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Parse a genbank file using regular expressions

  • Public
By Nishi Singh 3151 days ago
#! /usr/local/bin/perl -w $genbank = "genbank_file.txt"; open (GENBANK, $genbank) || die "cannot open $gb_report for reading: $!"; # Flag for multiline translation; 1 means translation "in progress" $trans = 0; while (<GENBANK>) { if (/(LOCUS\s*)(\w*)(.*)/) { print "Locus: $2\n"; } elsif (/(VERSION.*GI:)(\d*)/) { print "GI: $2\n"; } elsif (/(DEFINITION\s*)(.*)(\.)/) { print "Sequence name: $2\n"; } elsif (/(ORGANISM\s*)(.*)/) { print "Organism: $2\n"; } elsif(/(gene)(\s*)(\d*)(\.\.)(\d*)/) { print "Gene length: $5\n"; } elsif (/(CDS\s*)(\d*)(\.\.)(\d*)/) { # ex: CDS 357..1541 $cds_start = $2; $cds_end = $4; print "CDS: $cds_start - $cds_end\n"; } elsif (/(\/translation=")(.*)/) { # protein product begins print "Translation: "; $protein = $2; $trans = 1; } elsif ($trans) { # translation still going on if (!/"/) { # no terminal quote; translation continues $protein .= $_; } elsif (/(.*)(")/) { # terminal quote; end of translation $protein .= $1; $protein =~ s/\s*//g; print "$protein\n"; $trans = 0; } else { print "Problems: end of translation product not found.\n"; } } else { # Skip this data } }