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extract_selected_IDs.py
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extract_selected_IDs.py
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#make a dictionary of sequence naame and fastaa sequence
#get start and end position from gff file
#extract the region
import sys
import subprocess
from Bio import SeqIO
import re
import pandas as pd
import textwrap
def main():
description="Extract sequences from a fasta file for selected IDs, using information in gff file."\
"\nUsage:\t"\
"python extract_gene_sequences.py <fasta_filename> <gff_filename> <comma separated list of IDs>"
try:
if sys.argv[1] == "-help" or sys.argv[1]=='--h':
print(description)
exit()
fasta_file = sys.argv[1]
gff_file=sys.argv[2]
id_list=sys.argv[3].split(",")
except IndexError:
print ("Enough arguments not provided or too many arguments")
print (description)
exit()
#its_seq_file = sys.argv[2]
fasta_dict = SeqIO.to_dict(SeqIO.parse(fasta_file, "fasta"))
gffs=pd.read_csv(gff_file, sep = '\t', names= ['seq_id', 'source', 'type', 'start', 'stop','a', 'b', 'c', 'description'])
out_handle = open('extracted_sequences.fasta', 'w+')
my_wrap = textwrap.TextWrapper(width = 80)
for index, row in gffs.iterrows():
type = row['type']
seq_id = row['seq_id']
description = row['description']
#print (description)
if pd.isna(description):
continue
for variable in id_list:
if re.search('ID='+variable ,description):
ID= variable
start = int(row['start'] -1)
stop=int(row['stop'] -1)
seq_id = row['seq_id']
#print (start, stop)
text_1 = str(fasta_dict[seq_id].seq[start:stop])
sequence = my_wrap.fill(text = text_1)
out_handle.write(">%s\n%s\n" % (ID,sequence))
sequence=''
out_handle.close()
if __name__ == "__main__":
del_file=subprocess.run(["rm","extracted_sequences.fasta"], stdout=subprocess.PIPE)
#print ('the exitcode was %d' % del_file.returncode)
main()