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--- tech [2019/03/29 11:02]
fplmarques [Extract features from NCBI/GenBank annotation]
+++ tech [2019/03/29 13:34] (current)
fplmarques [Extract features from NCBI/GenBank annotation]
@@ Line 108: / Line 108: @@
  <code>for file in *.gb ; do python extract_*.py ${file} ${file%.*}.fas ; done </code>
+This code extracts individual genomes from concatenated genomes in GenBank (*.gb) format.
+<code perl | get_individual_genomes.pl>
+#!/usr/bin/perl
+#
+# usage:
+#	perl  get_individual_genomes.pl input_file.gb
+#
+#
+$file = $ARGV[0];
+open (FILE, $file);
+ while (<FILE>) {
+   if ($_ =~ m/^LOCUS\s+(\w+).*/){
+	$output_file = "$1\.gb";
+	open($out, '>', $output_file);
+	print $out "$_";
+   }
+   if (($_ =~ m/^[\w|\s|\d].*/) ne ($_ =~ m/^LOCUS.*/)){
+	print $out "$_";
+   }
+   if ($_ =~ m/^\/\/\n/){
+	print $out "$_";
+	close ($out);
+   }
+ }
+close (FILE);
+ </code>
 ===== Sequence submission to the NCBI/GenBank =====