Using Bio.SeqIO to write single-line FASTA

Question

QIIME requests this (here) regarding the fasta files it receives as input:

The file is a FASTA file, with sequences in the single line format. That is, sequences are not broken up into multiple lines of a particular length, but instead the entire sequence occupies a single line.

Bio.SeqIO.write of course follows the format recommendations, and splits the sequence every 80 bps. I could write my own writer to write those "single-line" fastas - but my question is if there's a way that I missed to make SeqIO do that.

Cheryllches

Bioinformatics questions may find a more specialized audience at biostars.org – Carbonari

Lucky me you were here then. SO is where I'm used to go to... :) – Cheryllches

Answer 1

BioPython's SeqIO module uses the FastaIO submodule to read and write in FASTA format.

The FastaIO.FastaWriter class can output a different number of characters per line but this part of the interface is not exposed via SeqIO. You would need to use FastaIO directly.

So instead of using:

from Bio import SeqIO
SeqIO.write(data, handle, format)

use:

from Bio.SeqIO import FastaIO
fasta_out = FastaIO.FastaWriter(handle, wrap=None)
fasta_out.write_file(data)

or

for record in data:
    fasta_out.write_record(record)

Carbonari

write_file() and write_record() are marked OBSOLETE in BioPython (now). – Brakeman

Answer 2

Though both @unode and @HongboZhu provided working answers to the question, they used FastaIO.
SeqIO (now at least, and in Python3) provides functionality to write in the format you desire:

from Bio import SeqIO
SeqIO.write(data, handle, 'fasta-2line')

Samarium

Answer 3

@unode answered the question. I just want to add that write_file() and write_record() from FastaIO are marked OBSOLETE as of today. So an alternative solution is to use as_fasta_2line() function, which converts a fasta record into a plain two-line string.

from Bio.SeqIO import FastaIO
records_list = [FastaIO.as_fasta_2line(record) for record in records]
handle.writelines(records_list)

Brakeman

Answer 4

Or just write text.

g=open("outfile.fasta",'w')

for x in data:
    g.write(f">{x.description}\n{x.seq}\n")

Basso