Hi,
I have a code bioperl (below) that does the job of extracting CDS locations (e.g., (234..1234) from a GenBank file, but does not extract the complement statement when they are indicated such as complement(234530..235249). How can I extract the complement statement together with the location whenever they indicated as mentioned.
if ($feat_object->primary_tag eq "CDS") {
my $start = $feat_object->location->start;
my $end = $feat_object->location->end;
print $start . ".." . $end . "\n";
}
Thanks
•
written
by
robjohn7000
will it help to use foreach?
if ( $feature->primary_tag eq 'CDS' ) {
foreach my $location ( $feature->location->each_Location ) {
print $location->start, "..", $location->end, "\n";
}
}
-- update with full code --
#!/bin/perl
use strict;
use Bio::SeqIO;
my $seqio_object = Bio::SeqIO->new(
-file => 'tmp/NC_017187.gbk',
-format => 'genbank'
);
my $seq_object = $seqio_object->next_seq;
foreach my $feature ( $seq_object->top_SeqFeatures ) {
if ( $feature->primary_tag eq 'CDS' ) {
foreach my $location ( $feature->location->each_Location ) {
print $location->start, "..", $location->end, "\n";
}
}
}
this code produces output:
...
2254886..2255341
2255356..2255934
2255982..2256446
from the "complement" statement
$ grep "2255356..2255934" NC_017187.gbk
gene complement(2255356..2255934)
CDS complement(2255356..2255934)
Thanks seninp. Unfortunately, I got the following error: Can't call "location" on an undefined value at line: foreach my $location ( $feature->location->each_Location ).
just updated the reply
Many thanks Pavel, updated solution using grep did the trick. Very much appreciated!
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