comparison bin/piPipe.pl @ 29:0a47c6cf912d draft

Uploaded

28:aea6ed0da85b

use Rcall qw (pie_chart bg_to_png );
use align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm BWA_call get_fastq_seq extract_sam sam_to_bam_bg );
use html qw ( main_page details_pages menu_page ppp_page );
use File::Copy;

my ( @fastq, @fastq_n, $dir, $min, $max, $mis, $misTE, $help, $Pcheck, $Dcheck, $mapnumf, $html_out);
my ( $ref, $tRNAs, $rRNAs, $snRNAs, $miRNAs, $exons, $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 $max_procs = 8;

	"pi_max:i" => \$pi_max,
	"mis:i" => \$mis,
	"misTE:i" => \$misTE,
	"html:s" => \$html_out,
	"PPPon:s" => \$Pcheck,
	"Dison:s" => \$Dcheck,
	"help"   =>  \$help,
	"ref:s" => \$ref,
	"tRNAs:s" => \$tRNAs,
	"rRNAs:s" => \$rRNAs,
	"snRNAs:s" => \$snRNAs,

		my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs );
		my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt';
		my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt';
		my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt';
		rpms_rpkm( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo );
		rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_M, $pi, $mi, $bo );
		rpms_rpkm( $TEs_count_M, $TEs_ref_size, $ma, $TEs_count_file_noM, $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_uni_TEs, $grand_child ); 

		bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_unique_plus.bedgraph', $type_dir.$type_prefix.'genome_unique_minus.bedgraph', $Gviz_genome_uni, 'Mb' );
		bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_plus.bedgraph', $type_dir.$type_prefix.'genome_minus.bedgraph', $Gviz_genome_rand, 'Mb' );

		#HTML Details
		my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child];
		details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir );

		$pm2->finish();
	}
	$pm2->wait_all_children;

29:0a47c6cf912d

use Rcall qw (pie_chart bg_to_png );
use align qw ( to_build get_unique sam_count sam_count_mis sam_sorted_bam rpms_rpkm BWA_call get_fastq_seq extract_sam sam_to_bam_bg );
use html qw ( main_page details_pages menu_page ppp_page );
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 ( $si_min, $si_max, $pi_min, $pi_max );
my ( $build_index, $build_tRNAs, $build_rRNAs, $build_snRNAs, $build_miRNAs, $build_exons, $build_TE );
my $max_procs = 8;

	"pi_max:i" => \$pi_max,
	"mis:i" => \$mis,
	"misTE:i" => \$misTE,
	"html:s" => \$html_out,
	"PPPon:s" => \$Pcheck,
	"help"   =>  \$help,
	"ref:s" => \$ref,
	"tRNAs:s" => \$tRNAs,
	"rRNAs:s" => \$rRNAs,
	"snRNAs:s" => \$snRNAs,

		my ( $TEs_count, $TEs_ref_size, $TEs_count_NoM, $TEs_count_M ) = sam_count_mis ( $type_sam_TEs );
		my $TEs_count_file = $type_dir.$type_prefix.'TEs_reads_counts.txt';
		my $TEs_count_file_M = $type_dir.$type_prefix.'TEs_reads_counts_mismatches.txt';
		my $TEs_count_file_noM = $type_dir.$type_prefix.'TEs_reads_counts_nomismatches.txt';
		rpms_rpkm( $TEs_count, $TEs_ref_size, $ma, $TEs_count_file, $pi, $mi, $bo );
		rpms_rpkm( $TEs_count_NoM, $TEs_ref_size, $ma, $TEs_count_file_noM, $pi, $mi, $bo );
		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_uni_TEs, $grand_child ); 

		bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_unique_plus.bedgraph', $type_dir.$type_prefix.'genome_unique_minus.bedgraph', $Gviz_genome_uni, 'Mb' );
		bg_to_png ( $fai_file, $type_dir.$type_prefix.'genome_plus.bedgraph', $type_dir.$type_prefix.'genome_minus.bedgraph', $Gviz_genome_rand, 'Mb' );

		#HTML Details
		my $prefix_details_pages = $dir.$fastq_n[$child].'-'.$types_names[$grand_child];
		details_pages ( $type_dir, $prefix_details_pages, \@fastq_n, $fastq_n[$child], $misTE, $dir, $Pcheck );

		$pm2->finish();
	}
	$pm2->wait_all_children;