python extracting sequences from gene prediction output

Question

I've done a gene prediction using SoftBerry and it returns output like this:

Predicted protein(s):

>FGENESH:[mRNA]   1  12 exon (s)   4267  -   6782  1296 bp, chain +
ATGATACGCACTGCGCTTTCACGAGCAGCGGCCATCGTCGCCGCCCGCACCTCCGCCAAG
CTCCGCCCTTCCCTCCTCGCTCGATCTCCGCCGTCCAGACTCCTCCACGATGGGATTAAC
GCCAACCCAGTTGCTCTTCAGATGATCAACTACGCCGTCTCTCTCGCCAGGTCTCAGAAA
>FGENESH:   1  12 exon (s)   4267  -   6782   431 aa, chain +
MIRTALSRAAAIVAARTSAKLRPSLLARSPPSRLLHDGINANPVALQMINYAVSLARSQK
SDESYGQAQLVLEQCLSSQPSEGQDLATHNSRAMVLMAMSTLLSERGKLDEAIEKLQKVE

etc: an extensive output so manual editing is not trivial. I need to fish out the sequences that start with '>FGENESH:[mRNA]'. So, I try this:

for line in infile:
    if line.startswith('>FGENESH:[mRNA]'):
        print(line)
        outfile.write(line)

Which gives me only the header lines:

>FGENESH:[mRNA]   1  12 exon (s)   4267  -   6782  1296 bp, chain +

However, I would like the output to look like this:

>FGENESH:[mRNA]   1  12 exon (s)   4267  -   6782  1296 bp, chain +
ATGATACGCACTGCGCTTTCACGAGCAGCGGCCATCGTCGCCGCCCGCACCTCCGCCAAG
CTCCGCCCTTCCCTCCTCGCTCGATCTCCGCCGTCCAGACTCCTCCACGATGGGATTAAC
GCCAACCCAGTTGCTCTTCAGATGATCAACTACGCCGTCTCTCTCGCCAGGTCTCAGAAA

Could anyone advice me how to obtain that? I would be much obliged - being a novice and all. Thank you.

jd

Answer 1

flag = False

for line in infile:
    if flag is True:
        if line.startswith('>'):
            flag = False
        else:
            outfile.write(line)
    if line.startswith('>FGENESH:[mRNA]'):
        flag = True
        outfile.write(line)