Mercurial > repos > jdv > b2b_summarize_assembly

comparison summarize_run.pl @ 1:5def63878840 draft default tip

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"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"
author jdv
date Tue, 28 Sep 2021 06:16:07 +0000
parents 114353d77370
children
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0:114353d77370 1:5def63878840
15 my $fn_qc1; 15 my $fn_qc1;
16 my $fn_qc2; 16 my $fn_qc2;
17 my $fn_consensus; 17 my $fn_consensus;
18 my $fn_out; 18 my $fn_out;
19 my $n_threads = 1; 19 my $n_threads = 1;
20 my $max_aln = 100000;
21 20
22 GetOptions( 21 GetOptions(
23 'raw_1=s' => \$fn_raw1, 22 'raw_1=s' => \$fn_raw1,
24 'raw_2=s' => \$fn_raw2, 23 'raw_2=s' => \$fn_raw2,
25 'filt_1=s' => \$fn_filt1, 24 'filt_1=s' => \$fn_filt1,
28 'fastqc_1=s' => \$fn_qc1, 27 'fastqc_1=s' => \$fn_qc1,
29 'fastqc_2=s' => \$fn_qc2, 28 'fastqc_2=s' => \$fn_qc2,
30 'consensus=s' => \$fn_consensus, 29 'consensus=s' => \$fn_consensus,
31 'out=s' => \$fn_out, 30 'out=s' => \$fn_out,
32 'threads=i' => \$n_threads, 31 'threads=i' => \$n_threads,
33 'max_aln=i' => \$max_aln,
34 ); 32 );
35 33
36 34
37 my @counts; 35 my @counts;
38 for ($fn_raw1, $fn_raw2, $fn_filt1, $fn_filt2) { 36 for ($fn_raw1, $fn_raw2, $fn_filt1, $fn_filt2) {
48 46
49 47
50 die "raw pair count mismatch\n" if ($counts[0] != $counts[1]); 48 die "raw pair count mismatch\n" if ($counts[0] != $counts[1]);
51 die "filtered pair count mismatch\n" if ($counts[2] != $counts[3]); 49 die "filtered pair count mismatch\n" if ($counts[2] != $counts[3]);
52 50
53 #warn "calculating fragment length stats...\n"; 51 # read fragment stats from STDIN
54 my @lens; 52 my @lens;
55 open my $stream, '-|', "frag_lens","--forward",$fn_filt1,"--reverse",$fn_filt2,"--ref",$fn_consensus,"--threads",$n_threads,"--max_aln",$max_aln; 53 while (<STDIN>) {
56 while (<$stream>) {
57 chomp $_; 54 chomp $_;
58 push @lens, $_; 55 push @lens, $_;
59 } 56 }
60 close $stream;
61 57
62 my $frag_mean = int( sum(@lens)/scalar(@lens)+0.5 ); 58 my $frag_mean = int( sum(@lens)/scalar(@lens)+0.5 );
63 my $frag_sd = int( sqrt( sum( map {($_ - $frag_mean)**2} @lens)/(scalar(@lens)-1) )+0.5 ); 59 my $frag_sd = int( sqrt( sum( map {($_ - $frag_mean)**2} @lens)/(scalar(@lens)-1) )+0.5 );
64 60
65 # extract FastQC data 61 # extract FastQC data