20251125

2025-11-25 00:28:51 +08:00
commit eb3f16c30e
406 changed files with 91653 additions and 0 deletions
@@ -0,0 +1,40 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+use lib ($ENV{EUK_MODULES});
+use Fasta_reader;
+
+my $usage = "usage: $0 targets.fasta\n\n";
+
+my $target_fasta_file = $ARGV[0] or die $usage;
+
+
+main: {
+    
+    my $fasta_reader = new Fasta_reader($target_fasta_file);
+
+    my %seqs = $fasta_reader->retrieve_all_seqs_hash();
+    
+    foreach my $acc (keys %seqs) {
+	my $sequence = $seqs{$acc};
+
+	my $seq_len = length($sequence);
+	if ($seq_len < 500) { next; }
+
+	my $bubble_missing_seq = $sequence;
+	$bubble_missing_seq = substr($bubble_missing_seq, 0, 200) . substr($bubble_missing_seq, 350);
+	
+	my $new_gene_acc = $acc;
+	$new_gene_acc =~ s/\W/_/g;
+
+	print ">isoA-$new_gene_acc;$new_gene_acc\n$sequence\n"
+	    . ">isoB-$new_gene_acc;$new_gene_acc\n$bubble_missing_seq\n";
+
+    }
+    
+
+    exit(0);
+}
+