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about bioperl script for extracting sequences from a fasta file(get orf output file) with ids which has less than 30 amino acids

i want the script to get sequences from a fasta file which is an output of jemboss(get orf) which has less than 30 amino acids

rna-seq bioperl python
• 2,039 views • link
updated by Nitin Narwade Nitin Narwade • written by yaminivadapally • yaminivadapally

Smell of a homework assignment ! Although, Nitin Narwade has answered your question, you are supposed to write your own code and ask for help in case of errors or problems. You cannot ask for the complete ready made solution. This is not the way this forum is supposed to be used.

For trivial tasks like this , I would recommend using tools like seqkit however, if that is your programming assignment, please make some efforts or show us your efforts here before posting.

• 1 views • link
written by lakhujanivijay lakhujanivijay

1 answer

A plain python code:

fread = open("inputFileName.fasta", "r")
fwrite = open("output.fasta", "w")

header = ""
seq = ""

for line in fread:
    line = line.strip()
    if(line[0] == ">"):     
        if(header != ""):
            if(len(seq) < 30):
                fwrite.write (header + "\n" + seq + "\n")
            header = ""
            seq = ""
        header = line
    else:
        seq += line
if(len(seq) < 30):
    fwrite.write (header + "\n" + seq + "\n")

fread.close()
fwrite.close()
• 1 views • link
written by Nitin Narwade Nitin Narwade

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