Mercurial > repos > jtilman > flexbar

comparison flexbar.pl @ 40:2fcee21876db draft

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Uploaded
author jtilman
date Sun, 01 Jul 2018 08:00:26 -0400
parents 216a55a39b52
children e1f80a81ba2c
comparison
equal deleted inserted replaced
39:ae7d2b47ad07 40:2fcee21876db
11 my @outFiles; 11 my @outFiles;
12 12
13 foreach(0..$#ARGV){ 13 foreach(0..$#ARGV){
14 my $arg = $ARGV[$_]; 14 my $arg = $ARGV[$_];
15 15
16 if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/){ 16 if($arg =~ /\.(fastq\w+)$/ || $arg =~ /\.(fastq\w+\.gz)$/ || $arg =~ /\.(fastq\w+\.bz2)$/){
17 17
18 if(defined $format && $format ne $1){
19 print STDERR "Paired read files should have the same format.\n";
20 exit 1;
21 }
18 $format = $1; 22 $format = $1;
23
19 my $file = $arg; 24 my $file = $arg;
20 25
21 $arg =~ s/\.fastq\w+$/\.fastq/; 26 $arg =~ s/\.fastq\w+$/\.fastq/;
22 $arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/; 27 $arg =~ s/\.fastq\w+\.gz$/\.fastq\.gz/;
28 $arg =~ s/\.fastq\w+\.bz2$/\.fastq\.bz2/;
29
30 push @inFiles, $arg if $arg =~ /\.dat_input\.fastq$/ || $arg =~ /\.dat_input\.fastq\.gz$/ || $arg =~ /\.dat_input\.fastq\.bz2$/;
31 push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/ || $arg =~ /\.dat\.fastq\.bz2$/;
23 32
24 $ARGV[$_] = $arg; 33 $ARGV[$_] = $arg;
25 rename $file, $arg; 34 rename $file, $arg;
26
27 push @inFiles, $arg if $arg =~ /\.dat_input\.fastq$/ || $arg =~ /\.dat_input\.fastq\.gz$/;
28 push @outFiles, $arg if $arg =~ /\.dat\.fastq$/ || $arg =~ /\.dat\.fastq\.gz$/;
29 } 35 }
30 } 36 }
31 37
32 my $call = join " ", @ARGV; 38 my $call = join " ", @ARGV;
33 39
40 46
41 my $file = $_; 47 my $file = $_;
42 48
43 s/\.fastq$//; 49 s/\.fastq$//;
44 s/\.fastq\.gz$//; 50 s/\.fastq\.gz$//;
51 s/\.fastq\.bz2$//;
45 52
46 rename $file, $_; 53 rename $file, $_;
47 } 54 }
48 55