From 2c642559f8b9efd6aa817ad2d793206650f3f72f Mon Sep 17 00:00:00 2001 From: jason Date: Tue, 16 Sep 2008 18:27:31 +0000 Subject: [PATCH] match '*' and '?' as well svn path=/bioperl-live/trunk/; revision=14883 --- Bio/AlignIO/msf.pm | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/Bio/AlignIO/msf.pm b/Bio/AlignIO/msf.pm index e51c0ed49..af7c4804c 100644 --- a/Bio/AlignIO/msf.pm +++ b/Bio/AlignIO/msf.pm @@ -126,14 +126,15 @@ sub next_aln { $seqname = $name; $start = 1; $str = $hash{$name}; - $str =~ s/[^A-Za-z]//g; + $str =~ s/[^0-9A-Za-z$Bio::LocatableSeq::OTHER_SYMBOLS]//g; + $end = length($str); } $seq = Bio::LocatableSeq->new(-seq => $hash{$name}, - -id => $seqname, - -start => $start, - -end => $end, + -id => $seqname, + -start => $start, + -end => $end, ); $aln->add_seq($seq); -- 2.11.4.GIT