaaaacca +cacaactacatggaaactgaacaacctgctcctgaacgactactgggtaaataacgaaat +gaaggcagaaataaagatgttctttgaaaccaatgagaacaaagacacaacatatcagaa +tctctgggacacatttaagcagtgtgtagagggaaatttatagcactaaatgcccgcaag +agaaagcaggaaagatctaacatcagcaccctaacatcacaattaaaagaactagagaag +caacagtaaacaaattcaaaagctagcagaaggcaagaaataactaagatcagagcagaa +ctgaaggagatagagacacaaaaaacccttcaaaaaatcaatgcatctaggagctggttt +tttgaaaagatcaacaaaataaatagaatctaatagaaacaataaaaaatgataaagggg +atatcaccactgatcccacagaaatacaaactaccatcagagaatactataaacacctct +atgcaaataaactagaaaatctagaagaaatggataaattcctggacacatacaccctcc +caagactaaaccaggaagaagttgaatccctgaatagaccaataacagactctgaaattg +aggcaataattaatagcctaccaaccaaaaaagcccaggacaagaccaattcacagtcaa +attctaccagaggtacaaagaggagctgacaccattccttctgaaactattccaatcaat +agaaaaagagggaatcctccctaactcattttatgagttatgaggccagcatcatcctga +taccaaagcctggcagagacacaacaaaaaaagagaattttagaccaatatccctgatga +acattggtgcaaatatcctcaataaaatactggcaaactgaatccagcagcacctcaaaa +agcttatccaccacgatcaagttggctacatccctgggatgcaagcctggttcaacattc +gcaaaacaataaatgtaatccatcacgtaaacaaaatcaaagacaaaaaccacatgatta +tctcaatagatgcaaaaaaggcctttgacaaaattcaacagcccttcatgctaaaaactc +tcaataaactattttgatgggatgtatctcaaaatactaagagctattttttgacaaacc +cacagccaatatcatactgaatgggcaaaaactcctttgaaaactggcacaagacaggga +cgccctctctcaccactcctattcaacatagagttggaagttctggacagggcaatcagg +cgggagaaagaaataaagggcattcaattaggaaaagaggaagtcaaattgtccctgttt +gcagatgacatgattgcatatttagaaaaccccatcatatcagcccaaaatctccttaag +ctgataagcaactttggcaaagtctcaggatacaaaatcaatgtgcaaaaatcacaagca +ttcttatacaccaataacaaggcaaacagagagccaaatcatgagtgaactcccactcac +aattgcttcaaagagaataaaatacctaggaatccaacttacaagggatgtgaaggacct +cttcaaggagaacaacaaaccactgctcaacaaaaaaaaagaggacacaaacaaatggaa +gaacattccatgctcatggataggaagagtctatatcataa +>chr18:62900000-62910000 +TAAAAAGTTTGTCTGggccaggtgcagtggctcctgcctgtaatctcagcactttgggag +gccgaggcaggtggatcacctgaggtcaggagttcaagaccagcctggccaacatggcaa +aaccccgcctctactaaaaatgcaaaaattagctggctgtggtggcatgttcctgtagtc +ccaactactcggtaggctaaggcaggagacttgtttgaacccaggaggcggaggttgcag +tgggccaagatcgcaccactgcactccaacctgggtgacagagcaagactttgccttaaa +ataataaataaataaataaataaataaataaataaataaataaataaataaaAAGTTTGT +CCTAGTTACATCATGGTGACTGTGGTCAACAATATGTTGTAGTTGTTTGTAttcttgttt +tttctttttctttcttttttttttttttttttttttttttttgagacagggtctcacttt +gttacccaagctggaatgcaatcacagcttgttacccaagctgtggtgcaatcacagttc +actgcagcctcaaactcctgggttcgagtgatcttcctgccccagcctctcaaatagctg +ggagtataggcacgtgccaccatggctggctaattttttattttttgtagagatggggtc +ttgctctgttgcccagtctggtctcaaacgaaccttctacttcagcctcccaaagtggta +ggattacagagtttgagctaccacaccctgccataatatattgtattcttgaacaatgct +aagagagtggatgtattttcaccacaaaagtgaaatatctcacaaataactatgtgagat +agtgcatgtgaactagctagaattagtcacttcacagtttacgtatatttcaaaagtcat +gctgtacacaataaatatgtacagttttatctgtcaattaaacaaaTAATAAAACGGTTC +ATCCTAAGTAGCTGAATTACTGTGTGAACCTGAAAACTTGGTATTTCAGTCATGGTGAGA +GTTAACAACTTAAGCCAAATGTTAGCTTTCTTTTTTGTTACATTAACTTTGCTTTTGTTA +TAGATTTTTTTGTCTCCTTATTAATTCAATGCTTATTATTTTAGTACTAATACAATTTCA +TTGTATTGAATGAAATTGTGTGTGGCTCTTTCAAGTGAAGATGATAAAGCCATTATGAAG +GTTATTTGAAGTGTAGATTGGGAAGAAGATGGGACATTTGTTCCATTCCTGCAGTCTGTT +GTACCCAAGATGAGATGTGTTTTTTCTTTTTTATTCTGTTTACACATTCTAGTAATCTAG +TGAGCATTTGGAAATAAGCAGATTGCTGGGTCAAGGCCAGTTTTTAAATCTTACAACCTG +GAATAAAAAAAGAGAAAGAGCCAAAAAAACATCCTCTTAGGGCCATTGGAAAAGGCCATA +TGCTGTGCTTGCGTGTTGACAAATCCCAGCTCTTTGCTGGAACTCATCCTTGTGTTTCAG +TGGCTTTAGGATATTATTCTTAATTCATTTTCCATAGGTTTATTTTATTTTTTTAAAGGA +CAGAAATTCACTATAGAGAAACTCTAGCTTTTTCCTGTACTCTAGACTTATATTAATACT +CCttttttctttttttttttttgagatggagtctcgctctgtcgcccaggctagagtgca +atggcgtgatcttggctcaccacaacctccacctcctgggtttaagcagttctcctgcct +cagcttcccgagtagctgggattacaggcgtgtgccaccatgcccagctaattttttgta +ttttttttttagtagagatggggtttcaccatgctggccaggctggtctcgaactcctga +cctcgtgaaacacccacctcagcctcccaaagtgctgggattacaggtgtgagccatcgc +acccATCCTATATTAATACTTTTCTAAACAAGTGCATCATCTCAGCACTTTGCTGGCTTT +GTAATGGAAAATAGATGGTTTTTGTTGTTTGTTTTTAAAGGAGTTAGACATAGCCTAACA +AACTGGAAATTGACATTTCCATCTATTTTTCTCCCTTTTGAAGCTAAATATGTCTTTGTT +ATTTTGGTTCCTAGTCCCCATTACTACTTATTTTCTGATAGTTCATCCACAGCAACTTCA +GTCAGTTAGCTCACTAGTTCTTATGGCTAGAGATTCCGCCAGTTTTCCCCTGTGCCTTGC +TTCATCACAGAGGTGTTGGTTCCCATTTTTGTCCGGCATTCTAAGATTTCTCAATGGATT +CTAGATGCCGGATTTCAGTATTTTCTGCACTTCACTCTATCAAGCAGTATTTTATAGACA +GAGATAGTTTTGGTGGTTCATCCTGGTCCTGAGCAGTTGGGAGTCATGTACTTGCATTCC +CATCTCTGGTGCTCCCATTCAGTGTGCAACTCTTATTCGTTGTGTGACTCCCGTCCATTA +CTGTTTTTCCACCTCAACCTTTAATTCCATGCTACTCATCCGCCTGTTCATGCATCCTCT +CTCCTTCATTAAATATTCGTTGTAGTTGTGATGTGCCTAACAGTTGTTCTGAGTTTTGTT +TCTTATGTTCTTTTCGGTATGGTGTAGATAGTTTCACAGTTCCTTGGATGTCAGTTCCTA +GTTCTTTGGAAGTCAGTGCTTAAGTGGAATTTTTTTCCCTCTTGAAGTGAATTAAGGTAA +AGTCAATGTGCTTATTCCTCTCCCAGCTGTAGTGGTGTCACTTGTGTTTCAGAATATATT +GTGAAGGTTAAAACCTCCTGGAATTATAGCTAAAAATAGATACTCTGGCTAGTTAAGAAA +GGCCGGATGCTGAGATTCCAAAAATCATGGAGAACTATAATACAGAGAGAACTGAGTTCT +TTCTCGCTATTTCTCATATTAGGGTGTGCCCATTTACTTATAGCATTGCAGTTAATTATA +GTCTCTATGTCCTTTGCCCTCAAGGTTGAACGTAATTAGGAAGCTGATAGCAGATGAAGT +GGACTTTCTACAGCATGTTACTCAGCTTGACCTACGAGACAATAAGCTTGGTGATCTAGA +TGCTATGATTTTCAACAACATTGAAGTTTTACACTGTGAAAGGAATCAACTGGTCACATT +AGACATCTGTGGCTATTTCCTAAAAGCGCTCTATGCCTCTTCTAATGGTATGTATCATAG +GCTACATCAAAGTTGCTCTTTTGGTTCCAGGAATTTACCCAGCATCATTATTTCTGCTTC +TGATTATTCTTTGCTCAAGTAGTTAGTAAAATAGCTCAAATTTTGCTAAAATAAAAGTCA +CAAAAGAAAAATGCTGACTTATTGTTTAAAGGACTCAAAAAGGAAAATTTTATTGTCCCT +AATTTTTTTCTCGTATTGTGATTTGGATAAGTTACTCCCACTTTTGATTTGATTTTTCTG +CTTAAAGGAAGAGAGAAAAGTGAACTATTTCTTGGGCTACATTACCAAGATCTAGAGATC +TTTACTACCTTATTACTAAATCTGGAACCTTTATTTAATACTGGAGAATGAAAGGAAGTT +TTATTTTGACTCCATTCGGGATCTCCAGTTTCATGTTTGACTAACAAAGAACTCACCTTA +ATATAAACCAGAATGttagctgggcgtggtggtgtatgcctgtagtcccagctacttggg +aatgggaagctgaggcaggaggattgctggagcccaggaggtggaggctgcggtcgtctg +agatcacactactgcactccagcctggttgacagagcgagaccctgtctcaaaaaaaaaa +aaaagacaagaaaaGATAATTTAAAAAAGATAAACTAGAATGATATATGCACAAGAAGGA +CACCATGAAGCTAGAGTCTTAATCATTTAATAATATTTCTTCCTAAGAATCTGAAAATCA +GGGCAGTTCCAAAAAAGAAAAGGTAGTATGGGCATATGTTTGCTAAGATGAAGGTTTCCA +TTCCCTACAGTCAGTAAACTGAATGAAAACAAGTGTTCACTACTGCAAGTTGAACATATG +TTTATCACGCACTTGTTTTATGCATAGTGCAGCTCATGAGCTCTGAAAGATGAAGGATTT +TTCAAATGTGATTACTGTTATCTCAGAAAAACAAGCCAAGCCTCAAATAGGTATATTTTC +TAGTGTAATCAGTTTGGCTGAGCACTGAAGGGTTATAGGATTTAGATAACCAGTGGGAAT +GAAGTAGGAAGAAAGAATCTGAATGTGGCTTGTTCGGCAGTTGGGAGAAAACAGGGAATT +CTGAACCCATAGAAGTAATTAGGGGATGCATGCTTTTGTCAGATGGTCAAGCATTGCCCT +TAGCTTAGTAAGCGATAGAGAACCAGTAGAGACTCTAAAGTGGAGGAGACTTGATGGAAG +TGATGCTTTAAGGCAGTTAATGTGAAAATAGTGTGTACAGAATGCATTTATAGAAGAAGG +TTGAGGGTAATCCACTACTCCACTAATCCAAGTTATTGTGATGGGCTTCATGTGGGTTAA +TGGGAACTTGTAGTCAAGATTACATATGTTGATTTGAGACTTACCTGCTCAGAGGTGATA +CCTGAAACCAGGGAAGTAAGGTAACTGGAAGAGAGGAGAGTGCTAGTACCAAAGGTCAAC +TTACAAGCCCCTCACACTTAGCTGCAGCCAGACTGGGCAACCAGATAGGAGCTGCACCTG +TGAATTACTTGGTAATTGTTTAGAGAAGCAGAAGGACATTTACAAACTACTCTTGTCCAA +GAAACACAGTGACAGGGGACAGTGGTGTCATATTTCATAAAGTGTTCAGGAAGTGTTTCA +gatttaagtaaaataagtcatttgtgacccactggagtgctgtttcagtaaggtgatgag +ggcaaaagACAAGAAGCATTACTTGGTTTTATGGAAGGACCCTTGGGTTTTAAAAGGATG +GTACTCGTGGTTAATCTTTCAGATGTGATACAGCCTGCATAACAATAAGAGCAACAGTAA +ATGGATAGCAAAGAGGTAGGAAATTAGAATGCATGATGTATTTCAATCTCTGAAGAAGAT +CTTGTGATTAAAAGTTCTTTTTTACTTTTCCTGCACTTTCAAAGTTAAACAAATGATGTA +TTGTACTTCCTAAACTAAACAAACAATAGAGAATAAAGCACAGTAATGACGTTCCACATA +CAAAAAGAGTCTCTATGTCATTTGTATAGTAATGTCTTTGTGGGGTTTTTTTTTTTCTTC +CTAGAACTTGTTCAACTTGATGTTTACCCAGTTCCAAATTATCTGTCCTACATGGATGTT +TCAAGGTAAGAAGTCAAGTCTTAGAGCCCTCTAGAGTCTACTAGAAAATTATTTAGTAAT +TCTGTCTGAGCTTATGCACAAGTACTTTTTAATATTTTGAAGGTAAATGCTAAAAAATTA +ATGATTTTTACTTTATTCTCTAAAATTATATATATCTATTGATTAAAATACATTTGTAGT +TCAAACCAGAGCATCAAAGTGCCTGTGCACACCAATTTGAACACACATTTGGACTTGAAA +GGTGAGTAAGTTGAGGGCCATATGGCTTAAAGCTCTAATAACTCTTTTCATTATATGAAT +CATATTTTTTTGTCTTTCCCTGAAGTAATGTTAATTTTATTTTTTATTTTCAAAATTTTT +TTTCAAACTCTGCCAAGTCTTAGGATGATTTAATTTTTTAAGTGCTTTATTTCTTTGGAT +TTCTTACACCCCTTGTTTAGACATATATCTCTTCGCTAAAAATTCTTAGGAAATAATGAC +AAAGCCTATCAAAATAGAAATTCTCTACAACCTGCTTGGTTTTCTTAGCTCCTTTTTGAA +TATGCTAACTATTTTACCTTTTATGGTAATTTGCTTCTGCAGTGTATTATATTTATTGCG +GTTCCCACAAATATTATAGTAGACTTTTTCTTGAAGGCACAAAGGCTTGACAGTGTCTAC +AGTATGTATTTATACCACGTAAACTTAAAAATTTTTAACAATGAATTTTAAAATTGCaac +tcatttggaaggtaactccaaaggagatacacaaaaatgttctaaacatagggagtttgt +ggcccactcaaggtgacaactgttaactcatttcagggcttaaattctggtgtgtttatt +aacagtcaccatgctttttaatcacaactATTGTATGATTTGTCTTCTACAGAATTTTGC +CTTTTATCTTGAGATTACACAGGCTTAGCTATTTTAATAATCTATTCAATCATAATTATG +CAAGATGTGTCAGTACTTAGCTATTGGGAAAATATTACAGTTAAATTTTTATTgggggag +gagccaagatggccgaataggaacagctccggtctacagctcccagcgtgagcgacgcag +aagacgggtgatttctgcatttccatctgaggtaccgggttcatctcactagggagtgcc +agacagtgggcgcaggccagtgtgtgtgtgcaccatgcgcgagccgaagcagggcgaggc +attgcctcacctgggaagcgcaaggggtcagggagttccctttccgagtcaaagaaaggg +gtgacggacgcacctggaaaatcgggtcactcccacccgaatattgcgcttttcagaccg +gcttaagaaacggcgcaccacgagactatatcccacacctggctcagagggtcctacgcc +cacggaatctcgctgattgctagcacagcagtctgagatcaaactgcaaggcggcaacga +ggctgggggaggggcgcccgccattgcccaggcttgcttaggtaaacaaagcagccggga +agctcgaactgggtggagcccaccacagctcaaggaggcctgcctgcctctgtaggctcc +acctctgggggcagggcacagacaaacaaaaagacagcagtaacctctgcagacttaagt +gtccctgtctgacagctttgaagagagcagtggttctcccagcacgcagctggagatctg +agaacgggcagactgcctcctcaagtgggtccctgacacctgacccccgagcagcctaac +tgggaggcaccccccagcaggggcacactgacacctcacacggcagggtattccaacaga +cctgcagctgagggtcctgtctgttagaaggaaaactaacaaccagaaaggacatctaca +ccgaaaacccatctgtacatcaccatcatcaaagaccaaaagtagataaaaccacaaaga +tggggaaaaaacagaacagaaaaactggaaactctaaaacgcagagcgcctctcctcctc +caaaggaacgcagttcctcaccagcaacagaacaaagctggatggagaatgattttgacg +agctgagagaagaaggcttcagacgatcaaattactctgagctacgggaggacattcaaa +ccaaaggcaaagaagttgaaaactttgaaaaaaatttagaagaatgtataactagaataa +ccaatacagagaagtgcttaaaggagctgatggagctgaaaaccaaggctcgagaactac +gtgaagaatgcagaagcctcaggagccgatgcgatcaactggaagaaagggtatcagcaa +tggaagatgaaatgaagcgagaagggaagtttagagaaaaaagaataaaaagaaatgagc +aaagcctccaagaaatatgggactatgtgaaaagaccaaatctacgtctgattggtgtac +ctgaaagtgatgtggagaatggaaccaagttggaaaacactctgcaggatattatccagg +agaacttccccaatctagcaaggcaggccaacgttcagattcaggaaatacagagaacgc +cacaaagatactcctcgagaagagcaactccaagacacataattgtcagattcaccaaag +ttgaaatgaaggaaaaaatgttaagggcagccagagagaaaggtcgggttaccctcaaag +gaaagcccatcagactaacagcggatctctcggcagaaaccctacaagccagaagagagt +gggggccaatattcaacattcttaaagaaaagaattttcaaaccagaatttcatatccag +ccaaactaagcttcataagtgaaggagaaataaaatactttatagacaagcaaatgctga +gagattttgtcaccaccaggcctgccctaaaagagctcctgaaggaagcgctaaacatgg +aaaggaacaaccggtaccagccgctgcaaaatcatgccaaaatgtaaagaccatcgagac +taggaagaaactgcatcaactaatgagcaaaatcaccagctaacatcataatgacaggat +caaattcacacataacaatattaactttaaatgtaaatggactaaattctgcaattaaaa +gacacagactggcaagttggataaagagtcaagacccatcagtgtgctgtattcaggaaa +cccatctcacgtgcagagacacacataggctcaaaataaaaggatggaggaagatctacc +aagccaatggaaaacaaaaaaaggcaggggttgcaatcctagtctctgataaaacagact +ttaaaccaacaaagatcaaaagagacaaagaaggccattacataatggtaaagggatcaa +tccaacaagaggagctaactatcctaaatatttatgcacccaatacaggagcacccagat +tcataaagcaagtcctgagtgacctacaaagagacttagactcccacacattaataatgg +gagactttaacaccccactgtcaacattagacagatcaatgagacagaaagtcaacaagg +atacccaggaattgaactcagctctgcaccaagcagacctaatagacatctacagaactc +tccaccccaaatcaacagaatatacatttttttcagcaccacaccacacctattccaaaa +ttgaccacatagttggaagtaaagctctcctcagcaaatgtaaaagaacagaaattataa +caaactatctctcagaccacagtgcaatcaaactagaactcaggattaagaatctcactc +aaagccgctcaactacatggaaactgaacaacctgctcctgaatgactactgggtacgta +acgaaatgaaggcagaaataaagatgttctttgaaaccaacgagaacaaagacaccacat +accagaatctctgggacgcattcaaagcagtgtgtagagggaaatttatagcactaaatg +cctacaagagaaagcaggaaagatccaaaattgacaccctaacatcacaattaaaagaac +tagaaaagcaagagcaaacacattcaaaagctagcagaaggcaagaaataactaaaatca +gagcagaactgaaggaaatagagacacaaaaaacccttcaaaaaatcaatgaatccagga +gctggttttttgaaaggatcaacaaaattgatagaccgctagcaagactaataaagaaaa +aaagagagaagaatcaaatagacacaataaaaaatgataaaggggatatcaccaccgatc +ccacagaaatacaaactaccatcagagaatactacaaacacctctacgcaaataaactag +aaaagctagaagaaatggatacattcctcgacacatacactctcccaagactaaaccagg +aagaagttgaatctctgaatagaccaataacaggctctgaaattgtggcaataatcaata +gtttaccaaccaaaaagagtccaggaccagatggattcacagccgaattctaccagaggt +acaaggaggaactggtaccattccttctgaaactattccaatcaatagaaaaagagggaa +tcctccctaactcattttatgaggccagcatcattctgataccaaagccgggcagagaca +caaccaaaaaagagaattttagaccaatatccttgatgaacattgacgcaaaaatcctca +ataaaatactggcaaaccgaatccagcagcacatcaaaaagcttatccaccatgatcaag +tgggcttcatccctgggatgcaaggctggttcaatatatgc
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/one.fastq Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,100 @@ +@HWI-ST584:365:C37MVACXX:1:1305:19372:56141 1:N:0:GCCAAT +CTCGTATACCCTTGACCGAAGACCGGTCCTCCTCTATCGGGGATGGTCGTCCTCTTCGACCGAGCGCGCAGCTTCGGGAGGGACGCACATGGAGCGGTGAG ++ +CCCFFFFFHHHHHHJJIJJJIIIJJIJJIJJGGJJFJJHIJJGBHFCCBFDDDEDDDBABDDDDDDDDDDDDDDD@@B@BBB@BD@BDBDDDCDCBD@BDD +@HWI-ST584:365:C37MVACXX:1:2301:7296:160148 1:N:0:GCCAAT +CTGGGATATAAGACTCCTACCTCGGCCTCCTAATGAAGGCTGAGACGATTGGTACACAGCTCCAGCGTGGTGTCAGGCACACAACAGGTGCTCTCCCTAAG ++ +@CCFFFFFHGHHHJJJJIJIIIJIGGIJJJJJJJIIJJJJJJJJEGIJIJJJJIIIJJJIJJIIIHHCFF=BBCEDDCBDDDDDDDDD@CCDDDDDDDDDD +@HWI-ST584:365:C37MVACXX:1:1205:13370:110105 1:N:0:GCCAAT +CCTGAACTTAGGCTTGCTCTGCAGAAGAGGACCCAGACCGAAGCTGGATAACGCTGGTGCATGCCTCCCTGGCTCCCTTGGCTTTTTTTGGTCACAGGGCC ++ +@@?DADDDHHHFHGIBG<FHGI>FHGFEG?DGHDBC;6?GIHGG@FA@FGHG?HEHA?DDDCCCCCE?@C>;=?A88<@?CCCBCCC@B>BCCCCCCBC?B +@HWI-ST584:365:C37MVACXX:1:2308:12673:6166 1:N:0:GCCAAT +CATAAATGTGTGCACGAGTTACTTTATATGCATTATGAATTTGTTGAAAGAACAATTTCAAAACTGATGATTACCTCTGGCCTCATTCTCACATGCCACTA ++ +BCCFFFFFHHHHGJJJIIHIHIJJJJJGJJIIJJJJIJJJJJJJJJJIJJJJIJJJIJIJJGIJJJJJJJIJJJJCHIIHGHHHFFFFFFFEEEEDEDDDD +@HWI-ST584:365:C37MVACXX:1:2207:7253:147412 1:N:0:GCCAAT +NCTGTTTCCATCTGGGGGCCTCAGGAGTATCTGGGTTCTCCTCCAACAGCTCTGTCAATTTGTCTTTCAACTCCTGTACTTTGTTTACATTCTGCTTCAGT ++ +#1BDDFFFHHHHHJJJIJJJJJJJJJJFGIJJJJJGHIIJJIJJJJJIIJJJJJIJJJJJHHHHHHHFFFFFFEECEEEFFEDDDDDDDEEDEEDDDDDDF +@HWI-ST584:365:C37MVACXX:1:2308:14918:56009 1:N:0:GCCAAT +GCAGTCTTTGGAGAAGAAATATTCTAAACATTTAAGCAAGGAGGAGGCTTCCTAAACTGCATTTTTGTTTCTTATCTCACCATTTTTGTGGTGTGTTTCAC ++ +CCCFFFFFHHHHHIJJJJJIJJJJJJJJJIIJJJJJIJJJJIJIJJJJIJJJJJJJJJJHIIJJJJJJIJHHHHHHHFFFFFFEEEEDDDDCDDDDDDDED +@HWI-ST584:365:C37MVACXX:1:1201:11510:45354 1:N:0:GCCAAT +GTAGTTTTGAGAAATTTTCCACAATTGTCCTCTGAGCAACTACTATACTTCCAAATCTTACTTTCCCTCGGATTAAGAAATAGAGAATGCAGAGGATCTTG ++ +@@@FBDFFHDHHHGHGIIGIJJIJIJHHIIHGIEEHIJJJJIHIJJJIJIIGECGIIJEBGHIIJCGFHAB@EEEE=??CEED@@CEDDEEDDBBB;:CDD +@HWI-ST584:365:C37MVACXX:1:2108:4159:38107 1:N:0:GCCAAT +GTCAAAAAATAGGGTCAACTGTGTTAGACTAAATTACATTATTGTATATGCTGCACTGAATGGAACCTTTGTATTGTAATTATCATAGAGAAGCACAGTTT ++ +?::A???=DD?D<E+AB:FEDA4C@??E?@C>DDCCDE<?DDDDDEADEDEC<BDEBDCDEICACDDCACD=@CC=7?=:;CDA;@;ADAAAAAA??=A;> +@HWI-ST584:365:C37MVACXX:1:1203:20582:36223 1:N:0:GCCAAT +GCCACCTTTCATTTTCCTTGCATTGGACACACCTACAGGGCTTCGCTGCACCGACATCTGAGGCAACATCCCATCATGCAGCCAACTTAACTGCACTACCA ++ +@@@FDDEFGFDFFI>EHGEGGHGI@HEHHCGGGGEIHIFIHHEHBFHHDEIGIBGGBAHFFEB?BDA@ACCBCCC;>@ACCCBBCCCCCC@ACCCCC@?AC +@HWI-ST584:365:C37MVACXX:1:1307:2892:120144 1:N:0:GCCAAT +GGCTGCTGTTTGAGGTTTATTTTGTTCTTATTCTTTGGAAGATATTCCTTAAGGCTTCCCGAAGGCAGAAATTCCATGATGAGCTTAATACCATTTCCTCC ++ +?@@DDDDFHHHHFGHBHGIIIIJJIIGGGEHIEGGIJIEEFGGIHGIIJJIJIDFIIIJJI>BBEHHJFHHEEHH;A@?CEDEEEEEE@@A>5>>CD>ACA +@HWI-ST584:365:C37MVACXX:1:1305:12954:25279 1:N:0:GCCAAT +GGGAATGCTGACTCGGCAGGTCAAGGCCTTGTGGCTGGTGGCCCCATCGGGGCCCTTTGTCTCATGAAGGTTTAGCACTTCTCCTTTCCCCCGCCAACTGT ++ +CCCFFFFFHHHHHJIJJJIJACFFFH?D>GF1CGGC################################################################# +@HWI-ST584:365:C37MVACXX:1:2304:18056:150403 1:N:0:GCCAAT +CATTGAACAGTTTTTTCCTCTTGAAAGGGTAATTTTAGAGGATATTATTTTTTAAGTCACTAAAGATAGTTTTGCTTACAGAGAAATTTGTTTAAAAGGGG ++ +@CCFFFFFGHHHHJJJJJJJJJIIJJJJJ?GHIJJJIIIJJJJIIIJJJJJJJJJJJJJJJJJJJJJHHHHHHHFEFFFFEEEEEDDDDDEDDDDDDDDDB +@HWI-ST584:365:C37MVACXX:1:1102:1484:117821 1:N:0:GCCAAT +CCCTATTATCTATAGTTATCTCATTAAAACTGGATCTGGTTATAACATATAAAGGGCTGGATAGACCATTTTAAAAATAAAATCTATTTACTGCAAATGAA ++ +@@@DADDDFHHHHEH:CFHEHGEHGGEGIIIIGBHCHICGHEHIIIIIGIIFBEAHIGHIFHEIBFBBFHAFFGA@DHHIFCEEHFCEEDEBBCCCCC@C< +@HWI-ST584:365:C37MVACXX:1:2107:13215:154024 1:N:0:GCCAAT +ATTCATTACTCAGAACAAACCTAAAAAAAAAATAAAACCCTTTTGAAATTTAAGCAATGACTCATAAGAGATTGGAATTGGACTCAAATTACTGGCTTAAT ++ +CCCADFFFHGHHGJJJJJIJJJJJJJJJJJJIJJJJJIJGHIJJJIHHHHFHC@CDDECDEEECDDDDDDDDDDDCDCDDDDDDCCDCCCDCCDD@CDDDD +@HWI-ST584:365:C37MVACXX:1:2305:14375:146794 1:N:0:GCCAAT +CTTTTTTATGTTCAAGTCTTTCTTTTTGCAAGGATTTCTCTAATCTTGATCTGTGTTCATATACAACTTGTAACTGGGCGGAGAGGGACTCCTGGTGCTGC ++ +BBCFFFFFHHHHHJJJIJIJJIJJJJJJJJJJJIJJJJJJJJJJJJJJJJJJJIJIIJJJIJJJJJJIJJIJIJIHJHHGDBDBDDDDDDDDDDDDDDCDD +@HWI-ST584:365:C37MVACXX:1:2102:21132:28209 1:N:0:GCCAAT +CAGAAAGTGGGCCATTCATCTGAACCAAGTTCAGAGAATTTCCAGCACGGTGAAAAGATATGTTATGCAAGCACATAGATGTATTCAGTGGGGGTAGACAG ++ +CCCFFFFDHGHHHIJJJIJIJJIJJJJIJEHIJIFHIIGJJJFIJGHJJJFFGGEGGIIJJJEHIJJJFGIHHHFHBDFFFDFEDEDECCDDDB9@DDDDD +@HWI-ST584:365:C37MVACXX:1:1203:3094:151750 1:N:0:GCCAAT +GTTCGATAAGGTGTGAGGAGGAAGCAAAGGCTTTCCCACACTCCTTACATATGTAGGGTTTCTCACCGGTGTGGGTTCTTATGTGCACGATAAGGTGTGAG ++ +C@CFFFFFHHHDFCFHIJIJIGGGIIJJJJJJJJJJJGJGIIJIIIJJIIIJJHIJJJCGGIJJIJJHH=BBDDD;?BDDDDDFEDDDDDDDDDD>A@BCC +@HWI-ST584:365:C37MVACXX:1:1102:15558:4133 1:N:0:GCCAAT +AGAAAGGATATTCCAGTTTTTTTCCTTACCATTTAAAATATCAATAACTACCAAGATCACTCCTTCTGTCCAGAACAGTAAAACCTTGAGACTCCATGGTA ++ +CCCFFFFFHHHHHJJJIIJJJJJIJJJJJIIJJJJJIJIGIJJJIJJJJJJJJJJJIJJJJJJJJJJJIHGHHHFDFFFFEEEEDDDDDDDDDDDDDDDCC +@HWI-ST584:365:C37MVACXX:1:1306:11209:39712 1:N:0:GCCAAT +GGGCCATCAGGTTTCTCTTCTGTTAAATGTTTTAATCCATATTTTGAATCCACAATAGTTATGATACCATCAAGATAAATATCACTCCCTAATTCAGCATC ++ +CCCFFFFFHHHCFHIJJJJGIIHICIIJJFHIJJJJEGIIGIIJJIIGGHIIJJIJJGEIIJJJJIGHIJJJJJGGE=@@CHIAHFHCEFFFFFEDEEEED +@HWI-ST584:365:C37MVACXX:1:1108:5887:31082 1:N:0:GCCAAT +CGTGGAGGGTGGCGGGGCTCCTGGCCTCGTCTGGGTGAGGTTGGGAGCCTCGCTGGGGCTGCGGTCCCAGAGCTTCGGCAAAGCCACCAGGCCTTGGGGAG ++ +@@=DDDDFH<CFHIGGDIEFH@BBEFFCBBD?BCC5;?ADAACDD@DDBDDBDDDDBDDDDDDDBBDBCDDDDDD:<@BBB<>?A<AABBDDDDDDDDDB> +@HWI-ST584:365:C37MVACXX:1:1105:7280:52404 1:N:0:GCCAAT +ACGGGCTTAAAAAACGGCACACCAGGAGATTATATCCCGCACGTGGCTCAGAGGGTCCAACACCCACAGAGTCTCGTTGACTGCTAGCACAGCAGTCTGAG ++ +CCCFFFFFHGHDHIIHIIIHIJFIHIFGDGHGIIJJJJJJFIIHHHFFFFFEDDD?ABCDDDBDDDDBBACA>CDA?BCBCCDDDDDDDD?CDCBACDCCC +@HWI-ST584:365:C37MVACXX:1:1304:18748:121360 1:N:0:GCCAAT +GTGCAGGACAGTGGGTGCAGTGCACCGAGCGTGAGCCGAAGCAGGGCAAGGCATCACCTCCCCCGGGAAGTACAAGGGGTGAGGGAATTCCCTTTCCTAGC ++ +C@BFFFFFHHHFHJJGHGJJHHIJJJJIJIIFHGIIJJJDIIIGII<EHFFFFEDEEDEDDDDDDDDDDDCCCCCCBDD9>?BDDDDDCDDDDDDDDDDDD +@HWI-ST584:365:C37MVACXX:1:2308:16415:46106 1:N:0:GCCAAT +CGGCTATGGAGAAAAGGTAATTCATATATACTGCTGGTGGGAATGTAAATTAGTTCAGCCACTGTGGAAAGCAGTTTGGAGATTTCTCAAAGAACTGAAAA ++ +@@@FFFFFGHHBFG@GGHIIIGHI?AA?FH>BBFH>FEFIGIGGH?DDFGGGHBFFGDHGHGGGFGIIIGIIEHEACAEDEDFDECDCEEECCBCCCCCC> +@HWI-ST584:365:C37MVACXX:1:2207:3186:50907 1:N:0:GCCAAT +NCCCTACCCAGGCCAGGCATTTGCCAGATGCTTAATAAATACTTTTTGAGTTAATGCTACAATGCATCACTGGACATCTTTTAAAAGTAATATTCTTTTGG ++ +#1:BDDDDGHFHHGIGBEFC>HHGHGH>DFHGGIGEFEHCHGHGIIIIGH?DFFHIIIIIIIEDEHGH=@@D?CCEHFDDCEFBECCCCC@DDDDCDCCC# +@HWI-ST584:365:C37MVACXX:1:2307:4484:32118 1:N:0:GCCAAT +GCTTCGGCTCGCGCATGGTGCACACACACACTGGCCTGCGCCCACTGTCTGGCACTCCCTAGTGAGATGAACCCGGTACCTCAGATGGAAATGCAGAAATC ++ +@<@DDDDDFD@DD<<CF<FCEFHIEEG?H?FHGG?CFCCABBE<=6);;>36((;;-;?C39@C@C@>:>:(85<-)95>>CCCCC@C?############
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/refseq-small.txt Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,89 @@ +#bin name chrom strand txStart txEnd cdsStart cdsEnd exonCount exonStarts exonEnds score name2 cdsStartStat cdsEndStat exonFrames +10 NR_125367.1 chr17 + 10286448 10528857 10528857 10528857 11 10286448,10309464,10470853,10491705,10493959,10501389,10511461,10511670,10515775,10517061,10526068, 10286524,10309555,10470929,10491740,10494092,10501539,10511540,10511932,10515891,10517194,10528857, 0 MYHAS none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, +10 NM_001372.3 chr17 + 11501747 11873065 11501815 11872844 69 11501747,11511445,11513712,11514966,11520727,11522864,11532733,11535903,11539950,11543586,11547947,11550388,11554385,11556077,11568149,11572380,11572686,11583073,11584039,11592882,11597184,11597637,11603047,11604438,11607519,11608341,11622650,11631134,11642196,11645491,11648113,11650872,11656149,11659884,11660861,11666756,11671769,11672438,11684325,11686962,11687616,11696819,11700913,11711048,11713562,11725236,11725754,11726117,11737954,11757319,11772450,11774914,11778265,11783394,11784525,11786902,11790141,11795093,11797690,11806035,11808977,11827130,11833182,11835330,11837196,11840668,11845619,11865183,11872616, 11502232,11511642,11513871,11515097,11520939,11523098,11532901,11536020,11540101,11543701,11548016,11550515,11554641,11556319,11568285,11572577,11573111,11583296,11584206,11593753,11597315,11597764,11603200,11604564,11607759,11608502,11622807,11631239,11642354,11645630,11648401,11651083,11656277,11659993,11661009,11666931,11671943,11672646,11684491,11687065,11687856,11696981,11701110,11711211,11713686,11725379,11725916,11726351,11738215,11757745,11772570,11775103,11778501,11783517,11784730,11787067,11790282,11795264,11797813,11806229,11809126,11827258,11833410,11835522,11837388,11840839,11845802,11865573,11873065, 0 DNAH9 cmpl cmpl 0,0,2,2,1,0,0,0,0,1,2,2,0,1,0,1,0,2,0,2,0,2,0,0,0,0,2,0,0,2,0,0,1,0,1,2,0,0,1,2,0,0,0,2,0,1,0,0,0,0,0,0,0,2,2,0,0,0,0,0,2,1,0,0,0,0,0,0,0, +10 NM_153604.3 chr17 + 12569206 12672266 12569505 12666961 13 12569206,12608444,12618835,12620662,12626163,12639477,12642519,12647499,12649235,12655730,12661401,12663966,12666389, 12569560,12608510,12618891,12620738,12626325,12639653,12642645,12647753,12649389,12656663,12661530,12664024,12672266, 0 MYOCD cmpl cmpl 0,1,1,0,1,1,0,0,2,0,0,0,1, +10 NM_001146312.2 chr17 + 12569206 12672266 12569505 12666961 14 12569206,12608444,12618835,12620662,12626163,12639477,12642519,12647499,12649235,12655730,12659730,12661401,12663966,12666389, 12569560,12608510,12618891,12620738,12626325,12639653,12642645,12647753,12649389,12656663,12659874,12661530,12664024,12672266, 0 MYOCD cmpl cmpl 0,1,1,0,1,1,0,0,2,0,0,0,0,1, +10 NR_104605.1 chr17 - 12575178 12609452 12609452 12609452 3 12575178,12608250,12608689, 12575508,12608300,12609452, 0 LOC101928418 none none -1,-1,-1, +82 NM_201433.1 chr17 - 9813925 10101868 9820544 10101707 14 9813925,9821317,9822942,9828792,9829957,9837482,9843442,9846437,9850210,9862518,9872993,9885120,9923093,10101524, 9820658,9821416,9823022,9828916,9830086,9837561,9843517,9846553,9850300,9862572,9873079,9885201,9923214,10101868, 0 GAS7 cmpl cmpl 0,0,1,0,0,2,2,0,0,0,1,1,0,0, +82 NM_003802.2 chr17 - 10204182 10276322 10204267 10267847 41 10204182,10204885,10206512,10206710,10209775,10210255,10212550,10212838,10214419,10215227,10215890,10216474,10219009,10219215,10222106,10223469,10223667,10224848,10227338,10231182,10233703,10235415,10236390,10243466,10243644,10247116,10248518,10248783,10249996,10253872,10257996,10258211,10258400,10261051,10263276,10263477,10265434,10265676,10267643,10274525,10276295, 10204282,10205020,10206608,10206815,10209946,10210381,10212754,10213147,10214544,10215393,10216074,10216671,10219128,10219342,10222496,10223560,10223813,10225025,10227581,10231438,10233840,10235539,10236508,10243554,10243718,10247426,10248689,10248933,10250115,10254011,10258100,10258310,10258464,10261144,10263388,10263505,10265591,10265820,10267859,10274576,10276322, 0 MYH13 cmpl cmpl 0,0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +82 NM_017533.2 chr17 - 10346606 10372876 10346691 10370062 40 10346606,10347920,10348111,10348292,10348553,10350329,10351134,10351712,10351934,10352180,10353769,10354093,10354642,10355257,10355732,10356103,10356468,10356959,10357871,10358257,10358488,10358930,10359130,10359801,10360736,10362567,10363268,10363519,10364232,10366181,10366406,10366654,10366867,10367788,10367997,10368758,10369589,10369858,10372604,10372853, 10346844,10348016,10348216,10348463,10348679,10350533,10351443,10351837,10352100,10352364,10353966,10354212,10354769,10355647,10355823,10356249,10356645,10357202,10358127,10358394,10358612,10359048,10359218,10359872,10361046,10362738,10363418,10363638,10364371,10366285,10366505,10366718,10366960,10367903,10368025,10368915,10369733,10370101,10372653,10372876, 0 MYH4 cmpl cmpl 0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +83 NM_001330139.1 chr17 - 10616611 10633646 10618769 10633168 5 10616611,10626586,10628327,10629520,10633096, 10618905,10626646,10628451,10629581,10633646, 0 TMEM220 cmpl cmpl 2,2,1,0,0, +83 NM_001330140.1 chr17 - 10616611 10633646 10618769 10633168 4 10616611,10628327,10629520,10633096, 10618905,10628451,10629581,10633646, 0 TMEM220 cmpl cmpl 2,1,0,0, +83 NM_001004313.1 chr17 - 10616638 10633646 10618769 10633168 6 10616638,10626586,10628327,10629520,10632347,10633096, 10618905,10626646,10628451,10629581,10632377,10633646, 0 TMEM220 cmpl cmpl 2,2,1,0,0,0, +83 NM_001173461.1 chr17 + 11144739 11467380 11144739 11461621 4 11144739,11166682,11459056,11461070, 11145377,11166843,11459209,11467380, 0 SHISA6 cmpl cmpl 0,2,1,1, +83 NM_001173462.1 chr17 + 11144739 11467380 11144739 11461621 5 11144739,11166682,11282730,11459056,11461070, 11145377,11166843,11282826,11459209,11467380, 0 SHISA6 cmpl cmpl 0,2,1,1,1, +83 NM_207386.3 chr17 + 11144739 11467380 11144739 11461621 6 11144739,11166682,11282730,11455212,11459056,11461070, 11145377,11166843,11282826,11455269,11459209,11467380, 0 SHISA6 cmpl cmpl 0,2,1,1,1,1, +84 NM_004662.2 chr17 + 11786218 11873065 11790234 11872844 15 11786218,11786902,11790141,11795093,11797690,11806035,11808977,11827130,11833182,11835330,11837196,11840668,11845619,11865183,11872616, 11786489,11787067,11790282,11795264,11797813,11806229,11809126,11827258,11833410,11835522,11837388,11840839,11845802,11865573,11873065, 0 DNAH9 cmpl cmpl -1,-1,0,0,0,0,2,1,0,0,0,0,0,0,0, +84 NM_003010.3 chr17 + 11924134 12047148 11924203 12044577 11 11924134,11958205,11984672,11998891,12011106,12013691,12016549,12028610,12032455,12043155,12044463, 11924318,11958308,11984847,11999011,12011226,12013743,12016677,12028688,12032604,12043201,12047148, 0 MAP2K4 cmpl cmpl 0,1,2,0,0,0,1,0,0,2,0, +84 NM_001281435.1 chr17 + 11924134 12047148 11924203 12044577 12 11924134,11935582,11958205,11984672,11998891,12011106,12013691,12016549,12028610,12032455,12043155,12044463, 11924318,11935615,11958308,11984847,11999011,12011226,12013743,12016677,12028688,12032604,12043201,12047148, 0 MAP2K4 cmpl cmpl 0,1,1,2,0,0,0,1,0,0,2,0, +85 NM_001321168.1 chr17 + 12692828 12894961 12844390 12890425 20 12692828,12798256,12799723,12812213,12819216,12823071,12844372,12846904,12847385,12852456,12852965,12855817,12859183,12859971,12862033,12877405,12883374,12887847,12890417,12893348, 12693208,12798296,12799828,12812290,12819328,12823148,12844441,12846986,12847513,12852568,12853047,12855898,12859297,12860063,12862214,12877627,12883550,12888225,12890469,12894961, 0 ARHGAP44 cmpl cmpl -1,-1,-1,-1,-1,-1,0,0,1,0,1,2,2,2,1,2,2,1,1,-1, +85 NR_135569.1 chr17 + 12692828 12894961 12894961 12894961 18 12692828,12798256,12799723,12812213,12819216,12823071,12832245,12844372,12846904,12847385,12852456,12852965,12855817,12859183,12859971,12862033,12887847,12893348, 12693208,12798296,12799828,12812290,12819328,12823148,12832363,12844441,12846986,12847513,12852568,12853047,12855898,12859297,12860063,12862214,12888225,12894961, 0 ARHGAP44 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, +85 NM_001321166.1 chr17 + 12692828 12894961 12693155 12893488 20 12692828,12798256,12799723,12812213,12819216,12823071,12832245,12844372,12846904,12847385,12852456,12852965,12855817,12859183,12859971,12862033,12877405,12883374,12887847,12893348, 12693208,12798296,12799828,12812290,12819328,12823148,12832363,12844441,12846986,12847513,12852568,12853047,12855898,12859297,12860063,12862214,12877627,12883550,12888225,12894961, 0 ARHGAP44 cmpl cmpl 0,2,0,0,2,0,2,0,0,1,0,1,2,2,2,1,2,2,1,1, +85 NM_001321164.1 chr17 + 12692828 12894961 12693155 12890425 21 12692828,12798256,12799723,12812213,12819216,12823071,12832245,12844372,12846904,12847385,12852456,12852965,12855817,12859183,12859971,12862033,12877405,12883374,12887847,12890417,12893348, 12693208,12798296,12799828,12812290,12819328,12823148,12832363,12844441,12846986,12847513,12852568,12853047,12855898,12859297,12860063,12862214,12877627,12883550,12888225,12890469,12894961, 0 ARHGAP44 cmpl cmpl 0,2,0,0,2,0,2,0,0,1,0,1,2,2,2,1,2,2,1,1,-1, +85 NM_014859.5 chr17 + 12692828 12894961 12693155 12893488 21 12692828,12798256,12799723,12812213,12819216,12823071,12832245,12844372,12846904,12847385,12852456,12852965,12855817,12859183,12859971,12862033,12876618,12877405,12883374,12887847,12893348, 12693208,12798296,12799828,12812290,12819328,12823148,12832363,12844441,12846986,12847513,12852568,12853047,12855898,12859297,12860063,12862214,12876636,12877627,12883550,12888225,12894961, 0 ARHGAP44 cmpl cmpl 0,2,0,0,2,0,2,0,0,1,0,1,2,2,2,1,2,2,2,1,1, +85 NM_001321167.1 chr17 + 12692828 12894961 12693155 12890425 22 12692828,12798256,12799723,12812213,12819216,12823071,12832245,12844372,12846904,12847385,12852456,12852965,12855817,12859183,12859971,12862033,12876618,12877405,12883374,12887847,12890417,12893348, 12693208,12798296,12799828,12812290,12819328,12823148,12832363,12844441,12846986,12847513,12852568,12853047,12855898,12859297,12860063,12862214,12876636,12877627,12883550,12888225,12890469,12894961, 0 ARHGAP44 cmpl cmpl 0,2,0,0,2,0,2,0,0,1,0,1,2,2,2,1,2,2,2,1,1,-1, +85 NM_006042.2 chr17 - 13397348 13505259 13399513 13504446 2 13397348,13503847, 13400135,13505259, 0 HS3ST3A1 cmpl cmpl 2,0, +663 NM_002472.2 chr17 - 10293641 10325267 10293770 10323544 40 10293641,10295198,10295858,10296147,10296401,10297565,10298449,10299646,10299869,10300119,10301760,10302084,10302859,10303706,10304185,10304362,10304591,10304859,10307646,10309357,10309590,10310006,10310208,10312413,10312595,10314093,10315686,10315926,10317218,10317508,10317702,10318432,10318608,10318788,10318997,10321961,10322203,10323334,10324979,10325246, 10293920,10295294,10295963,10296318,10296527,10297769,10298758,10299771,10300035,10300303,10301957,10302203,10302986,10304096,10304276,10304508,10304768,10305102,10307902,10309494,10309714,10310124,10310296,10312481,10312905,10314264,10315836,10316045,10317357,10317612,10317801,10318496,10318701,10318897,10319025,10322118,10322347,10323574,10325023,10325267, 0 MYH8 cmpl cmpl 0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +664 NM_005963.3 chr17 - 10395623 10421859 10395732 10419959 40 10395623,10397670,10397885,10398247,10398508,10399266,10399557,10400385,10400603,10401050,10401942,10402290,10403942,10404426,10404910,10405082,10406054,10406322,10408126,10408479,10408704,10409128,10409328,10411202,10411679,10412801,10415155,10415390,10415724,10415997,10416183,10416942,10417137,10417326,10418184,10419242,10419515,10419755,10421556,10421836, 10395885,10397766,10397990,10398418,10398634,10399470,10399866,10400510,10400769,10401234,10402139,10402409,10404069,10404816,10405001,10405228,10406231,10406565,10408382,10408616,10408828,10409246,10409416,10411273,10411989,10412972,10415305,10415509,10415863,10416101,10416282,10417006,10417230,10417441,10418212,10419399,10419659,10419999,10421587,10421859, 0 MYH1 cmpl cmpl 0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +664 NM_001100112.1 chr17 - 10424464 10452940 10424596 10451237 40 10424464,10426406,10426624,10426812,10427075,10427782,10428073,10428540,10428767,10429009,10429915,10430254,10431064,10432006,10432478,10432652,10432880,10433148,10434949,10436601,10436825,10438389,10438594,10439846,10440549,10440981,10442521,10442760,10443244,10443910,10446191,10446414,10447027,10447218,10447416,10448662,10450791,10451033,10452691,10452875, 10424749,10426502,10426729,10426983,10427201,10427986,10428382,10428665,10428933,10429193,10430112,10430373,10431191,10432396,10432569,10432798,10433057,10433391,10435205,10436738,10436949,10438507,10438682,10439923,10440859,10441152,10442671,10442879,10443383,10444014,10446290,10446478,10447120,10447333,10447444,10448819,10450935,10451257,10452734,10452940, 0 MYH2 cmpl cmpl 0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +664 NM_017534.5 chr17 - 10424464 10453017 10424596 10451237 40 10424464,10426406,10426624,10426812,10427075,10427782,10428073,10428540,10428767,10429009,10429915,10430254,10431064,10432006,10432478,10432652,10432880,10433148,10434949,10436601,10436825,10438389,10438594,10439846,10440549,10440981,10442521,10442760,10443244,10443910,10446191,10446414,10447027,10447218,10447416,10448662,10450791,10451033,10452691,10452952, 10424749,10426502,10426729,10426983,10427201,10427986,10428382,10428665,10428933,10429193,10430112,10430373,10431191,10432396,10432569,10432798,10433057,10433391,10435205,10436738,10436949,10438507,10438682,10439923,10440859,10441152,10442671,10442879,10443383,10444014,10446290,10446478,10447120,10447333,10447444,10448819,10450935,10451257,10452734,10453017, 0 MYH2 cmpl cmpl 0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +665 NM_002470.3 chr17 - 10531842 10560626 10531969 10558381 41 10531842,10532913,10533158,10533408,10533604,10534927,10535129,10535792,10536907,10537333,10538156,10538683,10539051,10541125,10541359,10542189,10542360,10542614,10542876,10543312,10543649,10543879,10544401,10544601,10545556,10545733,10546142,10547667,10547900,10549023,10549245,10550498,10550679,10551873,10552893,10553690,10554828,10555736,10558177,10559406,10560605, 10531996,10533051,10533254,10533513,10533775,10535053,10535333,10536101,10537032,10537499,10538340,10538880,10539170,10541252,10541749,10542280,10542506,10542791,10543119,10543568,10543786,10544003,10544519,10544689,10545627,10546040,10546313,10547817,10548019,10549162,10549349,10550597,10550743,10551966,10553002,10553718,10554985,10555880,10558389,10559465,10560626, 0 MYH3 cmpl cmpl 0,0,0,0,0,0,0,0,1,0,2,0,1,0,0,2,0,0,0,2,0,2,1,0,1,0,0,0,1,0,1,1,0,0,2,1,0,0,0,-1,-1, +665 NM_004589.3 chr17 - 10583648 10600885 10584435 10600824 6 10583648,10590043,10595188,10596080,10599057,10600551, 10584570,10590159,10595281,10596278,10599148,10600885, 0 SCO1 cmpl cmpl 0,1,1,1,0,0, +665 NM_020233.4 chr17 + 10600926 10614875 10608243 10614461 4 10600926,10608226,10609754,10614150, 10600984,10608844,10609871,10614875, 0 ADPRM cmpl cmpl -1,0,1,1, +666 NR_049723.1 chr17 - 10619259 10619899 10619899 10619899 1 10619259, 10619899, 0 MAGOH2P none none -1, +666 NR_073456.1 chr17 + 10633093 10670369 10670369 10670369 4 10633093,10639921,10657545,10669995, 10633193,10639955,10657679,10670369, 0 TMEM220-AS1 none none -1,-1,-1,-1, +666 NR_073455.1 chr17 + 10633093 10670369 10670369 10670369 5 10633093,10637155,10639918,10657545,10669995, 10633217,10637224,10639955,10657679,10670369, 0 TMEM220-AS1 none none -1,-1,-1,-1,-1, +666 NR_073457.1 chr17 + 10633093 10671347 10671347 10671347 4 10633093,10657545,10669995,10671181, 10633217,10657679,10670173,10671347, 0 TMEM220-AS1 none none -1,-1,-1,-1, +666 NR_073458.1 chr17 + 10633093 10718481 10718481 10718481 4 10633093,10705715,10709479,10718215, 10633217,10705825,10709559,10718481, 0 TMEM220-AS1 none none -1,-1,-1,-1, +666 NR_036581.1 chr17 - 10698229 10707416 10707416 10707416 2 10698229,10706922, 10699265,10707416, 0 LINC00675 none none -1,-1, +666 NM_001101387.1 chr17 - 10725791 10741418 10728548 10728962 2 10725791,10741261, 10729100,10741418, 0 PIRT cmpl cmpl 0,-1, +675 NM_144680.3 chr17 - 11880755 11900689 11881273 11896146 9 11880755,11886613,11887429,11893778,11894290,11895759,11898874,11900126,11900589, 11882061,11886724,11887514,11893867,11894480,11896228,11898996,11900427,11900689, 0 ZNF18 cmpl cmpl 1,1,0,1,0,0,-1,-1,-1, +675 NM_001303281.1 chr17 - 11880755 11900827 11881273 11896146 7 11880755,11886613,11887429,11893778,11894290,11895759,11900747, 11882061,11886724,11887514,11893867,11894480,11896228,11900827, 0 ZNF18 cmpl cmpl 1,1,0,1,0,0,-1, +675 NM_001303282.1 chr17 - 11880755 11900827 11881273 11896146 7 11880755,11886613,11887429,11893778,11894290,11895759,11900747, 11882061,11886721,11887514,11893867,11894480,11896228,11900827, 0 ZNF18 cmpl cmpl 1,1,0,1,0,0,-1, +676 NR_030613.1 chr17 + 11985215 11985313 11985313 11985313 1 11985215, 11985313, 0 MIR744 none none -1, +680 NR_034144.1 chr17 + 12453284 12540504 12540504 12540504 3 12453284,12493757,12538317, 12453394,12494065,12540504, 0 LINC00670 none none -1,-1,-1, +680 NR_034145.1 chr17 + 12453284 12540504 12540504 12540504 4 12453284,12487876,12493757,12538317, 12453394,12488038,12494065,12540504, 0 LINC00670 none none -1,-1,-1,-1, +681 NR_104607.1 chr17 - 12663450 12693601 12693601 12693601 2 12663450,12693459, 12667035,12693601, 0 LOC100128006 none none -1,-1, +682 NR_039747.1 chr17 - 12820584 12820659 12820659 12820659 1 12820584, 12820659, 0 MIR1269B none none -1, +683 NM_018127.6 chr17 - 12894928 12921381 12896134 12921264 24 12894928,12897003,12897741,12898080,12898279,12899019,12899256,12899863,12901728,12903472,12905590,12905757,12906795,12908305,12909069,12909237,12913929,12914979,12916523,12917755,12919084,12920178,12920387,12921019, 12896362,12897148,12897820,12898201,12898379,12899129,12899295,12900002,12901825,12903591,12905676,12905896,12906891,12908418,12909142,12909296,12913988,12915099,12916592,12917813,12919149,12920249,12920438,12921381, 0 ELAC2 cmpl cmpl 0,2,1,0,2,0,0,2,1,2,0,2,2,0,2,0,1,1,1,0,1,2,2,0, +683 NM_173717.1 chr17 - 12894928 12921381 12896134 12921264 24 12894928,12897003,12897741,12898080,12898279,12899019,12899256,12899863,12901728,12903472,12905590,12905757,12906795,12908305,12909069,12909237,12913929,12914979,12916523,12917755,12919084,12920178,12920387,12921019, 12896362,12897148,12897820,12898201,12898379,12899129,12899295,12900002,12901825,12903591,12905673,12905896,12906891,12908418,12909142,12909296,12913988,12915099,12916592,12917813,12919149,12920249,12920438,12921381, 0 ELAC2 cmpl cmpl 0,2,1,0,2,0,0,2,1,2,0,2,2,0,2,0,1,1,1,0,1,2,2,0, +683 NM_001165962.1 chr17 - 12894928 12921381 12896134 12921264 23 12894928,12897003,12897741,12898080,12898279,12899019,12899256,12899863,12901728,12903472,12905590,12905757,12906795,12908305,12909069,12909237,12913929,12916523,12917755,12919084,12920178,12920387,12921019, 12896362,12897148,12897820,12898201,12898379,12899129,12899295,12900002,12901825,12903591,12905676,12905896,12906891,12908418,12909142,12909296,12913988,12916592,12917813,12919149,12920249,12920438,12921381, 0 ELAC2 cmpl cmpl 0,2,1,0,2,0,0,2,1,2,0,2,2,0,2,0,1,1,0,1,2,2,0, +687 NR_031679.1 chr17 - 13446845 13446963 13446963 13446963 1 13446845, 13446963, 0 MIR548H3 none none -1, +16 NM_000633.2 chr18 - 60790578 60986613 60795857 60985899 3 60790578,60985314,60986406, 60795992,60986185,60986613, 0 BCL2 cmpl cmpl 0,0,-1, +16 NR_033881.1 chr18 + 61771324 62090836 62090836 62090836 10 61771324,61794618,61916535,61955029,61961161,62074355,62079539,62083166,62089964,62090166, 61771469,61794673,61916628,61955127,61961350,62074493,62079618,62083346,62090039,62090836, 0 LINC01924 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1, +130 NM_001278268.1 chr18 + 59992519 60054943 59992585 60052267 10 59992519,60015400,60017044,60021623,60025522,60027187,60028912,60033940,60035933,60051983, 59992660,60015482,60017170,60021767,60025574,60027282,60029026,60033993,60036717,60054943, 0 TNFRSF11A cmpl cmpl 0,0,1,1,1,2,1,1,0,1, +130 NM_001270951.1 chr18 + 59992519 60054943 59992585 60052267 7 59992519,60015400,60017044,60021623,60025480,60027187,60051983, 59992660,60015482,60017170,60021767,60025574,60027282,60054943, 0 TNFRSF11A cmpl cmpl 0,0,1,1,1,2,1, +130 NM_001270950.1 chr18 + 59992519 60054943 59992585 60052267 8 59992519,60015400,60017044,60021623,60025480,60027187,60028912,60051983, 59992660,60015482,60017170,60021767,60025574,60027282,60029026,60054943, 0 TNFRSF11A cmpl cmpl 0,0,1,1,1,2,1,1, +130 NM_001270949.1 chr18 + 59992519 60054943 59992585 60051992 9 59992519,60015400,60017044,60021623,60025480,60027187,60028912,60033940,60051983, 59992660,60015482,60017170,60021767,60025574,60027282,60029026,60033993,60054943, 0 TNFRSF11A cmpl cmpl 0,0,1,1,1,2,1,1,0, +130 NM_003839.3 chr18 + 59992519 60054943 59992585 60052267 10 59992519,60015400,60017044,60021623,60025480,60027187,60028912,60033940,60035933,60051983, 59992660,60015482,60017170,60021767,60025574,60027282,60029026,60033993,60036717,60054943, 0 TNFRSF11A cmpl cmpl 0,0,1,1,1,2,1,1,0,1, +130 NM_194449.3 chr18 + 60382671 60647676 60382916 60646664 17 60382671,60497267,60506016,60527667,60562243,60563013,60570196,60572456,60582145,60587191,60608950,60612341,60625861,60630600,60639746,60642629,60645494, 60384492,60497464,60506142,60527834,60562390,60563244,60570399,60572517,60582241,60587347,60609151,60612504,60625992,60630705,60639941,60642858,60647676, 0 PHLPP1 cmpl cmpl 0,1,0,0,2,2,2,1,2,2,2,2,0,2,2,2,0, +131 NM_004869.3 chr18 - 61056422 61089752 61058207 61089492 11 61056422,61060641,61064266,61066474,61067280,61067779,61070939,61074664,61077522,61078699,61089465, 61058309,61060782,61064486,61066556,61067429,61067936,61071059,61074732,61077679,61078811,61089752, 0 VPS4B cmpl cmpl 0,0,2,1,2,1,1,2,1,0,0, +1044 NM_017742.5 chr18 + 60190657 60245818 60190657 60243812 14 60190657,60206913,60209730,60212034,60217580,60223435,60225919,60227819,60230241,60231803,60232234,60237335,60241289,60243744, 60191596,60207025,60209807,60212106,60217693,60223530,60226003,60227877,60230377,60231868,60232329,60237464,60242783,60245818, 0 ZCCHC2 cmpl cmpl 0,0,1,0,0,2,1,1,2,0,2,1,1,1, +1044 NR_126534.1 chr18 + 60190657 60253976 60253976 60253976 15 60190657,60206913,60209730,60212034,60217580,60223435,60225919,60227819,60230241,60231803,60232234,60237335,60241289,60243744,60251678, 60191596,60207025,60209807,60212106,60217693,60223530,60226003,60227877,60230377,60231868,60232329,60237464,60242783,60243885,60253976, 0 ZCCHC2 none none -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, +1050 NM_000657.2 chr18 - 60985186 60986613 60985281 60985899 2 60985186,60986406, 60986185,60986613, 0 BCL2 cmpl cmpl 0,-1, +1050 NM_002035.2 chr18 - 60994970 61034506 60999014 61034351 10 60994970,61002489,61006032,61011642,61018120,61022436,61022730,61026968,61030011,61034243, 60999134,61002591,61006116,61011726,61018312,61022532,61022796,61027025,61030101,61034506, 0 KDSR cmpl cmpl 0,0,0,0,0,0,0,0,0,0, +1051 NM_002639.4 chr18 + 61144143 61172318 61151661 61170955 7 61144143,61151654,61154178,61156579,61160185,61166352,61170562, 61144278,61151829,61154316,61156697,61160328,61166520,61172318, 0 SERPINB5 cmpl cmpl -1,0,0,0,1,0,0, +1052 NM_080474.2 chr18 + 61223392 61236560 61223392 61234244 7 61223392,61225584,61226810,61228317,61231210,61232677,61233839, 61223560,61225659,61226951,61228435,61231353,61232845,61236560, 0 SERPINB12 cmpl cmpl 0,0,0,0,1,0,0, +1052 NM_001307928.1 chr18 + 61223392 61236560 61223392 61234244 7 61223392,61225584,61226810,61228317,61231210,61232677,61233839, 61223560,61225719,61226951,61228435,61231353,61232845,61236560, 0 SERPINB12 cmpl cmpl 0,0,0,0,1,0,0, +1052 NM_012397.3 chr18 + 61254533 61266433 61255901 61264597 8 61254533,61255884,61256889,61259581,61260087,61261588,61262262,61264192, 61254684,61256066,61256949,61259710,61260205,61261731,61262418,61266433, 0 SERPINB13 cmpl cmpl -1,0,0,0,0,1,0,0, +1052 NM_001307923.1 chr18 + 61254533 61266433 61255901 61264597 8 61254533,61255884,61256889,61259581,61260087,61261588,61262262,61264192, 61254684,61256066,61256976,61259710,61260205,61261731,61262418,61266433, 0 SERPINB13 cmpl cmpl -1,0,0,0,0,1,0,0, +1052 NM_002974.3 chr18 - 61304492 61311553 61304952 61310811 8 61304492,61306418,61306867,61308107,61308993,61310394,61310646,61311442, 61305357,61306574,61307010,61308225,61309122,61310451,61310837,61311553, 0 SERPINB4 cmpl cmpl 0,0,1,0,0,0,0,-1, +1052 NM_175041.1 chr18 - 61304492 61311553 61304952 61310811 8 61304492,61306418,61306867,61308107,61308993,61310394,61310646,61311442, 61305357,61306511,61307010,61308225,61309122,61310451,61310837,61311553, 0 SERPINB4 cmpl cmpl 0,0,1,0,0,0,0,-1, +1052 NM_006919.2 chr18 - 61322430 61329197 61322890 61328450 8 61322430,61324064,61324503,61325746,61326632,61328033,61328285,61329079, 61323295,61324220,61324646,61325864,61326761,61328090,61328476,61329197, 0 SERPINB3 cmpl cmpl 0,0,1,0,0,0,0,-1, +1053 NM_080475.3 chr18 + 61369537 61391127 61377427 61390633 9 61369537,61370084,61377412,61378568,61379798,61383268,61387246,61388064,61390228, 61369611,61370240,61377595,61378628,61379927,61383386,61387389,61388220,61391127, 0 SERPINB11 cmpl cmpl -1,-1,0,0,0,0,1,0,0, +1053 NM_001291278.1 chr18 + 61370192 61391127 61377427 61390633 6 61370192,61377412,61378568,61379798,61388064,61390228, 61370240,61377595,61378628,61379927,61388220,61391127, 0 SERPINB11 cmpl cmpl -1,0,0,0,0,0, +1053 NM_001291279.1 chr18 + 61370192 61391127 61387296 61390633 7 61370192,61377412,61378568,61379798,61387246,61388064,61390228, 61370240,61377595,61378628,61379927,61387389,61388220,61391127, 0 SERPINB11 cmpl cmpl -1,-1,-1,-1,0,0,0, +1053 NM_001040147.2 chr18 + 61420280 61472610 61449606 61471869 8 61420280,61449588,61459626,61460394,61463499,61465837,61468099,61471470, 61420354,61449774,61459677,61460511,61463617,61465980,61468246,61472610, 0 SERPINB7 cmpl cmpl -1,0,0,0,0,1,0,0, +1053 NM_001261831.1 chr18 + 61442608 61472610 61449606 61471869 7 61442608,61449588,61460394,61463499,61465837,61468099,61471470, 61442950,61449774,61460511,61463617,61465980,61468246,61472610, 0 SERPINB7 cmpl cmpl -1,0,0,0,1,0,0, +1053 NM_003784.3 chr18 + 61442608 61472610 61449606 61471869 8 61442608,61449588,61459626,61460394,61463499,61465837,61468099,61471470, 61442950,61449774,61459677,61460511,61463617,61465980,61468246,61472610, 0 SERPINB7 cmpl cmpl -1,0,0,0,0,1,0,0, +1053 NM_001261830.1 chr18 + 61445010 61472610 61449606 61471869 8 61445010,61449588,61459626,61460394,61463499,61465837,61468099,61471470, 61445059,61449774,61459677,61460511,61463617,61465980,61468246,61472610, 0 SERPINB7 cmpl cmpl -1,0,0,0,0,1,0,0, +1054 NM_002575.2 chr18 + 61554938 61571124 61558678 61570539 8 61554938,61558669,61562497,61564324,61564960,61568973,61569637,61570134, 61555004,61558846,61562617,61564453,61565078,61569116,61569802,61571124, 0 SERPINB2 cmpl cmpl -1,0,0,0,0,1,0,0, +1054 NM_001143818.1 chr18 + 61554938 61571124 61558678 61570539 9 61554938,61557071,61558669,61562497,61564324,61564960,61568973,61569637,61570134, 61555004,61557329,61558846,61562617,61564453,61565078,61569116,61569802,61571124, 0 SERPINB2 cmpl cmpl -1,-1,0,0,0,0,1,0,0, +1054 NM_005024.2 chr18 + 61575223 61603345 61582744 61602476 8 61575223,61582735,61584689,61585198,61587021,61597278,61600281,61602071, 61575274,61582912,61584755,61585336,61587139,61597421,61600437,61603345, 0 SERPINB10 cmpl cmpl -1,0,0,0,0,1,0,0, +1055 NM_001123366.1 chr18 + 61616587 61627646 61620689 61627589 4 61616587,61620587,61621641,61627391, 61616634,61620761,61621791,61627646, 0 HMSD cmpl cmpl -1,0,0,0, +1055 NM_001031848.1 chr18 + 61637262 61653887 61645542 61653500 7 61637262,61645532,61647034,61648954,61650812,61652326,61653491, 61637404,61645710,61647172,61649072,61650955,61652479,61653887, 0 SERPINB8 cmpl cmpl -1,0,0,0,1,0,0, +1055 NM_001276490.1 chr18 + 61637262 61656608 61650934 61654512 6 61637262,61647034,61648954,61650812,61652326,61654107, 61637404,61647172,61649072,61650955,61652479,61656608, 0 SERPINB8 cmpl cmpl -1,-1,-1,0,0,0, +1055 NM_002640.3 chr18 + 61637262 61656608 61645542 61654512 7 61637262,61645532,61647034,61648954,61650812,61652326,61654107, 61637404,61645710,61647172,61649072,61650955,61652479,61656608, 0 SERPINB8 cmpl cmpl -1,0,0,0,1,0,0, +1055 NM_198833.1 chr18 + 61637262 61656608 61645542 61654512 7 61637262,61645532,61647034,61648954,61650812,61652326,61654107, 61637421,61645710,61647172,61649072,61650955,61652479,61656608, 0 SERPINB8 cmpl cmpl -1,0,0,0,1,0,0, +1056 NR_027245.1 chr18 - 61747242 61816260 61816260 61816260 4 61747242,61765067,61765810,61816008, 61747636,61765226,61765874,61816260, 0 LINC00305 none none -1,-1,-1,-1, +1057 NR_033983.1 chr18 - 61880316 61927290 61927290 61927290 3 61880316,61925452,61927149, 61882281,61925754,61927290, 0 LINC01538 none none -1,-1,-1,
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res.html Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,141 @@ +<!DOCTYPE html> +<html> +<head> + <title>Chimerae</title> + <style type="text/css"> + body { font-family:Arial, Helvetica, Sans-Serif; font-size:0.8em;} + #report { border-collapse:collapse;} + #report h4 { margin:0px; padding:0px;} + #report img { float:right;} + #report ul { margin:10px 0 10px 40px; padding:0px;} + #report th { background:#7CB8E2 url(static/images/header_bkg.png) repeat-x scroll center left; color:#fff; padding:7px 15px; text-align:left;} + #report td { background:#C7DDEE none repeat-x scroll center left; color:#000; padding:7px 15px; } + #report tr.odd td { background:#fff url(static/images/row_bkg.png) repeat-x scroll center left; cursor:pointer; } + #report div.arrow { background:transparent url(static/images/arrows.png) no-repeat scroll 0px -16px; width:16px; height:16px; display:block;} + #report div.up { background-position:0px 0px;} + </style> + <script src="./js/jquery.min.js" type="text/javascript"></script> + <script type="text/javascript"> + $(document).ready(function(){ + $("#report tr:odd").addClass("odd"); + $("#report tr:not(.odd)").hide(); + $("#report tr:first-child").show(); + $("#report tr.odd").click(function(){ + $(this).next("tr").toggle(); + $(this).find(".arrow").toggleClass("up"); + }); + //$("#report").jExpand(); + }); + </script> +</head> +<body> + <table id="report"> + <tr> + <th>L1 chromosome</th> + <th>L1 start</th> + <th>L1 end</th> + <th>L1 strand</th> + <th>test read #</th> + <th>Chimera chromosome</th> + <th>Chimera start</th> + <th>Chimera end</th> + <th>Chimera strand</th> + <th>test read #</th> + <th>Known RNA</th> + <th>Known EST</th> + <th></th> + </tr> + <tr> + <td>chr17:13850000-13860000</td> + <td>5524</td> + <td>5625</td> + <td>-</td> + <td>1</td> + <td>chr17:13850000-13860000</td> + <td>5361</td> + <td>5462</td> + <td>+</td> + <td>1</td> + <td></td> + <td></td> + <td><div class="arrow"></div></td> + </tr> + <tr> + <td valign=top colspan=10></td> + <td valign=top> + </td> + <td valign=top> + </td> + <td></td> + </tr> + <tr> + <td>chr18:62900000-62910000</td> + <td>6369</td> + <td>6470</td> + <td>-</td> + <td>1</td> + <td>chr18:62900000-62910000</td> + <td>6229</td> + <td>6330</td> + <td>+</td> + <td>1</td> + <td><a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/NM_152538.2">NM_152538.2</a></td> + <td><a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA456960.1">DA456960.1</a></td> + <td><div class="arrow"></div></td> + </tr> + <tr> + <td valign=top colspan=10></td> + <td valign=top> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/NM_001143970.1">NM_001143970.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/NR_033888.1">NR_033888.1</a><br> + </td> + <td valign=top> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA439948.1">DA439948.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BQ343973.1">BQ343973.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/HY039921.1">HY039921.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/HY011359.1">HY011359.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/FY211757.1">FY211757.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/FY213409.1">FY213409.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/FY210726.1">FY210726.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/FY213828.1">FY213828.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/FY213215.1">FY213215.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/FY213186.1">FY213186.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DB059299.1">DB059299.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA848406.1">DA848406.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA452145.1">DA452145.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/CD300204.1">CD300204.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BM554436.1">BM554436.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BI829507.1">BI829507.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BI828564.1">BI828564.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BI462449.1">BI462449.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/AA292896.1">AA292896.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/HY264403.1">HY264403.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DB203607.1">DB203607.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DB084198.1">DB084198.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA760572.1">DA760572.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA739826.1">DA739826.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA456573.1">DA456573.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA461374.1">DA461374.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA587715.1">DA587715.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA395712.1">DA395712.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA686009.1">DA686009.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/DA568154.1">DA568154.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BP247141.1">BP247141.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/CF596224.1">CF596224.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BX479603.1">BX479603.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/CD657445.1">CD657445.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BQ900308.1">BQ900308.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BM910071.1">BM910071.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BM017308.1">BM017308.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BI052118.1">BI052118.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BF176186.1">BF176186.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BF680445.1">BF680445.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BF208422.1">BF208422.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/BE567163.1">BE567163.1</a><br> + <a target="_blank" rel="noopener noreferrer" href="https://www.ncbi.nlm.nih.gov/nuccore/AW894450.1">AW894450.1</a><br> + </td> + <td></td> + </tr> + </table> +</body> +</html>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/final_result_chimerae.txt Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,3 @@ +Chimera.Chr Chimera.Start Chimera.End Chimera.Strand L1.Chr L1.Start L1.End L1.Strand Unique.Chr Unique.Start Unique.End Unique.Strand ID_final info dataf...16..nfastq...16.. GeneName GeneStrand repName repStart repEnd repWidth repStrand +chr17:13850000-13860000 5361 5625 - chr17:13850000-13860000 5524 5625 - chr17:13850000-13860000 5361 5462 + Id_1 no 1 no_gene * no 0 0 0 * +chr18:62900000-62910000 6229 6470 - chr18:62900000-62910000 6369 6470 - chr18:62900000-62910000 6229 6330 + Id_2 no 1 no_gene * no 0 0 0 *
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/first_results.txt Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,3 @@ +Chimera.Chr Chimera.Start Chimera.End Chimera.Strand L1.Chr L1.Start L1.End L1.Strand Unique.Chr Unique.Start Unique.End Unique.Strand ID_final info dataf...16..nfastq...16.. +chr17:13850000-13860000 5361 5625 - chr17:13850000-13860000 5524 5625 - chr17:13850000-13860000 5361 5462 + Id_1 no 1 +chr18:62900000-62910000 6229 6470 - chr18:62900000-62910000 6369 6470 - chr18:62900000-62910000 6229 6330 + Id_2 no 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/res_files/results.txt Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,3 @@ +L1 chromosome L1 start L1 end L1 strand test read # Chimera chromosome Chimera start Chimera end Chimera strand test read # +chr17:13850000-13860000 5524 5625 - 1 chr17:13850000-13860000 5361 5462 + 1 +chr18:62900000-62910000 6369 6470 - 1 chr18:62900000-62910000 6229 6330 + 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/rmsk-small.txt Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,36 @@ +#bin swScore milliDiv milliDel milliIns genoName genoStart genoEnd genoLeft strand repName repClass repFamily repStart repEnd repLeft id +690 314 359 51 57 chr17 13850045 13850158 -67345052 - MER5B DNA hAT-Charlie -2 176 63 1 +690 2449 104 0 0 chr17 13850158 13850455 -67344755 - AluSg SINE Alu -13 297 1 1 +690 314 359 51 57 chr17 13850455 13850518 -67344692 - MER5B DNA hAT-Charlie -116 62 1 1 +690 652 181 233 25 chr17 13850644 13850803 -67344407 - MER53 DNA hAT -1 192 1 1 +690 906 295 147 10 chr17 13850865 13851252 -67343958 + MLT1K LTR ERVL-MaLR 5 444 -151 1 +690 1661 164 104 43 chr17 13851262 13851435 -67343775 + L1M3 LINE L1 4914 5074 -1066 1 +690 2169 146 3 22 chr17 13851435 13851750 -67343460 - AluSz SINE Alu -3 309 1 1 +690 1661 164 104 43 chr17 13851750 13851952 -67343258 + L1M3 LINE L1 5075 5312 -828 1 +690 421 241 72 43 chr17 13851952 13852091 -67343119 + MLT1K LTR ERVL-MaLR 453 595 0 1 +690 250 233 0 62 chr17 13852345 13852409 -67342801 + L2c LINE L2 3323 3382 -5 1 +690 415 316 96 129 chr17 13853970 13854135 -67341075 - L3 LINE CR1 -1 4488 4317 1 +690 856 225 33 0 chr17 13854135 13854286 -67340924 + AluJo SINE Alu 137 292 -20 1 +690 415 316 96 129 chr17 13854286 13854516 -67340694 - L3 LINE CR1 -173 4316 4106 1 +690 2240 82 14 25 chr17 13854795 13855076 -67340134 + AluSx SINE Alu 1 278 -34 1 +690 317 215 49 0 chr17 13856476 13856620 -67338590 + (TA)n Simple_repeat Simple_repeat 2 152 0 1 +690 22 0 0 0 chr17 13856642 13856664 -67338546 + AT_rich Low_complexity Low_complexity 1 22 0 1 +690 201 290 0 46 chr17 13856763 13856828 -67338382 + L2c LINE L2 3357 3418 -8 1 +690 207 111 0 100 chr17 13857811 13857861 -67337349 + L2a LINE L2 3382 3426 0 1 +690 234 283 7 143 chr17 13857864 13858004 -67337206 + L3 LINE CR1 4058 4178 -311 1 +690 573 251 51 6 chr17 13858004 13858180 -67337030 + MER96B DNA hAT 232 415 -2 1 +690 3018 86 0 5 chr17 13858486 13858873 -67336337 + MLT2A1 LTR ERVL 1 385 -59 1 +690 974 148 16 120 chr17 13858883 13859128 -67336082 + MLT1B LTR ERVL-MaLR 177 388 -2 1 +690 2255 134 3 7 chr17 13859736 13860043 -67335167 + AluSg SINE Alu 1 306 -4 1 +1064 9370 128 36 36 chr18 62899485 62901011 -15176237 + THE1C-int LTR ERVL-MaLR 1 1526 -54 1 +1064 1953 143 73 17 chr18 62901011 62901366 -15175882 + THE1C LTR ERVL-MaLR 1 375 0 1 +1064 195 320 23 31 chr18 62902099 62902233 -15175015 - MIRb SINE MIR -6 256 120 1 +1064 225 0 0 0 chr18 62902616 62902641 -15174607 + (CA)n Simple_repeat Simple_repeat 2 26 0 1 +1064 330 26 0 0 chr18 62902641 62902679 -15174569 + (GA)n Simple_repeat Simple_repeat 2 40 0 1 +1064 201 39 0 0 chr18 62903194 62903220 -15174028 + (TG)n Simple_repeat Simple_repeat 2 27 0 1 +1064 222 306 22 0 chr18 62904516 62904600 -15172648 - L2b LINE L2 -8 3418 3306 1 +1064 40 49 0 0 chr18 62904689 62904750 -15172498 + AT_rich Low_complexity Low_complexity 1 61 0 1 +1064 258 32 0 0 chr18 62904980 62905011 -15172237 + (TCTA)n Simple_repeat Simple_repeat 4 34 0 1 +1064 205 237 33 17 chr18 62905555 62905615 -15171633 + GA-rich Low_complexity Low_complexity 3 63 0 1 +1064 236 149 21 0 chr18 62907603 62907650 -15169598 + (CA)n Simple_repeat Simple_repeat 2 49 0 1 +1064 304 217 33 0 chr18 62907681 62907773 -15169475 + (TA)n Simple_repeat Simple_repeat 2 96 0 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/two.fastq Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,100 @@ +@HWI-ST584:365:C37MVACXX:1:1305:19372:56141 2:N:0:GCCAAT +CGATCTGGCTGCGACATCTGTCACCCCATTGATCGCCAGGGTTGATTCGGATGATCTGGCTGGCTAGGCGGGTGTCCCCTTCCTCCCTCACCGCTCCATGT ++ +@C@FFFEDFFFBHIIIIGGIJJIIIJJIIJGIJHIEHGJJEGGGIJJIJJDHGHHHHGFEFEFDD@BDCBBB&504+:?<A(9::3<9<(28?@BB>:3>4 +@HWI-ST584:365:C37MVACXX:1:2301:7296:160148 2:N:0:GCCAAT +GGGCTTTGTGTCTGGCCAGCTTGATTTTCCTAATGGTCTCATCTCCTTTGCTAGTGTCTTTGTCATGCGTCTCTGGCCCTCGTGGGTAAATGACAAACGGG ++ +@@CFFFFFHHFFHJJHJHHIGJJGIJJJJIIGEHGIEHGIICGGIJEGGHEGGHHIIJJJJJGHIIIJJIIJJIIFGHHFFEAADD?@CCDEDDDDDDDDB +@HWI-ST584:365:C37MVACXX:1:1205:13370:110105 2:N:0:GCCAAT +CGAAGCTCTGTGCAATCAGCTGGTGAATCTGCTGCTGCCGGTCCTTCTTTCGAACACTCTCATAGCTGGGCAGGCGAGCTGGCTGCCACAGGGGCAGCTGG ++ +@<@BDDDAHFHHFGHIGHGCHGGGA>@HDBEHHGGGBDCHG:@DGEGEHGH7;CH>AGC@EGGEEHEAADDFDB>B;=B;>C<<?82::?A?B<355?9>C +@HWI-ST584:365:C37MVACXX:1:2308:12673:6166 2:N:0:GCCAAT +CATTTTTCTATAACACTATTATAATAAATTCACATGGAAAAGTACAAGGATGAGCAATTTTTTACTTTAGAAATGTTTCAAAAGGGGAGGTAAACTTGATG ++ +CCCFFFFFHHHHHJJJJJJJJJIJJJJJJJJHHHIJIIIJJJFHIIJJJJHIJIJJIJJJJJJJJJJJJJIJHIJIHHHGGFHFFFDDDDDDDDDDDDCDD +@HWI-ST584:365:C37MVACXX:1:2207:7253:147412 2:N:0:GCCAAT +AAAAGGCTCAGGAAGAATCAAGTGCAATGATGCAGTGGTTACAGAAAATGAACAAAACTGCAACAAAATGGCAGCAGACACCTGCACCTACAGATACTGAA ++ +@CCFFFFFHHHHHIJJJJJJIJGHIIJIJGHIJJJHHIFHJJIIJJIIJJGHIJJIJJJJJJJJJIJJJJJHHHHFFFFFEDEEDDDDDDDDDDDDDDEDD +@HWI-ST584:365:C37MVACXX:1:2308:14918:56009 2:N:0:GCCAAT +AGAGCCCCACTTTTTCCGTTTTGTAATTATTTGGCGAAAAGAAATTTGCTTATAGACTATGTTTAATGGGATTAACCATGTCCTCATTTTTCTTTTCATCC ++ +CCCFFFFFGHHHHJJJIHHJJJJHGJJJJJJJIJJJJJJJJJJJJJJJJJGHIJJJJJJJJIJJHHHHHHFFFFFEEEEEEEFDDDDEFEDDDDDDDDEEC +@HWI-ST584:365:C37MVACXX:1:1201:11510:45354 2:N:0:GCCAAT +GTTATAGAAAGGAAAGATAAACATGTAAGGTTTCATACTAAAATTTTTATTACATTAAAGTTTGCTCTAACTTTTGTTTTCAAATACAGATTATGAGACAG ++ +@@BDDEFADFHFGIIIJJJIEHHHJEHGHGGIIJIIJIHFHIJJIJIJJJGIGBHGHGGGIECGGIIJJGHJIJIIFGGGGGHFFEFHBDFFFFDCCEDED +@HWI-ST584:365:C37MVACXX:1:2108:4159:38107 2:N:0:GCCAAT +GCAAGAGAACATTTTACTGTTGTACAATCATGTTCTGGGGGTTTGATTGTTTACAGGATATTCCAAAATAAAAGGTCTCTGGAAGATTTTCATTGAGGATA ++ +?7@?DD8DD+<CFEB??CFHHGIC@>EGIDAH9C?FGH):@)(/?9C)=.8=CCG>>2@CC@7)=?C9E@:??@1(6@A>>A;;55;A>>CDED@>@C@CC +@HWI-ST584:365:C37MVACXX:1:1203:20582:36223 2:N:0:GCCAAT +GTTGTTGACTTGCTGACGTTGGGGTGGTTGGTAGTGCAGTTAAGTTGGCTGCATGATGGGATGTTGCCTCAGATGTCGGTGCAGCGAAGCCCTGTAGGTGG ++ +B@@BDFDDFHFDAAH>CGFHI=FB8?@6DEH??DBDGAF)8@FBGHH@@FCDGHGA>HBA9@D@CCCEECACCD<ACA=;??C>C<<@B-?ACACCCA>@# +@HWI-ST584:365:C37MVACXX:1:1307:2892:120144 2:N:0:GCCAAT +CGAGATCTTAAGGAACCTCTATCATGAGAACATTGTGAAGTACAAAGGAATCTGCACAGAAGACGGAGGAAATGGTATTAAGCTCATCATGGAATTTCTGC ++ +@<@ADFFFHHHHFIIJIGHEEFHIICDFHGGGIJIEHGGH?DHGIHIEGC9?FHCIGJGIJICCHI:GEHHGGHC@DDFBBECECCCCA@ACCCDDDCEDD +@HWI-ST584:365:C37MVACXX:1:1305:12954:25279 2:N:0:GCCAAT +ACGAATTTGGGGCTACGAAGAGGAATAGCGAAAAAGCAAATCTGTTTCAACTGATGGGAACCCTATAGCTATAGAACTTGGGGGCTATCTCCTATGCCCCT ++ +CCCFFFFFHGHGHIJJJJJJJJIIJJJIGIGIJIGG;FHEF=BAHIGIJGDGDC;CECHADFFDCCC;@@CCCCC>@C>CDDD=59A>?CDCACDCCDDB8 +@HWI-ST584:365:C37MVACXX:1:2304:18056:150403 2:N:0:GCCAAT +CTTTAGAATAATTGTTTGCTTTCAGATGATTAAAAAAAGGAGATTGTATCTAGGAAAAAAGTGTGAATGCTTCAAAGGAGAGATACTGATAATTGTGACTT ++ +CCCFFFFFGHHHHJJJJJJJJJJJJIJJJJJIJJJJJJJJGJJJJJIJIJFGIJIJJJJJJEHEHHHFFFFFFFEEEEEDDDDDDDDEDDDDDEDCDDDDC +@HWI-ST584:365:C37MVACXX:1:1102:1484:117821 2:N:0:GCCAAT +AATAAAATTATAAATCACTACCGTGGCCACATTTTAAAAGATATAATATTTTATCTATATTGCATTATTGCCAATTCAAATTTAGTTATATAATAAAGGAA ++ +?@@DDFFDFFHAHJGIFIIJJ;EHIII>@CGGFIIIIJCGBDBDHGGGDHBFCHEGIJIGGGGGHG@FHHIGIJIGJIJHHGEHHHFEFEFCDFEDEEDA> +@HWI-ST584:365:C37MVACXX:1:2107:13215:154024 2:N:0:GCCAAT +GTTTGAAAAGGCAAGTTTGTCCCTGGGCAATTTTCAAAATATTTCTTTAATGTGTTTTCACAATACTGTTTACCTAATAAATCTTAAGTTTTTAAAAGCAA ++ +B@@FFFFFHHHHHJIHIJJJJJIJIJJJJJJJJIJJJJIJJJJJJJJJJJHIFHHIJJJJIIJJJJJJIJJIJJJIJJHHHHHHHFFFEFFFDDEEED=CD +@HWI-ST584:365:C37MVACXX:1:2305:14375:146794 2:N:0:GCCAAT +GTCTGGCATCTCCTCCTCATGCTGCGTCTGGCCACCTACTGCGGCGGCCGCTGCTGAGACGCTCGCTCGGACCAAGGGGAGGAGACGGCGGGGGCGGCCGC ++ +CCCFFFFFHHHHHJJJJJJIJJJJJJJJJJJIJGIJJJJJJIGIDHFCDD=BDDDDDDDDDBDDDDDDDDBDDDDDDDD<BD??ABBBDDDDDD.5@9<<5 +@HWI-ST584:365:C37MVACXX:1:2102:21132:28209 2:N:0:GCCAAT +GTTCCTCCCCTTCCCCAACCCTGGGGAAATAAGAAACAATTCATATACTAGATCTAAAGTTTCATTAAAATTGCTTATGCCCTGTCTCAGGCATTTTAAGT ++ +CCCFFFFFHHHHHJJJJJIJJGIJJIGIJBGHDGIJ;GHGIBGDECDADBBFHGJIJJB@FGHIIIGIGIEEBEHH@D>;CEEEECEDDD<?ACDDEB>@3 +@HWI-ST584:365:C37MVACXX:1:1203:3094:151750 2:N:0:GCCAAT +CTAAACACATGCGGACACACACCGGGGAGAAGCCCTATGAATGTAAGGACTGTGGGAAAGCCTACAATAGGGTTTATCTACTGAATGAGCATGTGAAAACT ++ +CCCFFFFFHHGGHJJJJJGHIJJJJJJIGIIIIJJJIIJHHHHHHHFFFECCCEEDDCDDDDDDDDDDDDDDAADDDDDEDEDDDDCDDDDCDCDEEDDDD +@HWI-ST584:365:C37MVACXX:1:1102:15558:4133 2:N:0:GCCAAT +CTGAAACTTTGTCTCTTCTTCCGAAATGCTCCTATCTGGAAATAAATTCCCCTGTTTAACTTCCTTCAATTTATATCTTCATTCTACCATGGAGTCTCAAG ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJIJIIJJJDGDHIJGIIIGHIJHIIIJHJJJJJJJJJJJJJJIIIJHHGHHGHEEEFFFDEECEDDDDD +@HWI-ST584:365:C37MVACXX:1:1306:11209:39712 2:N:0:GCCAAT +AGCAACATAGTAAAAGAGTAGCGGTCATTTTAAATGAATTTGGGGAAGGAAGTGCGCTGGAGAAATCCTTAGCTGTCAGCCAAGGTGGAGAGCTCTATGAA ++ +@C@FFFFDDDFFF<EFIICEECGIIIHIIGHHIFGGDGIIIJJJIABEEGFGIGIJJIIGHHFBEFFEEEEECDDCCDDCDBD9?5:?9?><A>CDAADA> +@HWI-ST584:365:C37MVACXX:1:1108:5887:31082 2:N:0:GCCAAT +TGAGTTAGTCATTGTTTTTCTCCGAGGCGGCCTGCTTGCCACAGCCCTGCTCCCCAAGGCCTGGTGGCTTTGCCGAAGCTCTGGGACCGCAGCCCCAGCGA ++ +B@CFDEBEBFFHGJHIIJJJJIJJJJIBGHJGEHGGGIIIIFEEHFFFFDCEEDDDDDBDDDDDCCDDDDDDDCDBBDDDDCCDDDDDDDDDDDDDDBDD@ +@HWI-ST584:365:C37MVACXX:1:1105:7280:52404 2:N:0:GCCAAT +GTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTCTAACACAGAGGACCCTCAGCGCAGGTCTGTTGGAGTTTGCTAGAGGTCCACTCCAGACC ++ +@B@FFFFDDDDHFIIIIIHHIBEIJAFGIIIHG?GHI?CFHIECGHCGGCEHIGIIHHGEHIIGEFFBBDEEEE@;?>CCDDDCDAABCCCDDCCDACABB +@HWI-ST584:365:C37MVACXX:1:1304:18748:121360 2:N:0:GCCAAT +CTCCAAGCCAATCGCGGGATACAATCTCCTGGTGTGCCGTTTGCTAAGACCATTGGAAAAGCACAGTATTAGGGTGGGAGTGACCCGAATTTCCAGGTACC ++ +CCCFFFFFHHHHHJJJJJJJJJJJJJJJJIJJDGFGGIJIIIJIJJJJHHEHHFFFFFFEECEDDD@CFEEEDDABDDDDBDDDDDDDDDDDDEEDDACDC +@HWI-ST584:365:C37MVACXX:1:2308:16415:46106 2:N:0:GCCAAT +AGGAAGCAGCAGAAAGGCCCTGGGAGCTCGGTGGGTCCCTTCACAGGCGGCGGAAGGGTTGTTCCCATCTTTATGTCCATGTGTACTCAGTGTTTAGTTCC ++ +@@?DDDFDFDDBAHG<EBGGEFHIEHIGE@FDB@G6BFGBGGCGCAAC@:'37560<5285;AACDCCDD>ACC@44:A@C:A:@C:@>C>@:(9:AA@C@ +@HWI-ST584:365:C37MVACXX:1:2207:3186:50907 2:N:0:GCCAAT +CCACTGTCCAACCAGTCCCAGTGAGATGAACCAGGCACCTCAGTTGGAAATGCAGAAATCACCTGTCTTCTGCATCGATCATGCTGGGAGCTGCAGAATGA ++ +CCCDFFFFHHFHFIGHHFHGGGHEGG@@FEHIIIGGHFGIGIIFIGIDHI@BGHHIJJHGGIJIGIIHIGCEEAHEACBFCEDDEE>??BBBDDAC@ACAC +@HWI-ST584:365:C37MVACXX:1:2307:4484:32118 2:N:0:GCCAAT +TCATAATTATGCAAGATGTGTCAGTACTTAGCTATTGGGAAAATATTACAGTTAAATTTTTATTGTGGGAGGAGCCAAGATGGCCGAATAGGAAAAGTTCC ++ +;8?BDDD?D>?>?E<:2A,3,3<AH@H<F@<+<4AF@A3:C;:<C<D4EB**0?B*?<9?<(?F?####################################
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/blastdb.loc.sample Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,31 @@ +#This is a sample file distributed with Galaxy that is used to define a +#list of nucleotide BLAST databases, using three columns tab separated +#(longer whitespace are TAB characters): +# +#<unique_id> <database_caption> <base_name_path> +# +#The captions typically contain spaces and might end with the release date. +#It is important that the actual database name does not have a space in it. +# +#So, for example, if your database is nt and the path to your base name +#is /galaxy/data/blastdb/nt/DDmmmYYYY/nt, then the blastdb.loc entry +#could look like this: +# +#02dec2009 nt 02-Dec-2009 /galaxy/data/blastdb/nt/02dec2009/nt +# +#A /galaxy/data/blastdb/nt/02dec2009 directory would contain all of +#the "nt" blast indexes from ftp://ftp.ncbi.nlm.nih.gov/blast/db/nt* (e.g.): +# +#-rw-r--r-- 1 wychung galaxy 23437408 2008-04-09 11:26 nt.chunk.00.nhr +#-rw-r--r-- 1 wychung galaxy 3689920 2008-04-09 11:26 nt.chunk.00.nin +#-rw-r--r-- 1 wychung galaxy 251215198 2008-04-09 11:26 nt.chunk.00.nsq +#...etc... +# +#The blastdb.loc file should include one entry per line for each database. +# +#See also blastdb_p.loc, used for protein BLAST database. +# +#Note that for backwards compatibility with workflows, the <unique_id> of +#an entry must be the path that was in the original loc file. +#The metadata <unique_id> is the value stored in workflows for "database". +# \ No newline at end of file
--- a/tool-data/bwa_index.loc.sample Wed Jan 31 09:59:07 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt -#...etc... -# -#Your bwa_index.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa -#...etc... \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwa_mem_index.loc.sample Tue Feb 11 09:28:56 2020 -0500 @@ -0,0 +1,38 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +#
--- a/tool_data_table_conf.xml.sample Wed Jan 31 09:59:07 2018 -0500 +++ b/tool_data_table_conf.xml.sample Tue Feb 11 09:28:56 2020 -0500 @@ -1,7 +1,13 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> <tables> - <!-- Locations of configurations --> - <table name="bwa_indexes" comment_char="#"> + <!-- Locations of indexes in the BWA mapper format for BWA versions 0.6 and higher including BWA MEM and ALN--> + <table name="bwa_mem_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/bwa_index.loc" /> + <file path="tool-data/bwa_mem_index.loc" /> </table> -</tables> \ No newline at end of file + <!-- Locations of nucleotide (mega)blast databases --> + <table name="blastdb" comment_char="#"> + <columns>value, name, path</columns> + <file path="tool-data/blastdb.loc" /> + </table> +</tables>
--- a/tool_dependencies.xml Wed Jan 31 09:59:07 2018 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,24 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="bwa" version="0.7.12"> - <repository changeset_revision="051eba708f43" name="bwa" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="package_blast_plus_2_2_28" version="2.2.28"> - <repository changeset_revision="222036f7cab6" name="package_blast_plus_2_2_28" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="bedtools" version="2.24.0"> - <repository changeset_revision="d25966c8ddeb" name="bedtools" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="fastx" version="0.0.13"> - <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="repeat_masker" version="0.1.2"> - <repository changeset_revision="5673e72241aa" name="repeat_masker" owner="bgruening" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - <package name="R" version="0.1.2"> - <repository changeset_revision="5673e72241aa" name="repeat_masker" owner="bgruening" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> - - - -</tool_dependency> \ No newline at end of file