Mercurial > repos > brasset_jensen > srnapipe
view bin/sRNAPipe.pl @ 9:4878b321f851 draft
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author | brasset_jensen |
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date | Wed, 20 Dec 2017 10:07:06 -0500 |
parents | 1df6aaac800e |
children | b80aa719069f |
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#!/usr/bin/perl use strict; use warnings; use Getopt::Long; use Parallel::ForkManager; use File::Basename; use File::Copy::Recursive qw( dircopy ); use POSIX; use FindBin; use lib $FindBin::Bin; use resize qw ( size_distribution ); use subgroups qw (subgroups ); use ppp qw ( ping_pong_partners ); use Rcall qw (pie_chart bg_to_png ); use align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm BWA_call get_fastq_seq extract_sam sam_to_bam_bg ); use html qw ( main_page details_pages menu_page ppp_page ); use File::Copy; my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out); my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE ); my ( $si_min, $si_max, $pi_min, $pi_max ); my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_transcripts, $build_TE ); my $max_procs = 8; ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_transcripts, $build_TE ) = (0,0,0,0,0,0,0); ( $min, $max, $mis, $misTE, $si_min, $si_max, $pi_min, $pi_max, $dir ) = ( 18, 29, 0, 3, 21, 21, 23, 29 ); $Pcheck ='true'; GetOptions ( "fastq=s" => \@fastq, "fastq_n=s" => \@fastq_n, "dir=s" => \$dir, "min:i" => \$min, "max:i" => \$max, "si_min:i" => \$si_min, "si_max:i" => \$si_max, "pi_min:i" => \$pi_min, "pi_max:i" => \$pi_max, "mis:i" => \$mis, "misTE:i" => \$misTE, "html:s" => \$html_out, "PPPon:s" => \$Pcheck, "help" => \$help, "ref:s" => \$ref, "tRNAs:s" => \$tRNAs, "rRNAs:s" => \$rRNAs, "snRNAs:s" => \$snRNAs, "miRNAs:s" => \$miRNAs, "transcripts:s" => \$transcripts, "TE:s" => \$TE, "build_index" => \$build_index, "build_tRNAs" => \$build_tRNAs, "build_snRNAs" => \$build_snRNAs, "build_miRNAs" => \$build_miRNAs, "build_transcripts" => \$build_transcripts, "build_rRNAs" => \$build_rRNAs, "build_TE" => \$build_TE ); my $fq_collection = 'fastq_dir/'; mkdir $dir; mkdir $fq_collection; $dir = $dir.'/' unless $dir =~ /\/$/; mkdir $dir.'/css';mkdir $dir.'/js'; dircopy( $FindBin::Bin.'/css', $dir.'/css' ); dircopy( $FindBin::Bin.'/js', $dir.'/js' ); my $file = $dir.'report.txt'; open my $report, '>', $file or die "Cannot open $file $!\n"; my @toBuild = ( [$build_index, \$ref], [$build_tRNAs, \$tRNAs], [$build_rRNAs, \$rRNAs], [$build_snRNAs, \$snRNAs], [$build_miRNAs, \$miRNAs], [$build_transcripts, \$transcripts], [$build_TE, \$TE] ); to_build ( \@toBuild, $report, $dir ); my $proc_child = ceil($max_procs / scalar(@fastq)); my $proc_grand_child = ceil($proc_child/4); my $pm = Parallel::ForkManager->new($max_procs); my $pm2 = Parallel::ForkManager->new($proc_grand_child); $pm->run_on_finish( sub { my ($pid, $exit_code, $ident) = @_; print $report "Fastq fork $ident just finished ". "with PID $pid and exit code: $exit_code\n"; die "Something went wrong!\n" if $exit_code != 0; }); $pm->run_on_start( sub { my ($pid,$ident)=@_; print $report "Fastq fork : $ident started, pid: $pid\n"; }); $pm2->run_on_finish( sub { my ($pid, $exit_code, $ident) = @_; print $report "** Subgroup fork $ident just finished ". "with PID $pid and exit code: $exit_code\n"; die "Something went wrong!\n" if $exit_code != 0; }); $pm2->run_on_start( sub { my ($pid,$ident)=@_; print $report "** Subgroup fork $ident started, pid: $pid\n"; }); foreach my $child ( 0 .. $#fastq ) { my @suffix = ('.fastq', '.fastq.gz,', '.fq', '.fq.gz', 'ref', '.dat', '.fa','.fas','.fasta', '.txt'); my ( $name, $path, $suffix ) = fileparse( $fastq[$child], @suffix ); my ( $ref_name, $ref_path, $ref_suffix ) = fileparse( $ref, @suffix ); my ( $TE_name, $TE_path, $TE_suffix ) = fileparse( $TE, @suffix ); my ( $ex_name, $ex_path, $ex_suffix ) = fileparse( $transcripts, @suffix ); $pm->start($fastq[$child]) and next; my $dir_fq = $dir.$fastq_n[$child].'/'; mkdir $dir_fq; my $gen_dir = $dir_fq.'genome/'; mkdir $gen_dir; my $size_dir = $dir_fq.'size/'; mkdir $size_dir; my $fastq_resized = $dir_fq.$name.'_'.$min.'-'.$max.'.fastq'; size_distribution ( $fastq[$child], $fastq_resized, $size_dir, $min, $max ); my $sam_genome = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'.sam'; my $sam_genome_unique = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max.'_unique.sam'; my $fastq_prefix = $gen_dir.$fastq_n[$child].'_'.$min.'-'.$max; BWA_call ( $ref, $fastq_resized, $sam_genome, $mis, $proc_child, $report ); my ( $fai_ref_hashP, $ma, $ma_uni ) = get_unique ( $sam_genome, $sam_genome_unique, $gen_dir, $fq_collection.$fastq_n[$child], 1, $report ); die "No Reads mapped on the genome reference!\n" if $ma == 0; my $scale = 1000000 / $ma; sam_to_bam_bg ( $sam_genome_unique, $scale, $proc_child ); sam_to_bam_bg ( $sam_genome, $scale, $proc_child ); my $Gviz_dir = $gen_dir.'Gviz/'; my $fai_file = $gen_dir.'fai'; mkdir $Gviz_dir; my $Gviz_dir_rand = $Gviz_dir.'rand/'; mkdir $Gviz_dir_rand; my $Gviz_dir_uni = $Gviz_dir.'unique/'; mkdir $Gviz_dir_uni; open my $gfai, '>', $fai_file; foreach my $k ( sort keys %{$fai_ref_hashP} ) { print $gfai "$k\t$fai_ref_hashP->{$k}\n"; } close $gfai; bg_to_png ( $fai_file, $fastq_prefix.'_unique_plus.bedgraph', $fastq_prefix.'_unique_minus.bedgraph', $Gviz_dir_uni, 'Mb' ); bg_to_png ( $fai_file, $fastq_prefix.'_plus.bedgraph', $fastq_prefix.'_minus.bedgraph', $Gviz_dir_rand, 'Mb' ); my $group_dir = $dir_fq.'subgroups/'; my $fastq_uni = $fq_collection.$fastq_n[$child].'_unique_mappers.fastq'; my $fastq_all = $fq_collection.$fastq_n[$child].'_all_mappers.fastq'; my ($bo, $mi, $pi) = subgroups ( $fastq_all, $group_dir, $mis, $misTE, $proc_child, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $si_min, $si_max, $pi_min, $pi_max, $report); pie_chart($group_dir); open (my $dupnum, $gen_dir.'dup_mapnum.txt') || die "cannot open dup_mapnum.txt $!"; my %dupnum_genome; my $header = <$dupnum>; while (<$dupnum>) { chomp $_; my @dupline = split /\t/, $_; $dupnum_genome{$dupline[0]} = [$dupline[1], $dupline[2]]; } close $dupnum; my $mi_sam = $group_dir.'miRNAs.sam'; mkdir $group_dir.'miRNAs/'; my $mi_count_file = $group_dir.'miRNAs/miRNAs_reads_counts.txt'; my ( $mi_count, $mi_ref_size ) = sam_count ( $mi_sam ); rpms_rpkm( $mi_count, $mi_ref_size, $ma, $mi_count_file, $pi, $mi, $bo ); my ( $sam_transcripts, $sam_TEs ) = ( $group_dir.'transcripts.sam', $group_dir.'TEs.sam' ); my @types = ($group_dir.'bonafide_reads.fastq', $group_dir.'miRNAs.fastq', $group_dir.'siRNAs.fastq', $group_dir.'piRNAs.fastq' ); my @types_names = ('bonafide_reads', 'miRNAs', 'siRNAs', 'piRNAs'); foreach my $grand_child ( 0 .. $#types ) { my $type_dir = $group_dir.$types_names[$grand_child].'/'; my $type_prefix = $types_names[$grand_child].'-'; mkdir $type_dir; $pm2->start($types[$grand_child]) and next; my ( $type_sam_genome, $type_sam_TEs, $type_sam_transcripts ) = ( $type_dir.$type_prefix.'genome.sam', $type_dir.$type_prefix.'TEs.sam', $type_dir.$type_prefix.'transcripts.sam' ); my ( $type_sam_uni_genome, $type_sam_uni_TEs, $type_sam_uni_transcripts ) = ( $type_dir.$type_prefix.'genome_unique.sam', $type_dir.$type_prefix.'TEs_unique.sam', $type_dir.$type_prefix.'transcripts_unique.sam' ); my ( $type_uni_genome_fastq, $type_uni_TEs_fastq, $type_uni_transcripts_fastq ) = ( $fq_collection.$fastq_n[$child].'-'.$type_prefix.'genome_uni.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'TEs_uni.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'transcripts_uni.fastq'); my ( $type_genome_fastq, $type_TEs_fastq, $type_transcripts_fastq ) = ( $fq_collection.$fastq_n[$child].'-'.$type_prefix.'genome.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'TEs.fastq', $fq_collection.$fastq_n[$child].'-'.$type_prefix.'transcripts.fastq'); my $type_sequence_hashP = get_fastq_seq ( $types[$grand_child] ); if ( $grand_child == 1 ) { BWA_call ( $TE, $types[$grand_child], $type_sam_TEs, $misTE, $proc_child, $report ); BWA_call ( $transcripts, $types[$grand_child], $type_sam_transcripts, $mis, $proc_child, $report ); BWA_call ( $ref, $types[$grand_child], $type_sam_genome, $mis, $proc_child, $report ); extract_sam ( undef, $type_sam_TEs, $type_sam_TEs, $type_sam_uni_TEs, $type_uni_TEs_fastq, $type_uni_TEs_fastq ); extract_sam ( undef, $type_sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); extract_sam ( undef, $type_sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); } else { extract_sam ( $type_sequence_hashP, $sam_TEs, $type_sam_TEs, $type_sam_uni_TEs, $type_TEs_fastq, $type_uni_TEs_fastq ); extract_sam ( $type_sequence_hashP, $sam_transcripts, $type_sam_transcripts, $type_sam_uni_transcripts, $type_transcripts_fastq, $type_uni_transcripts_fastq ); extract_sam ( $type_sequence_hashP, $sam_genome, $type_sam_genome, $type_sam_uni_genome, $type_genome_fastq, $type_uni_genome_fastq ); } my $ex_count_file = $type_dir.$type_prefix.'transcripts_reads_counts.txt'; my ( $ex_count, $ex_ref_size ) = sam_count ( $type_sam_transcripts ); rpms_rpkm( $ex_count, $ex_ref_size, $ma, $ex_count_file, $pi, $mi, $bo ); my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs ); my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt'; my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt'; my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt'; rpms_rpkm( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo ); rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo ); rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo ); sam_to_bam_bg ( $type_sam_TEs, $scale, $grand_child ); sam_sorted_bam ( $type_sam_transcripts, $grand_child ); sam_sorted_bam ( $type_sam_uni_transcripts, $grand_child ); sam_sorted_bam ( $type_sam_uni_TEs, $grand_child ); my $Gviz_TEs = $type_dir.'Gviz_TEs/'; mkdir $Gviz_TEs; bg_to_png ( $group_dir.'TEs.fai', $type_dir.$type_prefix.'TEs_plus.bedgraph', $type_dir.$type_prefix.'TEs_minus.bedgraph', $Gviz_TEs, 'Kb' ); my $Gviz_genome= $type_dir.'Gviz_genome/'; my $Gviz_genome_rand = $Gviz_genome.'rand/'; my $Gviz_genome_uni = $Gviz_genome.'unique/'; mkdir $Gviz_genome; mkdir $Gviz_genome_uni; mkdir $Gviz_genome_rand; sam_to_bam_bg ( $type_sam_genome, $scale, $grand_child ); sam_to_bam_bg ( $type_sam_uni_genome, $scale, $grand_child ); bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_unique_plus.bedgraph', $type_dir.$type_prefix.'genome_unique_minus.bedgraph', $Gviz_genome_uni, 'Mb' ); bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_plus.bedgraph', $type_dir.$type_prefix.'genome_minus.bedgraph', $Gviz_genome_rand, 'Mb' ); #HTML Details my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child]; details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir, $Pcheck ); $pm2->finish(); } $pm2->wait_all_children; if ( $Pcheck eq 'true' ) { my $ppp = $group_dir.'PPPartners/'; mkdir $ppp; print $report "ping_pong_partners $group_dir/piRNAs/TEs.sam $ppp\n"; ping_pong_partners ( $group_dir.'TEs.fai', $group_dir.'piRNAs/piRNAs-TEs_sorted.bam', $ppp, $pi_min ); my $ppp_page = $dir.$fastq_n[$child].'-piRNAs-PPP.html'; ppp_page ( $group_dir, $ppp_page, \@fastq_n, $fastq_n[$child], $ppp, $dir ); } #HTML Main Webpage my $index_page = $dir.$fastq_n[$child].'.html'; main_page ( $gen_dir, $index_page, \@fastq_n, $fastq_n[$child], $ma, $ma_uni, $dir ); copy ($index_page, $html_out) if $child == 0; #HTML Menu my $menu_page = $dir.$fastq_n[$child].'-sub.html'; menu_page ( $group_dir, $menu_page, \@fastq_n, $fastq_n[$child], $min, $max, $si_min, $si_max, $pi_min, $pi_max, $dir ); unlink glob "$group_dir*.sam"; unlink glob "$group_dir*.fastq"; $pm->finish(); # pass an exit code to finish } $pm->wait_all_children; unlink glob $dir."dataset_*symlink.fa*"; print $report "Job done!\n"; close $report;