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3
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1 '''
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2 Convert a VCF format file to Cravat format file
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3 '''
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4
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5 import os
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6 import argparse
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7 from vcf_converter import CravatConverter
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8
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9 # File read/write configuration variables
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10 vcf_sep = '\t'
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11 cr_sep = '\t'
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12 cr_newline = '\n'
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13
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14 # VCF Headers mapped to their index position in a row of VCF values
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15 vcf_mapping = {
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16 'CHROM': 0,
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17 'POS': 1,
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18 'ID': 2,
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19 'REF': 3,
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20 'ALT': 4,
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21 'QUAL': 5,
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22 'FILTER': 6,
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23 'INFO': 7,
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24 'FORMAT': 8,
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25 'NA00001': 9,
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26 'NA00002': 10,
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27 'NA00003': 11
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28 }
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29
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30
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31 def get_args():
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32 parser = argparse.ArgumentParser()
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33 parser.add_argument('--input',
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34 '-i',
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35 required = True,
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36 help='Input path to a VCF file for conversion',)
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37 parser.add_argument('--output',
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38 '-o',
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39 default = os.path.join(os.getcwd(), "cravat_converted.txt"),
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40 help = 'Output path to write the cravat file to')
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41 return parser.parse_args()
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42
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43
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44 def convert(in_path, out_path=None):
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45 if not out_path:
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46 base, _ = os.path.split(in_path)
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47 out_path = os.path.join(base, "cravat_converted.txt")
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48
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49 with open(in_path, 'r') as in_file, \
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50 open(out_path, 'w') as out_file:
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51
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52 # cr_count will be used to generate the 'TR' field of the cravat rows (first header)
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53 cr_count = 0
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54 # VCF lines are always assumed to be '+' strand, as VCF doesn't specify that attribute
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55 strand = '+'
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56 # VCF converter. Adjusts position, reference, and alternate for Cravat formatting.
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57 converter = CravatConverter()
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58
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59 for line in in_file:
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60 if line.startswith("#"):
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61 continue
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62 line = line.strip().split(vcf_sep)
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63 # row is dict of VCF headers mapped to corresponding values of this line
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64 row = { header: line[index] for header, index in vcf_mapping.items() }
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65 for alt in row["ALT"].split(","):
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66 new_pos, new_ref, new_alt = converter.extract_vcf_variant(strand, row["POS"], row["REF"], alt)
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67 new_pos, new_ref, new_alt = str(new_pos), str(new_ref), str(new_alt)
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68 cr_line = cr_sep.join([
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69 'TR' + str(cr_count), row['CHROM'], new_pos, strand, new_ref, new_alt, row['ID']
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70 ])
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71 out_file.write(cr_line + cr_newline)
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72 cr_count += 1
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73
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74
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75 if __name__ == "__main__":
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76 cli_args = get_args()
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77 convert(cli_args.input, cli_args.output)
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