comparison summarize_run.pl @ 1:20d941ecc1bb draft default tip

"planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/b2b_utils commit 9bf8a0462bd44f170c0371b6cae67dd0c3b3da9f-dirty"

0:6fb0eff46972

my $fn_qc1;
my $fn_qc2;
my $fn_consensus;
my $fn_out;
my $n_threads = 1;
my $max_aln = 100000;

GetOptions(
    'raw_1=s'     => \$fn_raw1,
    'raw_2=s'     => \$fn_raw2,
    'filt_1=s'    => \$fn_filt1,

    'fastqc_1=s'  => \$fn_qc1,
    'fastqc_2=s'  => \$fn_qc2,
    'consensus=s' => \$fn_consensus,
    'out=s'       => \$fn_out,
    'threads=i'   => \$n_threads,
    'max_aln=i'   => \$max_aln,
);


my @counts;
for ($fn_raw1, $fn_raw2, $fn_filt1, $fn_filt2) {

die "raw pair count mismatch\n" if ($counts[0] != $counts[1]);
die "filtered pair count mismatch\n" if ($counts[2] != $counts[3]);

#warn "calculating fragment length stats...\n";
my @lens;
open my $stream, '-|', "frag_lens","--forward",$fn_filt1,"--reverse",$fn_filt2,"--ref",$fn_consensus,"--threads",$n_threads,"--max_aln",$max_aln;
while (<$stream>) {
    chomp $_;
    push @lens, $_;
}
close $stream;

my $frag_mean = int( sum(@lens)/scalar(@lens)+0.5 );
my $frag_sd = int( sqrt( sum( map {($_ - $frag_mean)**2} @lens)/(scalar(@lens)-1) )+0.5 );

# extract FastQC data

1:20d941ecc1bb

my $fn_qc1;
my $fn_qc2;
my $fn_consensus;
my $fn_out;
my $n_threads = 1;

GetOptions(
    'raw_1=s'     => \$fn_raw1,
    'raw_2=s'     => \$fn_raw2,
    'filt_1=s'    => \$fn_filt1,

    'fastqc_1=s'  => \$fn_qc1,
    'fastqc_2=s'  => \$fn_qc2,
    'consensus=s' => \$fn_consensus,
    'out=s'       => \$fn_out,
    'threads=i'   => \$n_threads,
);


my @counts;
for ($fn_raw1, $fn_raw2, $fn_filt1, $fn_filt2) {

die "raw pair count mismatch\n" if ($counts[0] != $counts[1]);
die "filtered pair count mismatch\n" if ($counts[2] != $counts[3]);

# read fragment stats from STDIN
my @lens;
while (<STDIN>) {
    chomp $_;
    push @lens, $_;
}

my $frag_mean = int( sum(@lens)/scalar(@lens)+0.5 );
my $frag_sd = int( sqrt( sum( map {($_ - $frag_mean)**2} @lens)/(scalar(@lens)-1) )+0.5 );

# extract FastQC data