| Previous changeset 34:02c46c8164a8 (2017-11-28) Next changeset 36:dfe259eb1e6b (2017-11-28) |
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Commit message:
Uploaded |
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modified:
bin/piPipe.pl |
| b |
| diff -r 02c46c8164a8 -r 67edc34cf0ef bin/piPipe.pl --- a/bin/piPipe.pl Tue Nov 28 09:08:28 2017 -0500 +++ b/bin/piPipe.pl Tue Nov 28 09:15:29 2017 -0500 |
| [ |
| @@ -17,12 +17,12 @@ use File::Copy; my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $mapnumf, $html_out); -my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE ); +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_exons, $build_TE ); +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_exons, $build_TE ) = (0,0,0,0,0,0,0); +( $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'; @@ -46,13 +46,13 @@ "rRNAs:s" => \$rRNAs, "snRNAs:s" => \$snRNAs, "miRNAs:s" => \$miRNAs, - "exons:s" => \$exons, + "transcripts:s" => \$transcripts, "TE:s" => \$TE, "build_index" => \$build_index, "build_tRNAs" => \$build_tRNAs, "build_snRNAs" => \$build_snRNAs, "build_miRNAs" => \$build_miRNAs, - "build_exons" => \$build_exons, + "build_transcripts" => \$build_transcripts, "build_rRNAs" => \$build_rRNAs, "build_TE" => \$build_TE ); @@ -67,7 +67,7 @@ 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], [$build_exons, \$exons], [$build_TE, \$TE] ); +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)); @@ -103,7 +103,7 @@ 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( $exons,@suffix ); + my ( $ex_name, $ex_path, $ex_suffix ) = fileparse( $transcripts, @suffix ); $pm->start($fastq[$child]) and next; @@ -150,7 +150,7 @@ my $group_dir = $dir_fq.'subgroups/'; my $fastq_uni = $gen_dir.'unique.fastq'; my $fastq_all = $gen_dir.'all.fastq'; - my ($bo, $mi, $pi) = subgroups ( $fastq_all, $group_dir, $mis, $misTE, $proc_child, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $TE, $si_min, $si_max, $pi_min, $pi_max, $report); + my ($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); @@ -172,7 +172,7 @@ rpms_rpkm( $mi_count, $mi_ref_size, $ma, $mi_count_file, $pi, $mi, $bo ); - my ( $sam_exons, $sam_TEs ) = ( $group_dir.'exons.sam', $group_dir.'TEs.sam' ); + 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 ) @@ -181,30 +181,30 @@ 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_exons ) = ( $type_dir.$type_prefix.'genome.sam', $type_dir.$type_prefix.'TEs.sam', $type_dir.$type_prefix.'exons.sam' ); - my ( $type_sam_uni_genome, $type_sam_uni_TEs, $type_sam_uni_exons ) = ( $type_dir.$type_prefix.'genome_unique.sam', $type_dir.$type_prefix.'TEs_unique.sam', $type_dir.$type_prefix.'exons_unique.sam' ); - my ( $type_uni_genome_fastq, $type_uni_TEs_fastq, $type_uni_exons_fastq ) = ( $fq_collection.$type_prefix.'genome_uni.fastq', $fq_collection.$type_prefix.'TEs_uni.fastq', $fq_collection.$type_prefix.'exons_uni.fastq'); - my ( $type_genome_fastq, $type_TEs_fastq, $type_exons_fastq ) = ( $fq_collection.$type_prefix.'genome.fastq', $fq_collection.$type_prefix.'TEs.fastq', $fq_collection.$type_prefix.'exons.fastq'); + 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 ) = ( $fq_collection.$type_prefix.'genome_uni.fastq', $fq_collection.$type_prefix.'TEs_uni.fastq', $fq_collection.$type_prefix.'transcripts_uni.fastq'); + my ( $type_genome_fastq, $type_TEs_fastq, $type_transcripts_fastq ) = ( $fq_collection.$type_prefix.'genome.fastq', $fq_collection.$type_prefix.'TEs.fastq', $fq_collection.$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 ( $exons, $types[$grand_child], $type_sam_exons, $mis, $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_exons, $type_sam_exons, $type_sam_uni_exons, $type_exons_fastq, $type_uni_exons_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_exons, $type_sam_exons, $type_sam_uni_exons, $type_exons_fastq, $type_uni_exons_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.'exons_reads_counts.txt'; - my ( $ex_count, $ex_ref_size ) = sam_count ( $type_sam_exons ); + my $ex_count_file = $type_dir.'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 ); @@ -216,7 +216,7 @@ 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_exons, $grand_child ); sam_sorted_bam ( $type_sam_uni_exons, $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/'; |