https://bioinformaticsonline.com/snippets/view/27313/find-and-replace-ambiguous-characters-in-fasta-file-with-perl-and-bioperl? https://bioinformaticsonline.com/snippets/view/27313/find-and-replace-ambiguous-characters-in-fasta-file-with-perl-and-bioperl Fri, 13 May 2016 03:20:09 -0500 https://bioinformaticsonline.com/snippets/view/27313/find-and-replace-ambiguous-characters-in-fasta-file-with-perl-and-bioperl #!/usr/bin/perl -w my $usage="\nUsage: $0 [-h] [-m char] [fastaFileName1 ...]\n". " -h: help\n". " -m: missing character\n". "Print out the name of sequences with characters other than ATGC-.\n". "If -m is specified, the ambiguous characters are repleced with the\n". "specified character. e.g. -m '?' will place ? to the ambigous characters.\n" . "If multiple files are given, sequences in all files are marged. If no \n". "argument is given, it will take STDIN as the input\n"; our($opt_h, $opt_m); use Bio::SeqIO; use Getopt::Std; getopts('hm:') || die "$usage\n"; die "$usage\n" if (defined($opt_h)); my $format = "fasta"; my @seqArr = (); @ARGV = ('-') unless @ARGV; while (my $file = shift) { my $seqio_obj = Bio::SeqIO->new(-file => $file, -format => $format); while (my $seq = $seqio_obj->next_seq()) { push(@seqArr, $seq); } } #@seqArr = sort { $a->id() cmp $b->id() } @seqArr; foreach my $s (@seqArr) { my $thisSeq = $s->seq(); my $ambig = AmbiguousChar($thisSeq); if ($ambig ne "") { print STDERR $s->id(), "\t$ambig\n"; if (defined($opt_m)) { $thisSeq = ReplaceAmbiguousChar($thisSeq, $opt_m); $s->seq($thisSeq); } } } if (defined($opt_m)) { my $seqOut = Bio::SeqIO->new(-fs => \*STDOUT, -format => $format); foreach my $s (@seqArr) { $seqOut->write_seq($s); } } exit; sub AmbiguousChar { my $string = shift; $string =~ s/[ATGC-]//g; $string =~ s/\s+//g; return $string; } sub ReplaceAmbiguousChar { my ($string, $char) = @_; $string =~ s/[^ATGC-]/$char/g; return $string; }]]> Radha Agarkar