kkonganti@11: #!/usr/bin/env perl
kkonganti@11: 
kkonganti@11: # Kranti Konganti
kkonganti@11: # Takes in a gzipped multi-fasta file
kkonganti@11: # and joins contigs by 10 N's
kkonganti@11: 
kkonganti@11: use strict;
kkonganti@11: use warnings;
kkonganti@11: use Cwd;
kkonganti@11: use Bio::SeqIO;
kkonganti@11: use Getopt::Long;
kkonganti@11: use File::Find;
kkonganti@11: use File::Basename;
kkonganti@11: use File::Spec::Functions;
kkonganti@11: 
kkonganti@11: my ( $in_dir, $out_dir, $suffix, @uncatted_genomes );
kkonganti@11: 
kkonganti@11: GetOptions(
kkonganti@11:     'in_dir=s'  => \$in_dir,
kkonganti@11:     'out_dir=s' => \$out_dir,
kkonganti@11:     'suffix=s'  => \$suffix
kkonganti@11: ) or die usage();
kkonganti@11: 
kkonganti@11: $in_dir  = getcwd            if ( !defined $in_dir );
kkonganti@11: $out_dir = getcwd            if ( !defined $out_dir );
kkonganti@11: $suffix  = '_genomic.fna.gz' if ( !defined $suffix );
kkonganti@11: 
kkonganti@11: find(
kkonganti@11:     {
kkonganti@11:         wanted => sub {
kkonganti@11:             push @uncatted_genomes, $File::Find::name if ( $_ =~ m/$suffix$/ );
kkonganti@11:         }
kkonganti@11:     },
kkonganti@11:     $in_dir
kkonganti@11: );
kkonganti@11: 
kkonganti@11: if ( $out_dir ne getcwd && !-d $out_dir ) {
kkonganti@11:     mkdir $out_dir || die "\nCannot create directory $out_dir: $!\n\n";
kkonganti@11: }
kkonganti@11: 
kkonganti@11: open( my $geno_path, '>genome_paths.txt' )
kkonganti@11:   || die "\nCannot open file genome_paths.txt: $!\n\n";
kkonganti@11: 
kkonganti@11: foreach my $uncatted_genome_path (@uncatted_genomes) {
kkonganti@11:     my $catted_genome_header = '>' . basename( $uncatted_genome_path, $suffix );
kkonganti@11:     $catted_genome_header =~ s/(GC[AF]\_\d+\.\d+)\_*.*/$1/;
kkonganti@11: 
kkonganti@11:     my $catted_genome =
kkonganti@11:       catfile( $out_dir, $catted_genome_header . '_scaffolded' . $suffix );
kkonganti@11: 
kkonganti@11:     $catted_genome =~ s/\/\>(GC[AF])/\/$1/;
kkonganti@11: 
kkonganti@11:     print $geno_path "$catted_genome\n";
kkonganti@11: 
kkonganti@11:     open( my $fh, "gunzip -c $uncatted_genome_path |" )
kkonganti@11:       || die "\nCannot create pipe for $uncatted_genome_path: $!\n\n";
kkonganti@11: 
kkonganti@11:     open( my $fho, '|-', "gzip -c > $catted_genome" )
kkonganti@11:       || die "\nCannot pipe to gzip: $!\n\n";
kkonganti@11: 
kkonganti@11:     my $seq_obj = Bio::SeqIO->new(
kkonganti@11:         -fh     => $fh,
kkonganti@11:         -format => 'Fasta'
kkonganti@11:     );
kkonganti@11: 
kkonganti@11:     my $joined_seq = '';
kkonganti@11:     while ( my $seq = $seq_obj->next_seq ) {
kkonganti@11:         $joined_seq = $joined_seq . 'NNNNNNNNNN' . $seq->seq;
kkonganti@11:     }
kkonganti@11: 
kkonganti@11:     $joined_seq =~ s/NNNNNNNNNN$//;
kkonganti@11:     $joined_seq =~ s/^NNNNNNNNNN//;
kkonganti@11: 
kkonganti@11:     # $joined_seq =~ s/.{80}\K/\n/g;
kkonganti@11:     # $joined_seq =~ s/\n$//;
kkonganti@11:     print $fho $catted_genome_header, "\n", $joined_seq, "\n";
kkonganti@11: 
kkonganti@11:     $seq_obj->close();
kkonganti@11:     close $fh;
kkonganti@11:     close $fho;
kkonganti@11: }
kkonganti@11: 
kkonganti@11: sub usage {
kkonganti@11:     print
kkonganti@11: "\nUsage: $0 [-in IN_DIR] [-ou OUT_DIR] [-su Filename Suffix for Header]\n\n";
kkonganti@11:     exit;
kkonganti@11: }
kkonganti@11: