Mercurial > repos > brasset_jensen > srnapipe
view bin/subgroups.pm @ 26:b3be854a4273 draft
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author | brasset_jensen |
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date | Sun, 20 May 2018 16:55:31 -0400 |
parents | 4155dba0d57a |
children | 4bc00caa60b4 |
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package subgroups; use strict; use warnings; use Exporter; our @ISA = qw( Exporter ); our @EXPORT_OK = qw( &subgroups ); use POSIX; use File::Copy; use FindBin; use lib $FindBin::Bin; use align qw ( get_hash_alignment ); sub subgroups { my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_; my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref ); srand(); print $report "----------------------------\n"; print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n"; mkdir $dir; $dir = $dir.'/' unless $dir =~ /(.*)\/$/; my $accept_miRNas = $dir.'miRNAs.fastq'; my $reject_miRNAs = $dir.'miRNAs_rejected.fastq'; my $sam_miRNAs = $dir.'miRNAs.sam'; my @tmp = get_hash_alignment($miRNAs, $mis, 1, 1, $accept_miRNas, $reject_miRNAs, $fin, $proc, 'miRNAs',$sam_miRNAs, $report); my $mi = $tmp[0]; my $sam = ''; $repartition{'miRNAs'} = $mi; my $reject_rRNAs = $dir.'rRNAs_rejected.fastq'; if ( $rRNAs eq 'None') { move($reject_miRNAs,$reject_rRNAs); } else { $sam = new String::Random; $sam = $sam->randpattern("CCcccccc"); @tmp = get_hash_alignment($rRNAs, $mis, 0, 1, 'NA', $reject_rRNAs, $reject_miRNAs, $proc, 'rRNAs', $sam, $report); $repartition{'rRNAs'} = $tmp[0]; unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; } my $reject_tRNAs = $dir.'rRNAs_rejected.fastq'; if ( $rRNAs eq 'None') { move($reject_rRNAs,$reject_tRNAs); } else { $sam = new String::Random; $sam = $sam->randpattern("CCcccccc"); @tmp = get_hash_alignment($tRNAs, $mis, 0, 1, 'NA', $reject_tRNAs, $reject_rRNAs, $proc, 'tRNAs', $sam, $report); $repartition{'tRNAs'} = $tmp[0]; unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; } my $bonafide = $dir.'bonafide_reads.fastq'; if ( $rRNAs eq 'None') { move($reject_tRNAs,$bonafide); } else { $sam = new String::Random; $sam = $sam->randpattern("CCcccccc"); @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report); $repartition{'snRNAs'} = $tmp[0]; unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; } my $bo = $tmp[1]; my $sam_transcripts = $dir.'transcripts.sam'; my $reject_transcripts = $dir.'rejected_transcripts.fastq'; @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai'); $repartition{'transcripts'} = $tmp[0]; my $sam_TEs = $dir.'TEs.sam'; my $reject_TEs = $dir.'rejected.fastq'; @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' ); $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1]; unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; unlink $reject_transcripts; unlink $reject_rRNAs; unlink $reject_miRNAs; unlink $reject_tRNAs; #create repartition my $pi = fastqSubgroups($bonafide, $dir, $min_si, $max_si, $min_pi, $max_pi ); open (my $re, '>'.$dir.'repartition.txt') || die "cannot open $dir repartition.txt $!\n"; print $re "type\tnumber\tpercentage\n"; $sum += $_ foreach values %repartition; foreach my $k ( sort keys %repartition ) { my $prct = 0; $prct = $repartition{$k} / $sum * 100 if $sum != 0; print $re "$k\t$repartition{$k}\t"; printf $re "%.2f\n",$prct; } return ( $bo, $mi, $pi); } sub fastqSubgroups { my ( $fastq, $output_directory, $min_si, $max_si, $min_pi, $max_pi ) = @_; my $fastq_siRNA = $output_directory."siRNAs.fastq"; my $fastq_piRNA = $output_directory."piRNAs.fastq"; open my $fic, '<', $fastq || die "cannot open input file $! \n"; open my $si, '>', $fastq_siRNA || die "cannot open siRNA.fastq $! \n"; open my $pi, '>', $fastq_piRNA || die "cannot open piRNA.fastq $! \n"; my ($length, $cmp, $type, $siRNA_number, $miRNA_h_number, $piRNA_number, $not_pi_number) = (0,0,0,0,0,0,0); my (@fastq) =(); my $seq_name; my $out; while(<$fic>) { chomp $_; $cmp++; if ($cmp == 1) { die "file do not contain a @ at line $cmp\n" unless ($_ =~ /^\@/ ); $type = 0; @fastq = (); if ($_ =~ /^\@(.*)\s.*/) { $seq_name = $1;} elsif ($_ =~ /^\@(.*)/) {$seq_name = $1;} push(@fastq,$_); } elsif ($cmp == 2) { #die "unrecognized symbol at line $cmp\n" unless $_ =~ /[atcgATCGnN]+/; push(@fastq,$_); $length = length($_); $type = 0; if ( $length >= $min_si && $length <= $max_si ) { $type = 2; $siRNA_number++; } if ($length >= $min_pi && $length <= $max_pi ) { $type += 4; $piRNA_number++; } } elsif ($cmp == 3 ) { die "file do not contain a + at line $cmp\n" unless $_ =~ /^\+/; push(@fastq,$_); } elsif ($cmp == 4 ) { push(@fastq,$_); $cmp = 0; if ($type != 0) { if ($type & 4 ) { foreach my $t (@fastq) { print $pi $t."\n";} } if ($type & 2 ) { foreach my $t (@fastq) { print $si $t."\n";} } } } } close $fic; close $si; close $pi; return ($piRNA_number); } 1;