Mercurial > repos > romaingred > pirna_pipeline

comparison bin/align.pm @ 46:a03408665904 draft

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Uploaded
author romaingred
date Fri, 01 Dec 2017 08:14:22 -0500
parents bd4b30bff219
children 945d903dad5a
comparison
equal deleted inserted replaced
45:ffc66227835f 46:a03408665904
44 44
45 my $fout = $col_prefix.'all_mappers.fastq'; 45 my $fout = $col_prefix.'all_mappers.fastq';
46 my $funi = $col_prefix.'unique_mappers.fastq'; 46 my $funi = $col_prefix.'unique_mappers.fastq';
47 my $frej = $col_prefix.'unmapped.fastq'; 47 my $frej = $col_prefix.'unmapped.fastq';
48 48
49 my $repartition = $prefix.'distribution.txt'; 49 my $repartition = $out_prefix.'distribution.txt';
50 my $png_rep = $prefix.'distribution.png'; 50 my $png_rep = $out_prefix.'distribution.png';
51 my ( %duplicates, %genome_hits) ; 51 my ( %duplicates, %genome_hits) ;
52 52
53 #alignement to the first reference 53 #alignement to the first reference
54 my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report ); 54 my @return = sam_parse( $sam, $fout, $funi, $frej, $s_uni, \%duplicates, \%genome_hits, $report );
55 my $ref_fai = $return[4]; 55 my $ref_fai = $return[4];
75 } 75 }
76 76
77 histogram($size_mappedHashR, $png_rep, $total); 77 histogram($size_mappedHashR, $png_rep, $total);
78 78
79 79
80 my $dup = $prefix.'dup_mapnum.txt'; 80 my $dup = $out_prefix.'dup_mapnum.txt';
81 my $dup_u = $prefix .'dup_unique.txt'; 81 my $dup_u = $out_prefix .'dup_unique.txt';
82 my $dup_r = $prefix .'dup_nonmapp.txt'; 82 my $dup_r = $out_prefix .'dup_nonmapp.txt';
83 open(my $tab,">".$dup) || die "cannot open output txt file\n"; 83 open(my $tab,">".$dup) || die "cannot open output txt file\n";
84 open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n"; 84 open(my $tab_r,">".$dup_r) || die "cannot open output txt file\n";
85 open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n"; 85 open(my $tab_u,">".$dup_u) || die "cannot open output txt file\n";
86 print $tab "sequence\tcount\tmapnum\n"; 86 print $tab "sequence\tcount\tmapnum\n";
87 print $tab_u "sequence\tcount\n"; 87 print $tab_u "sequence\tcount\n";