Re^3: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl

Line 15 of the code
my $gb=Bio::DB::GenBank;
should be
my $gb = new Bio::DB::GenBank;
(indirect object notation), or better yet
my $gb = Bio::DB::GenBank->new;
or
my $gb = Bio::DB::GenBank->new();
which avoid the syntactic ambiguities of indirect object notation.

Give a man a fish: <%-{-{-{-<

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Re^4: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by dimitris852 (Acolyte) on Mar 21, 2016 at 05:28 UTC
thanks! but after fixing that I get this: `Undefined subroutine &main::write_sequence called at .... line 20.`	[reply] [d/l]
Re^5: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by 1nickt (Canon) on Mar 21, 2016 at 05:33 UTC
Do you have a sub called `write_sequence` in your main package? No. So you can't call it! Perhaps your object has a method of that name? Edit: Find where you copy-pasted `write_sequence` from and refer to the docs for that module. You'll need to `use` the module in your program. I leave it to you to figure out which module it is. Hint: it's not ... LOL, just saw you figured it out. Nice! The way forward always starts with a minimal test.	[reply] [d/l] [select]
Re^6: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by dimitris852 (Acolyte) on Mar 21, 2016 at 05:38 UTC
All it needed was to add `use Bio:perl;` and now works! thanks!!	[reply] [d/l]
Re^5: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by kevbot (Vicar) on Mar 21, 2016 at 05:39 UTC
You have not written a subroutine for write_sequence and the Bio::DB::Genbank module does not provide this method. It's likely that you want to add this to your code: `use Bio::Perl;` [download] as the Bio::Perl module does provide a write_sequence method. I recommend that you carefully read the documentation for Bio::DB::Genbank and Bio::Perl.	[reply] [d/l]
Re^5: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by AnomalousMonk (Archbishop) on Mar 21, 2016 at 05:36 UTC
I haven't read the Bio::DB::GenBank documentation (please feel free to do so ;-), but I suspect that `write_sequence` is a method of that class and so maybe needs to be called something like `$gb->write_sequence( ">>roar.fa", 'fasta', $seq );` Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]