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1 #!/usr/bin/python
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2
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3 import sys
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4 import optparse
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5 import csv
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6 import re
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7
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8 def main():
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9 parser = optparse.OptionParser()
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10 parser.add_option('-s', '--snpeff_file', dest = 'snpeff_file', action = 'store', type = 'string', default = None, help = "Path to the snpEff file")
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11 parser.add_option('-c', '--candidate_list', dest = 'candidate_list', action = 'store', type = 'string', default = None, help = "Two column tabular list of candidate Gene ID, Type")
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12 parser.add_option('-o', '--output', dest = 'output', action = 'store', type = 'string', default = None, help = "Output file name")
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13 (options, args) = parser.parse_args()
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14
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15 snpeff_file = options.snpeff_file
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16 candidate_list = options.candidate_list
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17
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18 candidates = parse_candidate_list(candidate_list = candidate_list)
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19 mark_snpeff_file(snpeff_file = snpeff_file, output = options.output, candidates = candidates)
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20
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21 def skip_and_write_headers(writer = None, reader = None, i_file = None):
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22 # count headers
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23 comment = 0
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24 while reader.next()[0].startswith('#'):
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25 comment = comment + 1
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26
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27 # skip and write headers
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28 i_file.seek(0)
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29 for i in range(0, comment):
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30 row = reader.next()
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31 writer.writerow(row)
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32
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33 def parse_candidate_list(candidate_list = ""):
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34 i_file = open(candidate_list, 'rU')
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35 reader = csv.reader(i_file, delimiter = '\t',)
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36
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37 candidates = {}
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38 for row in reader:
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39 gene_id = row[0]
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40 gene_type = row[1]
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41 candidates[gene_id] = gene_type
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42
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43 i_file.close()
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44
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45 return candidates
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46
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47 def mark_snpeff_file(snpeff_file = "", output = "", candidates = None):
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48 i_file = open(snpeff_file, 'rU')
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49 reader = csv.reader(i_file, delimiter = '\t')
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50
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51 o_file = open(output, 'wb')
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52 writer = csv.writer(o_file, delimiter = '\t')
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53
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54 skip_and_write_headers(writer = writer, reader = reader, i_file = i_file)
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55
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56 for row in reader:
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57 gene_id = row[9]
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58 if gene_id in candidates:
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59 gene_type = candidates[gene_id]
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60 row.append(gene_type)
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61 else:
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62 row.append('')
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63
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64 writer.writerow(row)
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65
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66 o_file.close()
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67 i_file.close()
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68
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69 if __name__ == "__main__":
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70 main()
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