Re^2: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl

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Re^3: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by AnomalousMonk (Archbishop) on Mar 21, 2016 at 05:20 UTC
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 $gb = Bio::DB::GenBank->new();` which avoid the syntactic ambiguities of indirect object notation. Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]
Re^4: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by dimitris852 (Acolyte) on Mar 21, 2016 at 05:28 UTC
thanks! but after fixing that I get this: `Undefined subroutine &main::write_sequence called at .... line 20.`	[reply] [d/l]
Re^5: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by 1nickt (Canon) on Mar 21, 2016 at 05:33 UTC
Do you have a sub called `write_sequence` in your main package? No. So you can't call it! Perhaps your object has a method of that name? Edit: Find where you copy-pasted `write_sequence` from and refer to the docs for that module. You'll need to `use` the module in your program. I leave it to you to figure out which module it is. Hint: it's not ... LOL, just saw you figured it out. Nice! The way forward always starts with a minimal test.	[reply] [d/l] [select]
Re^6: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by dimitris852 (Acolyte) on Mar 21, 2016 at 05:38 UTC
Re^5: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by kevbot (Vicar) on Mar 21, 2016 at 05:39 UTC
You have not written a subroutine for write_sequence and the Bio::DB::Genbank module does not provide this method. It's likely that you want to add this to your code: `use Bio::Perl;` [download] as the Bio::Perl module does provide a write_sequence method. I recommend that you carefully read the documentation for Bio::DB::Genbank and Bio::Perl.	[reply] [d/l]
Re^5: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by AnomalousMonk (Archbishop) on Mar 21, 2016 at 05:36 UTC
I haven't read the Bio::DB::GenBank documentation (please feel free to do so ;-), but I suspect that `write_sequence` is a method of that class and so maybe needs to be called something like `$gb->write_sequence( ">>roar.fa", 'fasta', $seq );` Give a man a fish: `<%-{-{-{-<`	[reply] [d/l] [select]
Re^3: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by 1nickt (Canon) on Mar 21, 2016 at 05:27 UTC
Sure you do. If something stops working, go back and look at what worked. Your OP had: `my $gb=new Bio::DB::GenBank;` [download] Now this is actually deprecated syntax and should be written as: `my $gb = Bio::DB::GenBank->new();` [download] ... but either style shows the point: you need to call the new() method to get an instance of the class Bio::DB::GenBank, aka, an object, and store it in `$gb`. Your existing code just assigns the bareword 'Bio::DB::GenBank' to `$gb` -- or tries to, but barewords are not allowed in your script because you're sensibly using `strict`. This is a great example of why to use `strict`: it tells you exactly what the problem is and where to find it. Also, don't use File::Slurp, it's broken. Use File::Slurper or Path::Tiny. Hope this helps! The way forward always starts with a minimal test.	[reply] [d/l] [select]
Re^3: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by kevbot (Vicar) on Mar 21, 2016 at 05:26 UTC
Change this: `my $gb=Bio::DB::GenBank;` [download] to this: `my $gb = new Bio::DB::GenBank;` [download] and see if that gets things working for you.	[reply] [d/l] [select]