How to change id for a number of sequence

Question

[sanjeet00001992]

I have a list of sequence which id’s I want to change. I have their tab separated coordinate file having their old ids and new id’s (my id’s).

For example, I have a sequence like

>Aquca_005_00546.1
KHMALQFAMNAMDELMKMCQMNEPLWIPNNSGTKEMLNMEEHAKMFPWLTNFKQQHSQVRTEATRDSAVVIMNSITLTDAFLDVNKWMDIFPSIISRAKTVQIISSGIAGHASGSLHLMYAELQVQSPLVPTREAHFLRYCQQNAEEGTWAIVDFPIDSFHDSLQYSFPRYRRRPSGCLIQDMPNGYSRVTWVEHAEVEDKPVHQIFNHFVNSGTAFGAQRWLAVLQQQC
>Aquca_014_00016.1
DGWKVLTFENGVEISKRTSASFHIFRSRWLLKSVSPQQFITVANAIDAAKQWDSDLVEAKYIKDLEDNLSIIRLRFGDGSKPLFKNREFIVYERRETMADGTLVVAVASLPKEIAAGLHPKGNNTIRGLLLQSGWVVEELGDDENSCMVTYVVQLDPAGWLPKFFVNRLNTKLVMIIDNLEKL

I want to change their original ids with my ids. For example, Aquca_005_00546.1 with RaAc00546A and Aquca_014_00016.1 with RaAc00016E. My tab separated file has

Original ids

Aquca_005_00546.1   
Aquca_014_00016.1

my ids

RaAc00546A
RaAc00016E

Original id's and my id's are in tab separated file aligned line by line (Aquca_005_00546.1 = RaAc00546A)

[venu]

As there is a perl tag, take a look at Bioperl module Bio::SeqIO. And also take a look at this(pure solution).

Answer 1

[WouterDeCoster]

Quick (bio)python script tested for your limited sample data:

from Bio import SeqIO
import sys

def changeids(fasfile, iddict):
    outlist = []
    for seq_record in SeqIO.parse(fasfile, "fasta"):
        seq_record.description = ""
        seq_record.id = iddict[seq_record.id]
        outlist.append(seq_record)
    SeqIO.write(outlist, "adaptedIDs.fa", "fasta")

def extractdict(identifierfile):
    with open(identifierfile) as idfile:
        return({line.split('\t')[0] : line.strip().split('\t')[1] for line in idfile.readlines()})

iddict = extractdict(sys.argv[2])
changeids(sys.argv[1], iddict)

Save as changeids.py and execute as python changeids.py yourfas.fa yourids.txt

Expecting a file without header in yourids.txt with in column 1 the identifiers as now and column 2 the identifiers you want, and nothing else. Requires biopython.