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annotate utils/get_msa.py @ 4:af383638de66 draft

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planemo upload commit 022984f323d3da44f70b3bf79c684cfd8dda3f61-dirty
author nick
date Mon, 23 Nov 2015 18:44:23 -0500
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4
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1 #!/usr/bin/env python
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2 from __future__ import division
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3 import os
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4 import sys
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5 import argparse
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6 import tempfile
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7 import subprocess
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8 sys.path.append(os.path.dirname(os.path.dirname(os.path.realpath(__file__))))
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9 import consensus
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10 import seqtools
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11
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12 OPT_DEFAULTS = {'format':'plain', 'qual':20, 'qual_format':'sanger'}
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13 USAGE = "%(prog)s [options]"
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14 DESCRIPTION = """"""
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15
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16
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17 def main(argv):
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18
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19 parser = argparse.ArgumentParser(description=DESCRIPTION)
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20 parser.set_defaults(**OPT_DEFAULTS)
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21
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22 parser.add_argument('seqs', metavar='sequence', nargs='*',
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23 help='The alignment.')
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24 parser.add_argument('-i', '--input',
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25 help='Provide the sequences in this input file instead of as command-line arguments. '
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26 'Give "-" to use stdin.')
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27 parser.add_argument('-f', '--format', choices=('plain', 'duplex'),
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28 help='Input format. "plain" is a simple list of the sequences, one on each line. "duplex" is '
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29 'the 8-column format of the family-sorted read data from the duplex pipeline. It must be '
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30 'the read pairs from a single alpha/beta barcode combination (both the alpha-beta and '
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31 'beta-alpha strands). If "duplex" is given, you must also specify which of the four '
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32 'possible alignments to output with --mate and --order.')
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33 parser.add_argument('-m', '--mate', type=int, choices=(1, 2))
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34 parser.add_argument('-o', '--order', choices=('ab', 'ba'))
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35 parser.add_argument('-F', '--qual-format', choices=('sanger',))
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36 parser.add_argument('-q', '--qual', type=int,
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37 help='Quality threshold: Default: %(default)s')
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38
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39 args = parser.parse_args(argv[1:])
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40
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41 qual_thres = ' '
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42 if args.qual_format == 'sanger':
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43 qual_thres = chr(args.qual + 33)
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44 else:
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45 fail('Error: Unsupported FASTQ quality format "{}".'.format(args.qual_format))
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46 # Check arguments.
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47 if not (args.seqs or args.input):
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48 fail('Error: You must provide sequences either in a file with --input or as arguments.')
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49 elif args.seqs and args.input:
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50 fail('Error: You cannot provide sequences in both a file and command-line arguments.')
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51 if args.format == 'duplex' and not (args.mate and args.order):
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52 fail('Error: If the --format is duplex, you must specify a --mate and --order.')
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53
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54 # Read input.
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55 quals = []
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56 if args.input:
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57 if args.format == 'plain':
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58 if args.input == '-':
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59 seqs = [line.strip() for line in sys.stdin]
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60 else:
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61 with open(args.input) as infile:
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62 seqs = [line.strip() for line in infile]
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63 elif args.format == 'duplex':
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64 if args.input == '-':
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65 (seqs, quals) = parse_duplex(sys.stdin, args.mate, args.order)
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66 else:
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67 with open(args.input) as infile:
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68 (seqs, quals) = parse_duplex(infile, args.mate, args.order)
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69 else:
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70 seqs = args.seqs
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71
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72 align = make_msa(seqs)
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73 if quals:
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74 quals = seqtools.transfer_gaps_multi(quals, align, gap_char_out=' ')
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75 cons = consensus.get_consensus(align, quals, qual_thres=qual_thres, gapped=True)
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76
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77 output = format_alignment(cons, align, quals, qual_thres=ord(qual_thres))
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78
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79 for seq in output:
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80 print seq
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81
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82
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83 def parse_duplex(infile, mate, order):
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84 seqs = []
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85 quals = []
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86 for line in infile:
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87 (bar, this_order, name1, seq1, qual1, name2, seq2, qual2) = line.rstrip('\r\n').split('\t')
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88 if this_order == order:
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89 if mate == 1:
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90 seqs.append(seq1)
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91 quals.append(qual1)
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92 elif mate == 2:
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93 seqs.append(seq2)
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94 quals.append(qual2)
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95 return seqs, quals
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96
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97
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98 def make_msa(seqs):
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99 """Perform a multiple sequence alignment on a set of sequences.
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100 Uses MAFFT."""
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101 i = 0
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102 #TODO: Replace with tempfile.mkstemp()?
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103 with tempfile.NamedTemporaryFile('w', delete=False, prefix='msa.') as family_file:
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104 for seq in seqs:
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105 i+=1
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106 header = '>{}\n'.format(i)
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107 family_file.write(header)
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108 family_file.write(seq+'\n')
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109 with open(os.devnull, 'w') as devnull:
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110 try:
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111 command = ['mafft', '--nuc', '--quiet', family_file.name]
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112 output = subprocess.check_output(command, stderr=devnull)
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113 except (OSError, subprocess.CalledProcessError):
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114 return None
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115 os.remove(family_file.name)
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116 return read_fasta(output)
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117
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118
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119 def read_fasta(fasta):
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120 """Quick and dirty FASTA parser. Return only the list of sequences (no names).
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121 Warning: Reads the entire contents of the file into memory at once."""
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122 sequences = []
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123 sequence = ''
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124 for line in fasta.splitlines():
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125 if line.startswith('>'):
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126 if sequence:
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127 sequences.append(sequence)
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128 sequence = ''
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129 continue
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130 sequence += line.strip()
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131 if sequence:
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132 sequences.append(sequence)
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133 return sequences
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134
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135
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136 def format_alignment(cons, seqs, quals=(), qual_thres=32, id_char='.'):
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137 output = [cons.upper()]
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138 for i, seq in enumerate(seqs):
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139 outseq = ''
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140 for j, seq_base in enumerate(seq.upper()):
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141 if quals and seq_base != '-' and ord(quals[i][j]) < qual_thres:
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142 outseq += ' '
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143 elif cons[j] == seq_base:
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144 outseq += id_char
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145 else:
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146 outseq += seq_base
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147 output.append(outseq)
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148 return output
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149
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150
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151 def fail(message):
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152 sys.stderr.write(message+"\n")
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153 sys.exit(1)
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154
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155 if __name__ == '__main__':
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156 sys.exit(main(sys.argv))