How to create a fasta file using a list of DNA sequences data
I have a file with the following structure:
Lcn.Chr1:75500000-95000000:1393900-1393947 gaaatgatttaattagattatttgaggtttgatgattaggattagag 1648480
Lcn.Chr1:75500000-95000000:1393980-1394025 AAATATGAACTCAGGGTTTTGAGATAAGCCAAACAACGATTCCAC 1648480
Lcn.Chr1:75500000-95000000:1394080-1394127 caccccaacttttataattgctatttaaattaattaattagtattgt 1648480
I've extracted the sequences using cut -f 2, now I need to make them as a .fasta format to use it as a database for a blast analysis. Any tips on how to add the fasta header to those sequences? The IDs could be numbers 001, 002, 003..
2 answers
Using your example file (let's call it seqs.txt).
cat seqs.txt| while read line; do printf "%s%s\n%s\n" ">" $(echo $line | cut -d " " -f 1) $(echo $line | cut -d " " -f 2); done
produces:
>Chr1:75500000-95000000:1393900-1393947
gaaatgatttaattagattatttgaggtttgatgattaggattagag
>Lcn.Chr1:75500000-95000000:1393980-1394025
AAATATGAACTCAGGGTTTTGAGATAAGCCAAACAACGATTCCAC
>Lcn.Chr1:75500000-95000000:1394080-1394127
caccccaacttttataattgctatttaaattaattaattagtattgt
That's a pretty ugly solution, but it should work.
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Dave Carlson
In Python3
import sys
with open(sys.argv[1], 'r') as sequences:
for idx,line in enumerate(sequences):
print(f">{idx:03d}")
print(line.rstrip().split('\t')[1])
Launch it as
python3 script.py your_input_file > output.fasta
It produces
>0001
gaaatgatttaattagattatttgaggtttgatgattaggattagag
>0002
AAATATGAACTCAGGGTTTTGAGATAAGCCAAACAACGATTCCAC
..
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