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comparison bin/align.pm @ 60:9645d995fb3c draft

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Fix for spaces in datasets names.
author pierre.pouchin
date Wed, 24 Oct 2018 07:40:20 -0400
parents 4bc00caa60b4
children 9185ca0a7b43
comparison
equal deleted inserted replaced
59:eeb89c3331ad 60:9645d995fb3c
32 sub build_index 32 sub build_index
33 { 33 {
34 my $to_index = shift; 34 my $to_index = shift;
35 my $log = shift; 35 my $log = shift;
36 my $index_log = $to_index.'_index.err'; 36 my $index_log = $to_index.'_index.err';
37 `bwa index $to_index 2> $index_log`; 37 `bwa index '$to_index' 2> '$index_log'`;
38 print $log "Creating index for $to_index\n"; 38 print $log "Creating index for $to_index\n";
39 } 39 }
40 40
41 sub get_unique 41 sub get_unique
42 { 42 {
410 $bedgraphP= $1.'_plus.bedgraph'; 410 $bedgraphP= $1.'_plus.bedgraph';
411 $bedgraphM = $1.'_minus.bedgraph'; 411 $bedgraphM = $1.'_minus.bedgraph';
412 $view_err = $1.'_view.err'; 412 $view_err = $1.'_view.err';
413 $sort_err = $1.'_sort.err'; 413 $sort_err = $1.'_sort.err';
414 } 414 }
415 `samtools view -Shb --threads $number_of_cpus $sam 2> $view_err | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> $sort_err > $bam_sorted`; 415 `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`;
416 `bedtools genomecov -scale $scale -strand + -bga -ibam $bam_sorted > $bedgraphP`; 416 `bedtools genomecov -scale $scale -strand + -bga -ibam '$bam_sorted' > '$bedgraphP'`;
417 `bedtools genomecov -scale $scale -strand - -bga -ibam $bam_sorted > $bedgraphM`; 417 `bedtools genomecov -scale $scale -strand - -bga -ibam '$bam_sorted' > '$bedgraphM'`;
418 } 418 }
419 419
420 sub sam_sorted_bam 420 sub sam_sorted_bam
421 { 421 {
422 my ( $sam, $number_of_cpus ) = @_; 422 my ( $sam, $number_of_cpus ) = @_;
426 $bam_sorted = $1.'_sorted.bam'; 426 $bam_sorted = $1.'_sorted.bam';
427 $view_err = $1.'_view.err'; 427 $view_err = $1.'_view.err';
428 $sort_err = $1.'_sort.err'; 428 $sort_err = $1.'_sort.err';
429 429
430 } 430 }
431 `samtools view -Shb --threads $number_of_cpus $sam 2> $view_err | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> $sort_err > $bam_sorted`; 431 `samtools view -Shb --threads $number_of_cpus '$sam' 2> '$view_err' | samtools sort -O BAM --threads $number_of_cpus /dev/stdin 2> '$sort_err' > '$bam_sorted'`;
432 } 432 }
433 433
434 sub BWA_call 434 sub BWA_call
435 { 435 {
436 my ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ) = @_; 436 my ( $index, $fastq, $sam, $mismatches, $number_of_cpus, $report ) = @_;
437 my ( $aln_err, $samse_err, $seq_num ) = ( $sam.'_aln.err', $sam.'_samse.err', 0 ); 437 my ( $aln_err, $samse_err, $seq_num ) = ( $sam.'_aln.err', $sam.'_samse.err', 0 );
438 print $report "-----------------------------\n"; 438 print $report "-----------------------------\n";
439 print $report "bwa aln -t $number_of_cpus -n $mismatches $index $fastq 2> $aln_err | bwa samse $index /dev/stdin $fastq 2> $samse_err > $sam\n"; 439 print $report "bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam'\n";
440 `bwa aln -t $number_of_cpus -n $mismatches $index $fastq 2> $aln_err | bwa samse $index /dev/stdin $fastq 2> $samse_err > $sam `; 440 `bwa aln -t $number_of_cpus -n $mismatches '$index' '$fastq' 2> '$aln_err' | bwa samse $index /dev/stdin '$fastq' 2> '$samse_err' > '$sam' `;
441 } 441 }
442 442
443 sub rpms_rpkm 443 sub rpms_rpkm
444 { 444 {
445 my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_; 445 my ( $counthashR, $sizehashR, $mapped, $out_file, $piRNA_number, $miRNA_number, $bonafide_number ) =@_;