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#!/usr/bin/env perl
use strict;
use warnings;
my $usage = "\n\n\tusage: $0 iworm_bundles_fasta_file sorted_reads_to_components_file\n\n\n";
my $iworm_bundles_fasta_file = $ARGV[0] or die $usage;
my $reads_to_components_file = $ARGV[1] or die $usage;
main: {
my %component_to_LRs;
{
open (my $fh, $reads_to_components_file) or die "Error, cannot open file: $reads_to_components_file";
while (<$fh>) {
chomp;
my @x = split(/\t/);
my $component_id = $x[0];
my $read_name = $x[1];
if ($read_name =~ /^>LR\$\|/) {
# got a long read!
my $seq = $x[3];
$component_to_LRs{$component_id} .= "X$seq";
}
}
close $fh;
}
## now add them to the compoennts:
open (my $fh, $iworm_bundles_fasta_file) or die "Error, cannot open file: $iworm_bundles_fasta_file";
while (my $header = <$fh>) {
chomp $header;
my $seq = <$fh>;
chomp $seq;
$header =~ /^>s_(\d+)/ or die "Error, cannot decipher component id";
my $component_id = $1;
if (my $LRs = $component_to_LRs{$component_id}) {
$seq .= $LRs;
}
print "$header\n$seq\n";
}
exit(0);
}
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