fasta file parsing for blast module

[msarrias]

Hi,

For the blast module, I think it would be convenient to modify the way fasta files are read, so that it is not sensitive to the number of lines in the file.

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update:

As I understand it, a sequence record in a Fasta format consists of a single line of description starting with >, followed by a line(s) of sequence data, i.e. the sequence can be split into multiple lines and does not necessarily have to be a single line (as required by gget).

For example, if the sequence record is as follows:

>ENSFALP00000003283
MVKAAKEIQMENPREAESPSTGATCSPPEEQAKKPSMLCFKKRKKSCKKELTVKDACEGAS
EEKSQCVSADQEEAKASNPSQSSQKGTWAAIKNLARPRKRQKSCSRKKVPSDSQVQLEVD
AEESCAQELPKKRASSGVKMPCVRFSRGKKKPSPSEAVEESEGSVQANEVMGVVNKASEE

gget will raise an exception since the sequence is split into 3 lines.

[lauraluebbert]

Hi Marina,

Thank you for your suggestion! :) The reason gget blast currently only takes into account the first sequence is that each sequence will have many rows of output. To BLAST all sequences in a fasta, I would have to concatenate the outputs while making clear which results belong to which sequence.

For now, I would recommend passing each sequence in a fasta to gget blast in a loop. For example, the code below will pass each sequence in "test.fa" to gget blast and then save the results in a csv named after the sequence ID (text next to the ">").

from Bio import SeqIO
import gget

for record in SeqIO.parse("test.fa", "fasta"):
    df = gget.blast(record.seq)
    df.to_csv(record.id)

[msarrias]

Hi Laura,

Thanks for your reply. I don't think I explained myself correctly, sorry for that. I have included an update in the discussion.

[lauraluebbert]

I understand; thank you for clarifying! I will take a look at it

[lauraluebbert]

Hi Marina,

A bit of a late reply, but gget blast (and all other modules that can take fasta files as input) should now be able to handle occurrences where the sequence is split into multiple lines. Please let me know if you encounter any other problems.