Mercurial > repos > romaingred > pirna_pipeline

comparison bin/subgroups.pm @ 38:15fbf3bdb553 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author romaingred
date Tue, 28 Nov 2017 10:11:00 -0500
parents 509d95c26dab
children
comparison
equal deleted inserted replaced
37:af4ee65eaffb 38:15fbf3bdb553
11 use lib $FindBin::Bin; 11 use lib $FindBin::Bin;
12 use align qw ( get_hash_alignment ); 12 use align qw ( get_hash_alignment );
13 13
14 sub subgroups 14 sub subgroups
15 { 15 {
16 my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_; 16 my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $transcripts, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_;
17 my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref ); 17 my (@files, $sum, $pie, $repar, %ismapped, %isjunk, %repartition, @junk_ref, @all_ref );
18 18
19 srand(); 19 srand();
20 print $report "----------------------------\n"; 20 print $report "----------------------------\n";
21 print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n"; 21 print $report "Create subgroups:\nfastq_in: $fin\ndirectory_out: $dir\nmismatches: $mis\nmismatches TE: $mis_TE\n";
50 @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report); 50 @tmp = get_hash_alignment($snRNAs, $mis, 0, 1, 'NA', $bonafide, $reject_tRNAs, $proc, 'snRNAs', $sam, $report);
51 $repartition{'snRNAs'} = $tmp[0]; 51 $repartition{'snRNAs'} = $tmp[0];
52 my $bo = $tmp[1]; 52 my $bo = $tmp[1];
53 unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; 53 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
54 54
55 my $sam_exons = $dir.'exons.sam'; 55 my $sam_transcripts = $dir.'transcripts.sam';
56 my $reject_exons = $dir.'rejected_exons.fastq'; 56 my $reject_transcripts = $dir.'rejected_transcripts.fastq';
57 @tmp = get_hash_alignment($exons, $mis, 0, 1, 'NA', $reject_exons, $bonafide, $proc, 'exons', $sam_exons, $report, $dir.'exons.fai'); 57 @tmp = get_hash_alignment($transcripts, $mis, 0, 1, 'NA', $reject_transcripts, $bonafide, $proc, 'transcripts', $sam_transcripts, $report, $dir.'transcripts.fai');
58 $repartition{'exons'} = $tmp[0]; 58 $repartition{'transcripts'} = $tmp[0];
59 59
60 60
61 my $sam_TEs = $dir.'TEs.sam'; 61 my $sam_TEs = $dir.'TEs.sam';
62 my $reject_TEs = $dir.'rejected.fastq'; 62 my $reject_TEs = $dir.'rejected.fastq';
63 @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_exons, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' ); 63 @tmp = get_hash_alignment($TE, $mis_TE, 0, 1, 'NA', $reject_TEs, $reject_transcripts, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' );
64 $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1]; 64 $repartition{'TEs'} = $tmp[0] ; $repartition{'others'} = $tmp[1];
65 unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; 65 unlink $sam, $sam.'_aln.err', $sam.'_samse.err';
66 unlink $reject_exons; 66 unlink $reject_transcripts;
67 unlink $reject_rRNAs; 67 unlink $reject_rRNAs;
68 unlink $reject_miRNAs; 68 unlink $reject_miRNAs;
69 unlink $reject_tRNAs; 69 unlink $reject_tRNAs;
70 70
71 #create repartition 71 #create repartition