Dear all
I have a question about an issue that I often find while doing my bioinformatic analyses and I often struggle to find a way around.
Let's say I have a fasta file like the one below
input.fasta
>ID1
ATGTGTCG.....
>ID2
CGCGTGTGATAT
>ID3
GCGCGCGCAAAA..
and then I have a tab-separated file where each ID is associated with a feature
input.txt
ID1 Nannochloropsis_oceanica
ID2 Nannochloropsis_gaditana
ID3 Nannochloropsis_oculata
and I'd like to edit the fasta identifiers by adding this feature, such that the desired output would be
output.fasta
>ID1_Nannochloropsis_oceanica
ATGTGTCG
>ID2_Nannochloropsis_gaditana
CGCGTGTGATAT
>ID3_Nannochloropsis_oculata
GCGCGCGCAAAA.
Does anyone know a simple unix/python/R code in order to automatically do that when working with thousands of sequences?
I used a python script from Tony Walters (https://gist.github.com/walterst/9147f9405cadf67a88471cc87b508333) to do that, but it is not working anymore in my own unix environment (some python error).
Thanks for your attention
Sergio
Hi Sergio Balzano
A easy way to do that is to use bash. You can do something like that
$ ID=`awk '{print ">" $1 "_" $2}' input.txt`
$ FASTA=`grep -v '>' input.fasta`
$ paste -d '\n'
Here are some resources that i recommend:
1- Python: https://gist.github.com/crazyhottommy/a59df92b48e6ad3f4630#file-change_fasta_header-py
2- Python: https://www.biostars.org/p/301242/#301255
3- Perl: https://gist.github.com/cabraham03/a7d3457919b08ac556d8
Hi Sergio Balzano
A easy way to do that is to use bash. You can do something like that
$ ID=`awk '{print ">" $1 "_" $2}' input.txt`
$ FASTA=`grep -v '>' input.fasta`
$ paste -d '\n'
import sys
from Bio import SeqIO
input_fasta = sys.argv[1]
input_ID = sys.argv[2]
output_fasta = sys.argv[3]
fr = open(input_ID,"r")
Seq_ID = {}
for line in fr:
ID = line.strip().split("\t")[0]
Species_name = line.strip().split("\t")[1]
Seq_ID[ID] = Species_name
fw = open(output_fasta,"w")
for rec in SeqIO.parse(input_fasta,"fasta"):
fw.write(">%s_%s\n%s\n"%(rec.id,Seq_ID[rec.id],str(rec.seq)))
fw.close()
#Usage python Change_SeqID.py input.fasta input.txt output.fasta
Hope my simple code can help you!
I have made such simple tools in the past, for a friend who knows nothing about programming. My tools are .jar files that executes ( in both Windows and Linux systems), a window opens asking for input files and the rest of story. If you often need to prepare such data, I can modify one of them to serve your purpose for free.
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