I am working on a project using the following command within nano
:
from Bio import SeqIO
import sys
import re
fasta_file = (sys.argv[1])
for myfile in SeqIO.parse(fasta_file, "fasta"):
if len(myfile) > 250:
gene_id = myfile.id
mylist = re.match(r"H149xcV_\w+_\w+_\w+", gene_id)
print (">"+list.group(0))
and its providing with the following outout:
>H149xcV_Fge342_r3_h2_d1
>H149xcV_bTr423_r3_h2_d1
>H149xcV_kN893_r3_h2_d1
>H149xcV_DNp021_r3_h2_d1
>H149xcV_JEP3324_r3_h2_d1
>H149xcV_JEP3324_r3_h2_d1
>H149xcV_JEP3324_r3_h2_d1
>H149xcV_JEP3324_r3_h2_d1
>H149xcV_SRt424234_r3_h2_d1
>H149xcV_SRt424234_r3_h2_d1
>H149xcV_SRt424234_r3_h2_d1
>H149xcV_SRt424234_r3_h2_d1
How can I change my command so that it provides me with and that are UNIQUE:
>H149xcV_Fge342_r3_h2
>H149xcV_bTr423_r3_h2
>H149xcV_kN893_r3_h2
>H149xcV_DNp021_r3_h2
>H149xcV_JEP3324_r3_h2
>H149xcV_SRt424234_r3_h2
You could use a capturing group and use that in the replacement.
To prevent unnecessary backtracking, you can exclude the underscore from the word characters using a negated character class [^\W_]+
(H149xcV_[^\W_]+_[^\W_]+)_[^\W_]+
list = re.match(r"(H149xcV_[^\W_]+_[^\W_]+)_[^\W_]+", gene_id)
print (">"+list.group(1))