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4
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1 '''This script takes a tab-delimited file containting position, ref base, mut base and splits any multicharacter ref or mut base entries into seperate lines and calculating the new positions'''
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2
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3 import sys
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4
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5 if len(sys.argv) != 3:
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6 exit("snpsplit takes exactly two arguments (input and output file), no more and no less")
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7
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8 input_name = sys.argv[1]
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9 output_name = sys.argv[2]
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10
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11 try:
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12 in_file = open(input_name)
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13 except IOError as e:
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14 exit("Error trying to open '"+input_name+"': {1}".format(e.errno, e.strerror))
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15
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16 try:
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17 out_file = open(output_name, 'w')
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18 except IOError as e:
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19 exit("Error trying to open '"+output_name+"': {1}".format(e.errno, e.strerror))
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20
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21 def splitter(cells):
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22 global out_lines
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23 for i in range(0,len(cells[1])):
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24 if cells[1][i] == cells[2][i]: continue
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25 out_file.write(str(int(cells[0])+i)+'\t'+cells[1][i]+'\t'+cells[2][i]+'\n')
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26 out_lines += 1
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27
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28 in_lines=out_lines=0
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29 out_file.write("Position\tRef\tMut\n")
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30 for line in in_file:
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31 in_lines += 1
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32 cells = line.rstrip().split('\t')
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33 if not str(line[0]).isdigit():
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34 out_file.write(line)
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35 continue
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36
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37 # Can only deal with SNPs/MNPs, not indels.
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38 if len(cells[1]) != len(cells[2]): continue
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39 splitter(cells)
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40
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41 in_file.close()
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42 out_file.close()
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43
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44 print "Lines read: %s" % in_lines
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45 print "Lines printed: %s" % out_lines
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