format uniprot fasta headers
Hi,
I have a multi-fasta file with a header in the following format:
>sp|Q9Y5Q8|TF3C5_HUMAN General transcription factor 3C polypeptide 5 OS=Homo sapiens GN=GTF3C5 PE=1 SV=2
I would like to format to extract the Uniprot ID or the Protein Name (ACC) to get the following:
>Q9Y5Q8
or
>TF3C5_HUMAN
I think sed can do it but I don't know the exact combination of regexp
Thanks
4 answers
awk -F '|' '/^>/ {printf(">%s\n",$2);next;} {print;}' input.fasta
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written
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Pierre Lindenbaum
save the script as script.py and run as
python script.py file.fasta and you will get this
>Q9Y5Q8
LASJDQSMLASKDNAL
#!/usr/bin/env python
#-*- coding: UTF-8 -*-
from __future__ import division
import sys
##########################################################################################
syntax = '''
------------------------------------------------------------------------------------
Usage: python script_.py file.fasta
------------------------------------------------------------------------------------
'''
##########################################################################################
if len(sys.argv) != 2:
print syntax
sys.exit()
##########################################################################################
dict = {}
seq = ""
prefix = sys.argv[1].split('.')[0]
outfile = open(prefix + '_' + 'extracted.fasta','w')
fasta_seqs = open(sys.argv[1], 'r')
for line in fasta_seqs:
line = line.rstrip('\n')
if line.startswith('>'):
if seq:
dict[name] = seq
seq = ""
name = line.split('|')[1]
else:
seq = seq + line
dict[name] = line
for key, value in dict.iteritems():
outfile.write('>' + key + '\n' + str(value) + '\n')
Feel free to modify it as you need
In this case, I would make it little easier for User using BioPython module:
from Bio import SeqIO
for seq_record in SeqIO.parse('sample.fasta', 'fasta'):
header = seq_record.id
UniprotID ='>'+str(header.split('|')[1])
ProteinName='>'+str((header.split('|')[-1]).split(' ')[0])
seqs = str(seq_record.seq)
print UniprotID
print seqs
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written
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Pallab Bhowmick •
Yes SeqIO.write() exists, or you can use print with the format() function for proper output.
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WouterDeCoster
If you only want the unique identifiers and not the sequences:
awk -F '|' '/^>/ {printf(">%s\n",$2);}' proteome.fasta | cut -c 2- > identifiers.txt
Example input:
>sp|O67453|Y1476_AQUAE Uncharacterized protein aq_1476 OS=Aquifex aeolicus (strain VF5) OX=224324 GN=aq_1476 PE=4 SV=1
MLKSLTMENVKVVTGEIEKLRERIEKVKETLDLIPKEIEELERELERVRQEIAKKEDEL
AVAREIRHKEHEFTEVKQKIAYHRKYLERADSPREYERLLQERQKLIERAYKLSEEIYE
RRKYEALREEEEKLHQKEDEIEEKIHKLKKEYRALLNELKGLIEELNRKAREIIEKYGL
>tr|A0A384D5E1|A0A384D5E1_URSMA Prokineticin-1 OS=Ursus maritimus OX=29073 GN=PROK1 PE=3 SV=1
MRGAMRVSIMFLLVTVSDCAVITGACERDVQCGAGTCCAISLWLRGLRMCTPLGREGEEC
HPGSHKVPFFRRRQHHTCPCLPSLLCSRCLDGRYRCSTDLKNINF
Example output:
O67453
A0A384D5E1
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GenoMax
•
written
by
katieostrouchov •
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katieostrouchov •
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What you need is
cut -d '|'sed -e 's/^>.\|//' -e 's/ .//' file
thanks but this approach gives me p|Q9Y5Q8|TF3C5_HUMANeneral transcription factor 3C polypeptide 5 OS=Homo sapiens GN=GTF3C5 PE=1 SV=2
sorry, my bad forgot the wild card