Permalink
Browse files

Fixed nasty bug coming from Ensembl missing the first line of repeatm…

…asker output file

svn path=/bioperl-run/trunk/; revision=13181
  • Loading branch information...
1 parent 8ae3a4f commit a098408df01b49aea32186859b927ec926e27720 elia committed Aug 16, 2002
Showing with 7 additions and 7 deletions.
  1. +7 −7 Bio/Tools/Run/RepeatMasker.pm
View
14 Bio/Tools/Run/RepeatMasker.pm
@@ -334,16 +334,16 @@ sub _parse_results {
open(REPOUT,"<$outfile") || $self->throw("Error opening $outfile\n");
my $filehandle = \*REPOUT;
my @repeat_features;
- #check if no repeats found
- if (<$filehandle> =~ /no repetitive sequences detected/)
- {
- print STDERR "RepeatMasker didn't find any repetitive sequences\n";
- close $filehandle;
- return;
}
#extract values
while (<$filehandle>) {
- if (/\d+/) { #ignore introductory lines
+ if (/$filehandle/ =~ /no repetitive sequences detected/)
+ {
+ print STDERR "RepeatMasker didn't find any repetitive sequences\n";
+ close $filehandle;
+ return;
+ }
+ if (/\d+/) { #ignore introductory lines
my @element = split;
# ignore features with negatives
next if ($element[11-13] =~ /-/);

0 comments on commit a098408

Please sign in to comment.