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dbSNPfasta2flank.py
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dbSNPfasta2flank.py
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import sys
file = open(sys.argv[1], "r");
width = input("Number of flanking nucleotides: ")
prevLine = ""
inMiddle = False
header = ""
def parse_header(arr):
"""
this functions receive an array with
and returns the proper header
"""
for element in arr:
element.replace(" ","")
if (len(element) > 0 and element.startswith("rs")):
return element.replace("=","")
for line in file:
if(line[0] == '>'):
prevLine = ""
# got a header line
fragments = line.split("|")
# print line
bases = [];
for element in fragments:
if element.startswith('alleles="'):
bases = element[9:12].split("/")
bases[0].strip()
bases[1].strip()
header = parse_header(fragments[2].split(" "))
# print "header", header
elif(len(line.replace(" ","")) == 2):
inMiddle = True
else:
if inMiddle:
line = line.replace(" ","")
line = line[0:width]
prevLine = prevLine[-width:]
print (">" + header.strip() + bases[0])
print (prevLine + bases[0] + line)
print "\n"
print (">" + header.strip() + bases[1])
print (prevLine + bases[1] + line)
print "\n"
inMiddle = False
if not inMiddle:
prevLine = prevLine + line.replace(" ","")
prevLine = prevLine.replace("\n","")