Mercurial > repos > romaingred > pirna_pipeline
changeset 38:15fbf3bdb553 draft
Uploaded
| author | romaingred |
|---|---|
| date | Tue, 28 Nov 2017 10:11:00 -0500 |
| parents | af4ee65eaffb |
| children | e36c4f4fe5fd |
| files | bin/subgroups.pm |
| diffstat | 1 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/bin/subgroups.pm Tue Nov 28 10:05:52 2017 -0500 +++ b/bin/subgroups.pm Tue Nov 28 10:11:00 2017 -0500 @@ -13,7 +13,7 @@ sub subgroups { - my ($fin, $dir, $mis, $mis_TE, $proc, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE, $min_si, $max_si, $min_pi, $max_pi, $report ) = @_; + my ($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(); @@ -52,18 +52,18 @@ my $bo = $tmp[1]; unlink $sam, $sam.'_aln.err', $sam.'_samse.err'; - my $sam_exons = $dir.'exons.sam'; - my $reject_exons = $dir.'rejected_exons.fastq'; - @tmp = get_hash_alignment($exons, $mis, 0, 1, 'NA', $reject_exons, $bonafide, $proc, 'exons', $sam_exons, $report, $dir.'exons.fai'); - $repartition{'exons'} = $tmp[0]; + 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_exons, $proc, 'TEs', $sam_TEs, $report, $dir.'TEs.fai' ); + @tmp = get_hash_alignment($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_exons; + unlink $reject_transcripts; unlink $reject_rRNAs; unlink $reject_miRNAs; unlink $reject_tRNAs;