Accessor methods for Bio::SeqIO
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7.5 years ago
Yaseen Ladak ▴ 30

Hello All,

I need some help.

I am trying to use Bio::SeqIO. How can I know what accessor functions does this module have like for example:

my $seqin  = Bio::SeqIO->new(-file => "myfile.fa",      -format => "fasta");
my $seqout = Bio::SeqIO->new(-file => ">myfile_100.fa", -format => "fasta");
while(my $seq = $seqin->next_seq) {
  if($seq->length <= 100) {
    $seqout->write_seq($seq);
  }
}

or for example $seq->desc

Is there a way to know what all methods each bio perl module may have? If so what is the right command? Is there a general command to be used on any bio perl module to find this out?

Thanks, Yaseen

Bio perl Fasta Sequence sequencing • 1.6k views
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Edited your post for clarity of the code block, you can use the 101010 button to do the same ;)

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Thank you for editing. What is 101010 button and is it for code formatting? When can I use that?

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When you write a reply you have a button bar to change the appearance of your text, including bold, italics, links. It's right above the text box and includes a 101010 button. Select the code, click the 101010 button and the code will be formatted. Alternatively, you can add the indentation yourself but this is more convenient.

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Thank you very much. Thats very helpfiul.

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