Writing fast about pyfastx HOT 3 CLOSED

You can replace or rewrite the header line of raw string like this:

import pyfastx
fa = pyfastx.Fasta(input.fasta)
representatives= fa.keys()
with open(output.faa,'w') as outf:
    for gene in fa:
        new_name= map_names[gene.name]
        rseq = gene.raw.lstrip('>{}'.format(gene.name))
        outf.write(">{}{}".format(new_name, rseq))

Hope this code can help you. In later version, I may add a functionality to help users to easily rename sequence.

from pyfastx.

I wondered how complicated it is to make some c-accelerated writing. Do you use cython for reading?

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Sorry, I'm not sure it's necessary to accelerate writing by using C. Because, the Python IO is comparable with C language. There are several reasons for me to use cpython (not cython) for accelerating reading sequence. 1) more time needed to build index by using python; 2) to resolve random access from gzipped sequence file; 3) python double memory when uppercase large sequence.

from pyfastx.