| Previous changeset 48:6936e45f6c80 (2017-12-01) Next changeset 50:d9059a181872 (2017-12-01) |
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Commit message:
Uploaded |
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modified:
bin/piPipe.pl |
| b |
| diff -r 6936e45f6c80 -r 71ac58e0d5be bin/piPipe.pl --- a/bin/piPipe.pl Fri Dec 01 08:49:08 2017 -0500 +++ b/bin/piPipe.pl Fri Dec 01 08:54:25 2017 -0500 |
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| @@ -119,7 +119,7 @@ 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 = $gen_dir.$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; @@ -148,8 +148,8 @@ 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 $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); @@ -183,8 +183,8 @@ $pm2->start($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_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 ) |