[Bioperl-guts-l] bioperl commit

Jason Stajich jason at pub.open-bio.org
Thu Jan 1 20:03:23 EST 2004


jason
Thu Jan  1 20:03:23 EST 2004
Update of /home/repository/bioperl/bioperl-live/Bio/SeqIO
In directory pub.open-bio.org:/tmp/cvs-serv22791/Bio/SeqIO

Modified Files:
	embl.pm 
Log Message:
Handle Feature Table-less records and set unknown id to something without spaces

bioperl-live/Bio/SeqIO embl.pm,1.69,1.70
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/SeqIO/embl.pm,v
retrieving revision 1.69
retrieving revision 1.70
diff -u -r1.69 -r1.70
--- /home/repository/bioperl/bioperl-live/Bio/SeqIO/embl.pm	2003/12/22 18:33:15	1.69
+++ /home/repository/bioperl/bioperl-live/Bio/SeqIO/embl.pm	2004/01/02 01:03:23	1.70
@@ -192,7 +192,7 @@
    $mol = $2;
    $div = $3;
    if(! $name) {
-       $name = "unknown id";
+       $name = "unknown_id";
    }
    my $alphabet;
 
@@ -225,8 +225,13 @@
    BEFORE_FEATURE_TABLE :
    until( !defined $buffer ) {
        $_ = $buffer;
-
-       # Exit at start of Feature table
+       warn($_);
+       # exit if we hit Sequence and there is no feature table
+       if( /^SQ/ ) {
+	   $self->_pushback($_);
+	   last;
+       }
+       # Exit at start of Feature table 
        last if /^F[HT]/;
 
        # Description line(s)
@@ -309,7 +314,7 @@
    }
 
    while( defined ($_ = $self->_readline) ) {
-       /^FT   \w/ && last;
+       /^FT\s{3}\w/ && last;
        /^SQ / && last;
        /^CO / && last;
    }
@@ -353,9 +358,9 @@
 	   /^SQ/ && last;
        }
    }
-   
    $seqc = "";	       
    while( defined ($_ = $self->_readline) ) {
+       warn($_);
        /^\/\// && last;
        $_ = uc($_);
        s/[^A-Za-z]//g;



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