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

Hello dimitris852,

The documentation for Bio::DB::GenBank states that the set_Seq_by_id method takes only one argument which is the id (as a string) of a sequence. It does not appear that you can supply a list of sequences as the argument.

So, if you want to write multiple sequences you will need to do something like this:

foreach my $id (@lines) {
    my $seq = $gb->get_Seq_by_id($id);
    write_sequence( ">>roar.fa", 'fasta', $seq );
}
[download]

Note that I changed the write mode from > to >> in order to append to the file. So, you should delete any old roar.fa file that may exist before running the script again.

Comment on Re: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl Select or Download Code

Replies are listed 'Best First'.
Re^2: Get Fasta file with Protein Sequences given a file with Genbank Ids using Perl by dimitris852 (Acolyte) on Mar 21, 2016 at 05:09 UTC
hello 1nickt and kevbot, I'm trying this code: `use strict; use warnings; use Bio::DB::GenBank; use File::Slurp; my @lines = read_file('sec.txt'); chomp @lines; print "@lines\n"; foreach my $id (@lines) { my $gb=Bio::DB::GenBank; my $seq = $gb->get_Seq_by_id($id); write_sequence( ">>roar.fa", 'fasta', $seq ); }` [download] Everything seem logic but I get this Error: `Bareword "Bio::DB::GenBank" not allowed while "strict subs" in use at .... line 15.` I have absolutely no idea how to fix it ....	[reply] [d/l] [select]
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
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
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
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]