kkonganti@17: #!/usr/bin/env perl
kkonganti@17: 
kkonganti@17: # Kranti Konganti
kkonganti@17: # Takes in a gzipped multi-fasta file
kkonganti@17: # and joins contigs by 10 N's
kkonganti@17: 
kkonganti@17: use strict;
kkonganti@17: use warnings;
kkonganti@17: use Cwd;
kkonganti@17: use Bio::SeqIO;
kkonganti@17: use Getopt::Long;
kkonganti@17: use File::Find;
kkonganti@17: use File::Basename;
kkonganti@17: use File::Spec::Functions;
kkonganti@17: 
kkonganti@17: my ( $in_dir, $out_dir, $suffix, @uncatted_genomes );
kkonganti@17: 
kkonganti@17: GetOptions(
kkonganti@17:     'in_dir=s'  => \$in_dir,
kkonganti@17:     'out_dir=s' => \$out_dir,
kkonganti@17:     'suffix=s'  => \$suffix
kkonganti@17: ) or die usage();
kkonganti@17: 
kkonganti@17: $in_dir  = getcwd            if ( !defined $in_dir );
kkonganti@17: $out_dir = getcwd            if ( !defined $out_dir );
kkonganti@17: $suffix  = '_genomic.fna.gz' if ( !defined $suffix );
kkonganti@17: 
kkonganti@17: find(
kkonganti@17:     {
kkonganti@17:         wanted => sub {
kkonganti@17:             push @uncatted_genomes, $File::Find::name if ( $_ =~ m/$suffix$/ );
kkonganti@17:         }
kkonganti@17:     },
kkonganti@17:     $in_dir
kkonganti@17: );
kkonganti@17: 
kkonganti@17: if ( $out_dir ne getcwd && !-d $out_dir ) {
kkonganti@17:     mkdir $out_dir || die "\nCannot create directory $out_dir: $!\n\n";
kkonganti@17: }
kkonganti@17: 
kkonganti@17: open( my $geno_path, '>genome_paths.txt' )
kkonganti@17:   || die "\nCannot open file genome_paths.txt: $!\n\n";
kkonganti@17: 
kkonganti@17: foreach my $uncatted_genome_path (@uncatted_genomes) {
kkonganti@17:     my $catted_genome_header = '>' . basename( $uncatted_genome_path, $suffix );
kkonganti@17:     $catted_genome_header =~ s/(GC[AF]\_\d+\.\d+)\_*.*/$1/;
kkonganti@17: 
kkonganti@17:     my $catted_genome =
kkonganti@17:       catfile( $out_dir, $catted_genome_header . '_scaffolded' . $suffix );
kkonganti@17: 
kkonganti@17:     $catted_genome =~ s/\/\>(GC[AF])/\/$1/;
kkonganti@17: 
kkonganti@17:     print $geno_path "$catted_genome\n";
kkonganti@17: 
kkonganti@17:     open( my $fh, "gunzip -c $uncatted_genome_path |" )
kkonganti@17:       || die "\nCannot create pipe for $uncatted_genome_path: $!\n\n";
kkonganti@17: 
kkonganti@17:     open( my $fho, '|-', "gzip -c > $catted_genome" )
kkonganti@17:       || die "\nCannot pipe to gzip: $!\n\n";
kkonganti@17: 
kkonganti@17:     my $seq_obj = Bio::SeqIO->new(
kkonganti@17:         -fh     => $fh,
kkonganti@17:         -format => 'Fasta'
kkonganti@17:     );
kkonganti@17: 
kkonganti@17:     my $joined_seq = '';
kkonganti@17:     while ( my $seq = $seq_obj->next_seq ) {
kkonganti@17:         $joined_seq = $joined_seq . 'NNNNNNNNNN' . $seq->seq;
kkonganti@17:     }
kkonganti@17: 
kkonganti@17:     $joined_seq =~ s/NNNNNNNNNN$//;
kkonganti@17:     $joined_seq =~ s/^NNNNNNNNNN//;
kkonganti@17: 
kkonganti@17:     # $joined_seq =~ s/.{80}\K/\n/g;
kkonganti@17:     # $joined_seq =~ s/\n$//;
kkonganti@17:     print $fho $catted_genome_header, "\n", $joined_seq, "\n";
kkonganti@17: 
kkonganti@17:     $seq_obj->close();
kkonganti@17:     close $fh;
kkonganti@17:     close $fho;
kkonganti@17: }
kkonganti@17: 
kkonganti@17: sub usage {
kkonganti@17:     print
kkonganti@17: "\nUsage: $0 [-in IN_DIR] [-ou OUT_DIR] [-su Filename Suffix for Header]\n\n";
kkonganti@17:     exit;
kkonganti@17: }
kkonganti@17: