Filter sequences by length and rename them with biopython

Question

[linlinli99013]

I guess this is a very simple question for most of the people here. But I really want to know how to solve it. Thanks.

When I got a fasta file from genbank, I want to remove sequences <500 aa and rename each sequence with gb accession number and common name. I wrote two small files to solve the problem. But I don't know how to write a main program to put them together. The input file is rdrp all ref.fasta

1 sequence length filter

from Bio import SeqIO

def long_seq(filename):
    long_sequences = []
    input_handle=open(filename,'rU')
    output_handle = open("long_seqs.fasta", "w")

    for record in SeqIO.parse(input_handle, "fasta") :
        if len(record.seq) >= 500 :
            # Add this record to our list
            long_sequences.append(record)

    print "Found %i long sequences" % len(long_sequences)

    SeqIO.write(long_sequences, output_handle, "fasta")
    input_handle.close()
    output_handle.close()

if __name__=="__main__":
    long_seq('rdrp all ref.fasta')

2 rename each sequence from genbank fasta file with gb number + common name

def rename_seq(filename):
    input_handle=open(filename)
    output_handle=open("rename_seq.fasta","w")

    for line in input_handle:
        if '>' in line:
            id_old=line.strip()
            a=id_old.find('.')
            b=id_old.find('[')
            c=id_old.find(']')
            id_new='>'+id_old[(a-8):a]+' '+id_old[(b+1):c]
            print>>output_handle, id_new
        else:
            seq=line.strip()
            print>>output_handle, seq    


    input_handle.close()
    output_handle.close()

if __name__=="__main__":
    rename_seq('long_seqs.fasta')

Answer 1

[Ram]

You could minimize the number of times you open the file by making long_seq(seq,X) simply about passing a flag if the len(seq)>X (though that would make the function meaningless).

Or, you could just put the files in the same directory and call one from the other - you'll just have to add an import with the file name of the file you're calling, which in your case would be:

import long_seq_filter.py

I'd also suggest using SeqIO in your second script so you can parse FASTA without worries.

Answer 2

[linlinli99013]

#shorter code.

# sequence length filter and
# rename the sequence with gb accession no. and common name
# input_file.fasta and output_file.fasta are given as two cmd args

from Bio import SeqIO
import sys

def long_seq(filename):
    long_sequences = []
    input_handle=open(sys.argv[1],'rU')
    output_handle = open(sys.argv[2], "w")

    for record in SeqIO.parse(input_handle, "fasta") :
        if len(record.seq) >= 500 :
            long_sequences.append(record)

    print "Found %i long sequences" % len(long_sequences)

    for item in long_sequences:
        id_old=item.description
        a=id_old.find('.')
        b=id_old.find('[')
        c=id_old.find(']')
        id_new='>'+id_old[(a-8):a]+' '+id_old[(b+1):c]
        print>>output_handle, id_new
        sequence=item.seq
        print>>output_handle, sequence


    input_handle.close()
    output_handle.close()

if __name__=="__main__":
    long_seq(sys.argv[1])