Changing the format of name of fasta sequences in a file including nucleotide number in sequence

Question

I don't know much programming but I am learning Linux and Python. I have a sequence file which has 13500 sequences in it. and the name of the sequences is in one form

>MP_scaffold_001_1

I want to count number of nucleotides in each sequence and want to change its name to

>MP_scaffold_001_1 <TAB> <Number_of_nucleotides>

Answer 1

If you're working with biological sequences in Python, you can't go wrong with Biopython . The SeqIO class contains tools for working with sequences, including those in FASTA format. The following code should get you started:

from Bio import SeqIO
with open("input.fasta", "r") as input, open("output.fasta", "w") as output:
    for seq in SeqIO.parse(input, "fasta"):
        length = "\t%d" % len(seq)
        seq.description += length
        SeqIO.write(seq, output, "fasta")

This code first opens two file handlers, input and output , that will automatically be closed when the processing is complete. Next, each sequence ( seq ) in input is iterated through using the SeqIO.parse() method. The length of the sequence is determined by using Python's built-in len() function, and a formatting string is built using the tab character \\t and the number returned by len() . Then, the description string of each seq is modified by adding the contents of the length variable onto the end of it. Finally, the newly-modified record is written to the output file in FASTA format.

I'd highly recommend reading through Biopython's Tutorial and Cookbook to familiarize yourself with all that the module provides.