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comparison htseq.pl @ 4:e0e1518e56f6 draft

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author rouan
date Thu, 26 Dec 2013 05:35:56 -0500
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3:0f51cd8ddfb0 4:e0e1518e56f6
1 #!/usr/bin/perl
2
3 use strict;
4 use warnings;
5 use Getopt::Std;
6 use File::Basename;
7 $| = 1;
8
9 # Grab and set all options
10 my %OPTIONS = (a => 0, i => "gene_id", m => "intersection-nonempty", s => "no", t => "exon");
11 getopts('a:cg:i:m:o:r:s:t:', \%OPTIONS);
12
13 die qq(
14 Usage: HTSeq.pl [OPTIONS] Group1=sample1=<SAM/BAM file> [Group1=sample2=<SAM/BAM file> ... Group2=sampleN=<SAM/BAM file> ...]
15
16 OPTIONS: -a STR skip all reads with alignment quality lower than the given minimum value (default: $OPTIONS{a})
17 -c reduce the matrix by removing any feature with no counts
18 -g STR the features file in the GFF/GTF format
19 -i STR GFF attribute to be used as feature ID (default: $OPTIONS{i})
20 -m STR mode to handle reads overlapping more than one feature. Possible values for <mode> are union, intersection-strict and intersection-nonempty (default: $OPTIONS{m})
21 -o STR output file name for expression matrix
22 -r STR the name of the output report
23 -s STR whether the data is from a strand-specific assay (default: $OPTIONS{s})
24 -t STR feature type (3rd column in GFF file) to be used, all features of other type are ignored (default, suitable for RNA-Seq and Ensembl GTF files: $OPTIONS{t})
25
26 ) if(@ARGV == 0);
27
28 my $sam_out;
29 my @counts;
30 my @features;
31 my %report;
32 my @samplenames;
33 my $current_group;
34 my @groups;
35 my @files;
36 my $groupcount = 0;
37 my %grouphash;
38
39 foreach my $input (@ARGV) {
40 my ($group, $sample, $input) = split "::", $input;
41 if(! defined $grouphash{$group}) {
42 $groupcount++;
43 $grouphash{$group} = "G${groupcount}:$group";
44 }
45 push @groups, $grouphash{$group};
46 push @samplenames, $sample;
47 push @files, $input;
48 }
49
50 for(my $index = 0; $index <= $#files; $index++) {
51 my $input_file = $files[$index];
52 my $sample = $samplenames[$index];
53
54 # run htseq
55 my @htseq;
56 my $COMM;
57 my $file_type = `file $input_file`;
58 if(grep /text$/, $file_type ) {
59 $COMM = "htseq-count -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} $input_file $OPTIONS{g}";
60 @htseq = `$COMM`;
61 } else {
62 $COMM = "samtools view $input_file | htseq-count -q -m $OPTIONS{m} -s $OPTIONS{s} -a $OPTIONS{a} -t $OPTIONS{t} -i $OPTIONS{i} - $OPTIONS{g}";
63 @htseq = `$COMM`;
64 }
65
66 my $row = 0;
67 $report{$sample} = "Command Used: $COMM\n";
68
69 for(my $row = 0; $row <= $#htseq; $row++) {
70 # store the report is an hash
71 if(grep /^no_feature|^ambiguous|^too_low_aQual|^not_aligned|^alignment_not_unique/, $htseq[$row]) {
72 $report{$sample} .= $htseq[$row];
73 } else {
74 # store the counts in a matrix
75 chomp $htseq[$row];
76 my ($feature, $value) = split "\t", $htseq[$row];
77 $counts[$row][$index] = $value;
78 if($input_file eq $files[0]) {
79 push @features, $feature;
80 }
81 }
82 }
83 }
84
85 # print the matrix
86 open(MATRIX, ">$OPTIONS{o}") || die "Could Not Create Output File $OPTIONS{o}!\n";
87 print MATRIX "#\t".join("\t", @groups)."\n";
88 print MATRIX "#Feature\t".join("\t", @samplenames)."\n";
89 for(my $row = 0; $row <= $#features; $row++) {
90 if(defined $OPTIONS{c}) {
91 my $rowsum = 0;
92 $rowsum += $_ foreach @{ $counts[$row] };
93 if(!$rowsum) {
94 next;
95 }
96 }
97 print MATRIX "$features[$row]\t".join("\t", @{ $counts[$row] })."\n";
98 }
99 close(MATRIX);
100
101 # print the report
102 open(REPORT, ">$OPTIONS{r}") || die "Could Not Create Output File $OPTIONS{r}!\n";
103 print REPORT "$groups[$_]:$samplenames[$_]\n$report{$samplenames[$_]}\n" foreach (0..$#samplenames);
104 close(REPORT);
105
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