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assign_sense_annotation.py
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assign_sense_annotation.py
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__author__ = 'asherkhb'
import sys
#Ensure correct number of arguments are entered.
if len(sys.argv) != 4:
print("Incorrect usage syntax: Must specify input FASTA, annotation list, and output file name./n")
print("Use 'rehead.py <Input FASTA> <Annotation List> <Output file name>'")
exit()
#Establish the inputs.
input_file = sys.argv[1]
annotation_list = sys.argv[2]
output_file = sys.argv[3]
id_dict = {}
#Create an output file for writing.
with open(output_file, 'w') as otpt:
#Open the input FASTA file for processing.
with open(input_file, 'r') as inpt:
#Establish annotation list
annotation_list = open(annotation_list, 'U')
for line in annotation_list:
#line_contents = line.strip().split(',') # Use this line for comma separated
line_contents = line.strip().split('\t') # Use this line for tab separated
id_dict[line_contents[0]] = line_contents[0]
annotation_list.close()
#Begin processing FASTA.
reading = True
while reading:
line = inpt.readline()
#Stop processing at end of input FASTA.
if line == '':
reading = False
#Process FASTA content lines.
else:
#Check header lines against list, rename if present in list. Write out appropriate header.
if line[0] == '>':
head = line.strip('>').strip('\n').strip(' ')
if head in id_dict:
line = '>%s_Known_Gene_Sense\n' % (head)
else:
pass
otpt.write(line)
#Write out sequence lines.
else:
otpt.write(line)