--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.5.0/bin/fasta_join.pl	Mon Jun 05 18:48:51 2023 -0400
@@ -0,0 +1,88 @@
+#!/usr/bin/env perl
+
+# Kranti Konganti
+# Takes in a gzipped multi-fasta file
+# and joins contigs by 10 N's
+
+use strict;
+use warnings;
+use Cwd;
+use Bio::SeqIO;
+use Getopt::Long;
+use File::Find;
+use File::Basename;
+use File::Spec::Functions;
+
+my ( $in_dir, $out_dir, $suffix, @uncatted_genomes );
+
+GetOptions(
+    'in_dir=s'  => \$in_dir,
+    'out_dir=s' => \$out_dir,
+    'suffix=s'  => \$suffix
+) or die usage();
+
+$in_dir  = getcwd            if ( !defined $in_dir );
+$out_dir = getcwd            if ( !defined $out_dir );
+$suffix  = '_genomic.fna.gz' if ( !defined $suffix );
+
+find(
+    {
+        wanted => sub {
+            push @uncatted_genomes, $File::Find::name if ( $_ =~ m/$suffix$/ );
+        }
+    },
+    $in_dir
+);
+
+if ( $out_dir ne getcwd && !-d $out_dir ) {
+    mkdir $out_dir || die "\nCannot create directory $out_dir: $!\n\n";
+}
+
+open( my $geno_path, '>genome_paths.txt' )
+  || die "\nCannot open file genome_paths.txt: $!\n\n";
+
+foreach my $uncatted_genome_path (@uncatted_genomes) {
+    my $catted_genome_header = '>' . basename( $uncatted_genome_path, $suffix );
+    $catted_genome_header =~ s/(GC[AF]\_\d+\.\d+)\_*.*/$1/;
+
+    my $catted_genome =
+      catfile( $out_dir, $catted_genome_header . '_scaffolded' . $suffix );
+
+    $catted_genome =~ s/\/\>(GC[AF])/\/$1/;
+
+    print $geno_path "$catted_genome\n";
+
+    open( my $fh, "gunzip -c $uncatted_genome_path |" )
+      || die "\nCannot create pipe for $uncatted_genome_path: $!\n\n";
+
+    open( my $fho, '|-', "gzip -c > $catted_genome" )
+      || die "\nCannot pipe to gzip: $!\n\n";
+
+    my $seq_obj = Bio::SeqIO->new(
+        -fh     => $fh,
+        -format => 'Fasta'
+    );
+
+    my $joined_seq = '';
+    while ( my $seq = $seq_obj->next_seq ) {
+        $joined_seq = $joined_seq . 'NNNNNNNNNN' . $seq->seq;
+    }
+
+    $joined_seq =~ s/NNNNNNNNNN$//;
+    $joined_seq =~ s/^NNNNNNNNNN//;
+
+    # $joined_seq =~ s/.{80}\K/\n/g;
+    # $joined_seq =~ s/\n$//;
+    print $fho $catted_genome_header, "\n", $joined_seq, "\n";
+
+    $seq_obj->close();
+    close $fh;
+    close $fho;
+}
+
+sub usage {
+    print
+"\nUsage: $0 [-in IN_DIR] [-ou OUT_DIR] [-su Filename Suffix for Header]\n\n";
+    exit;
+}
+