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1 #!/usr/bin/env python
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2 # Boris Rebolledo-Jaramillo (boris-at-bx.psu.edu)
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3 #
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4 #usage: getalleleseq.py [-h] [-l INT] [-j FILE] [-d DIR] alleles
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5 #
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6 #Given a table with minor and major alleles per position, it generates the
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7 #minor and major allele sequences in FASTA format
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8 #
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9 #positional arguments:
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10 # alleles Table containing minor and major allele base per
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11 # position. cols: [id, chr, pos, A, C, G, T, cvrg,
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12 # plody, major, minor, freq_minor]
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13 #
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14 #optional arguments:
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15 # -h, --help show this help message and exit
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16 # -l INT, --seq-length INT
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17 # Background sequence length. Bases in an artifical
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18 # all-N-sequence of length INT will be replaced by
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19 # either the major or minor allele base accordingly
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20 # -j FILE, --major-seq FILE
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21 # File to write major allele sequences in FASTA multiple
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22 # alignment format.
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23 # -d DIR, --minor-dir DIR
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24 # Per sample minor allele sequences will be written to
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25 # this directory
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26 #
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27 # The expected columns in the alleles table follow Nicholas Stoler's
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28 # Variant Annotator tool format. See Variant Annotator in Galaxy's tool shed
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29 # http://testtoolshed.g2.bx.psu.edu/repos/nick/allele_counts_1 for more details
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30 #
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31 # Expected columns:
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32 # 1. sample_id
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33 # 2. chr
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34 # 3. position
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35 # 4 counts for A's
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36 # 5. counts for C's
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37 # 6. counts for G's
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38 # 7. counts for T's
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39 # (8. counts for a's)
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40 # (9. counts for c's)
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41 # (10. counts for g's)
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42 # (11. counts for t's)
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43 # 8. (12.) Coverage
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44 # 9. (13.) Number of alleles passing a given criteria
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45 # 10. (14.) Major allele
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46 # 11. (15.) Minor allele
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47 # 12. (16.) Minor allele frequency in position
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48
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49 import sys
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50 import os
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51 import argparse
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52
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53 def createseq(sample, allele, seq_size, table):
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54 """Generate major or minor allele sequence"""
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55 out_sequence = ['N' for i in range(seq_size)]
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56 sample_data = [line for line in table if line[0] == sample]
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57
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58 for entry in sample_data:
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59 position = int(entry[2])
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60 if len(entry)==12:
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61 number_of_alleles = int(entry[8])
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62 major_allele = entry[9].strip()
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63 minor_allele = entry[10].strip()
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64 else:
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65 number_of_alleles = int(entry[12])
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66 major_allele = entry[13].strip()
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67 minor_allele = entry[14].strip()
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68
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69 if allele == 'major':
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70 out_sequence[position-1] = major_allele
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71 elif allele == 'minor':
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72 if number_of_alleles >= 2:
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73 out_sequence[position-1] = minor_allele
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74 else:
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75 out_sequence[position-1] = major_allele
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76 return out_sequence
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77
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78 def printseq(sample,allele,seq,output):
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79 """Print out sequence"""
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80 #print >> output, '>{0}_{1}'.format(sample,allele)
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81 print >> output, '>{0}{1}'.format(sample,allele)
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82 for i in range(0,len(seq),70):
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83 print >> output, ''.join(seq[i:i+70])
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84
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85 def main():
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86 parser = argparse.ArgumentParser(description='Given a table with minor and major alleles per position, it generates the minor and major allele sequences in FASTA format', epilog='Boris Rebolledo-Jaramillo (boris-at-bx.psu.edu)')
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87 parser.add_argument('alleles', type=str, help='Table containing minor and major allele base per position. cols: [id, chr, pos, A, C, G, T, cvrg, plody, major, minor, freq_minor] ')
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88 parser.add_argument('-l','--seq-length', type=int, metavar='INT', help='Background sequence length. Bases in an artifical all-N-sequence of length INT will be replaced by either the major or minor allele base accordingly')
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89 parser.add_argument('-j','--major-seq', type=str, metavar='FILE', help='File to write major allele sequences in FASTA multiple alignment format.')
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90 parser.add_argument('-d', '--minor-dir', type=str, metavar='DIR', default='.', help="Per sample minor allele sequences will be written to this directory (Default: current directory)")
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91 parser.add_argument('-p', '--minor-prefix', type=str, metavar='STR', nargs='?', const='', default='', help=argparse.SUPPRESS) #Galaxy compatibility
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92 args = parser.parse_args()
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93
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94
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95 try:
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96 table = [line.strip().split('\t') for line in list(open(args.alleles)) if "#" not in line]
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97 samples = sorted(list(set([ line[0] for line in table ])))
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98 except:
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99 sys.exit('\nERROR: Could not open %s\n' % args.alleles)
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100 try:
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101 major_out = open(args.major_seq, 'w+')
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102 except:
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103 sys.exit('\nCould not create %s\n' % args.major_seq)
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104
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105 # Single file for all major allele sequences in FASTA multiple alignment
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106 for sample in samples:
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107 sequence = createseq(sample,'major',args.seq_length,table)
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108 #printseq(sample,'major',sequence,major_out)
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109 printseq(sample,'',sequence,major_out)
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110 major_out.close()
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111
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112 # Sample specific minor allele sequence in FASTA format
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113 try:
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114 os.makedirs(args.minor_dir)
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115 except:
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116 pass
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117
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118 for sample in samples:
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119 if args.minor_prefix: # to fit Galaxy requirements
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120 name = sample.replace('_','')
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121 minor_name = "%s_%s_%s" % ('primary',args.minor_prefix,name+'-minor_visible_fasta')
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122 else: # for non-Galaxy
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123 minor_name = sample+'-minor.fa'
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124 minor_out = open(os.path.join(args.minor_dir, minor_name), 'w+')
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125 sequence = createseq(sample,'minor',args.seq_length,table)
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126 #printseq(sample,'minor',sequence,minor_out)
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127 printseq(sample,'_minor',sequence,minor_out)
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128 minor_out.close()
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129
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130 if __name__ == "__main__": main() |
