Question: error while executing code for parsing genbank file
0
gravatar for sharmatina189059
3 months ago by
United States
sharmatina18905910 wrote:

hello can anyone tell me what does this line mean? I am executing this script on Mac

use strict; use warnings; use feature 'say'; use Bio::GenBankParser;

my $file = shift; my $parser = Bio::GenBankParser->new( file => $file ); while ( my $seq = $parser->next_seq ) { my $feat = $seq->{'FEATURES'}; for my $f (@$feat) { my $tag = $f->{'feature'}{'locus_tag'}; my $prod = $f->{'feature'}{'product'}; if (defined $tag and defined $prod) { say join "\t", $tag, $prod; } } }

and I got an error like this: @INC (you may need to install the Bio::GenBankParser module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.2/darwin-thread-multi-2level /Library/Perl/Updates/5.18.2 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at script.pl line 4. BEGIN failed--compilation aborted at script.pl line 4.

can anyone tell me how can I parse genbank file if i want to get location product and locus_tag information. I am unable to execute this code.

ganbank file • 177 views
ADD COMMENTlink modified 3 months ago by Michael Dondrup43k • written 3 months ago by sharmatina18905910

Please format your code using 101010 button. People won't read a mess of code.

Didn't you see what it likes like after creating this post?

ADD REPLYlink written 3 months ago by shenwei3563.4k
1
gravatar for Michael Dondrup
3 months ago by
Bergen, Norway
Michael Dondrup43k wrote:

you may need to install the Bio::GenBankParser module

(In addition you need to read the error message ;)

ADD COMMENTlink written 3 months ago by Michael Dondrup43k

I have already install Bio::GenBankParser module, but while executing this code it is showing error.

ADD REPLYlink written 3 months ago by sharmatina18905910

Perl thinks otherwise, how did you install the module? EIther you used cpan or you are out of luck, so try:

cpan Bio::GenBankParser

possibly add a sudo if you need it.

ADD REPLYlink written 3 months ago by Michael Dondrup43k
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