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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 # import ipdb
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10
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11
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12 def get_vcf_mapping():
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13 """ : VCF Headers mapped to their index position in a row of VCF values.
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14 : These are only the mandatory columns, per the VCF spec.
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15 """
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16 return {
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17 'CHROM': 0,
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18 'POS': 1,
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19 'ID': 2,
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20 'REF': 3,
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21 'ALT': 4,
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22 'QUAL': 5,
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23 'FILTER': 6,
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24 'INFO': 7
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25 }
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26
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27
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28 def get_args():
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29 parser = argparse.ArgumentParser()
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30 parser.add_argument('--input',
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31 '-i',
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32 required = True,
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33 help='Input path to a VCF file for conversion',)
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34 parser.add_argument('--output',
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35 '-o',
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36 default = None,
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37 help = 'Output path to write the cravat file to')
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38 return parser.parse_args()
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39
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40
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41 def convert(in_path, out_path=None, cr_sep='\t', cr_newline='\n'):
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42 """ : Convert a VCF file to a Cravat file.
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43 : Arguments:
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44 : in_path: <str> path to input vcf file
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45 : out_path: <str> path to output cravat file. Will defualt to cravat_converted.txt in the input directory.
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46 : cr_sep: <str> the value delimiter for the output cravat file. Default value of '\\t'.
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47 : out_newline: <str> the newline delimiter in the output cravat file. Default of '\\n'
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48 """
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49 if not out_path:
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50 base, _ = os.path.split(in_path)
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51 out_path = os.path.join(base, "cravat_converted.txt")
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52
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53 with open(in_path, 'r') as in_file, \
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54 open(out_path, 'w') as out_file:
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55
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56 # cr_count will be used to generate the 'TR' field of the cravat rows (first header)
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57 cr_count = 0
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58 # VCF lines are always assumed to be '+' strand, as VCF doesn't specify that attribute
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59 strand = '+'
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60 # VCF converter. Adjusts position, reference, and alternate for Cravat formatting.
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61 converter = CravatConverter()
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62 # A dictionary of mandatory vcf headers mapped to their row indices
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63 vcf_mapping = get_vcf_mapping()
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64
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65 for line in in_file:
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66 if line.startswith("#"):
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67 continue
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68 line = line.strip().split()
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69 # row is dict of VCF headers mapped to corresponding values of this line
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70 row = { header: line[index] for header, index in vcf_mapping.items() }
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71 for alt in row["ALT"].split(","):
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72 new_pos, new_ref, new_alt = converter.extract_vcf_variant(strand, row["POS"], row["REF"], alt)
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73 new_pos, new_ref, new_alt = str(new_pos), str(new_ref), str(new_alt)
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74 cr_line = cr_sep.join([
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75 'TR' + str(cr_count), row['CHROM'], new_pos, strand, new_ref, new_alt, row['ID']
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76 ])
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77 out_file.write(cr_line + cr_newline)
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78 cr_count += 1
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79
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80
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81 if __name__ == "__main__":
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82 cli_args = get_args()
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83 if cli_args.output == None:
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84 base, _ = os.path.split(cli_args.input)
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85 cli_args.output = os.path.join(base, "cravat_converted.txt")
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86 convert(in_path = cli_args.input, out_path = cli_args.output)
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