[Biopython] Parsing FASTA headers

[Peter Cock]

Hi Alexey,

Norbert is right that because every database has their own FASTA
conventions, we do not attempt to parse the title lines more than
this.

Note if you use the low-level Bio.SeqIO.FastaIO.SimpleFastaParser
you just get tuples of two strings - the title line and the sequence -
so you can transform this yourself if you wish to.

Peter

On Tue, Aug 23, 2016 at 9:30 AM, Norbert Auer <norbert.auer at boku.ac.at> wrote:
> Hi Alexey!
>
> I don't think that there is such a support in Biopython. As you said
> yourself every database use its own format. But writing a parser is
> quite simple if you speak regular expressions.
>
> ...
>
> On 2016-08-23 05:13, Alexey Morozov wrote:
>> Hello everyone.
>> Is any support for FASTA dialects, so to say, in Biopython? For example,
>> NCBI headers include GI/new ID, human-readable sequence name, and a good
>> deal of them include species name in square brackets. Ones on JGI site
>> include two of their sequence IDs and a shortened species name. MMETSP
>> consists of lots and lots of tags. And so on and so forth, most
>> databases have some internal standart for FASTA headers that potentially
>> includes useful information.
>> Looking up docs, I found only SeqRecord.id and SeqRecord.description. If
>> I understood correctly, this just means "Stuff before or after first \s,
>> respectively". Can I get more fine-grained features without cooking up
>> my own parser?
>>
>>
>> --
>> Alexey Morozov,