allelefinder.py 8.87 KB
Newer Older
jhoogenboom's avatar
jhoogenboom committed
1
2
#!/usr/bin/env python
"""
3
4
Find true alleles in reference samples and detect possible
contaminations.
jhoogenboom's avatar
jhoogenboom committed
5
6
7

In each sample, the sequences with the highest read counts of each
marker are called alleles, with a user-defined maximum number of alleles
jhoogenboom's avatar
jhoogenboom committed
8
per marker.  The allele balance is kept within given bounds.  If the
jhoogenboom's avatar
jhoogenboom committed
9
10
11
highest non-allelic sequence exceeds a given limit, no alleles are
called for this marker.  If this happens for multiple markers in one
sample, no alleles are called for this sample at all.
jhoogenboom's avatar
jhoogenboom committed
12
13
14
"""
import argparse

15
16
17
from ..lib import pos_int_arg, add_input_output_args, get_input_output_files, \
                  ensure_sequence_format, get_sample_data, \
                  add_sequence_format_args
jhoogenboom's avatar
jhoogenboom committed
18
19
20
21

__version__ = "0.1dev"


22
23
24
25
26
27
28
29
30
# Default values for parameters are specified below.

# Default minimum number of reads required for the highest allele.
# This value can be overridden by the -n command line option.
_DEF_MIN_READS = 50

# Default minimum number of reads required for an allele to be called,
# as a percentage of the number of reads of the highest allele.
# This value can be overridden by the -m command line option.
jhoogenboom's avatar
jhoogenboom committed
31
_DEF_MIN_ALLELE_PCT = 30.0
32
33
34
35
36
37

# Default maximum amount of noise to allow, as a percentage of the
# number of reads of the highest allele of each marker.  If any noise
# (i.e., non-allelic sequences) above this threshold are detected, the
# sample is considered 'noisy' for this marker.
# This value can be overridden by the -M command line option.
jhoogenboom's avatar
jhoogenboom committed
38
_DEF_MAX_NOISE_PCT = 10.0
39
40
41

# Default maximum number of alleles to expect for each marker.
# This value can be overridden by the -a command line option.
jhoogenboom's avatar
jhoogenboom committed
42
43
_DEF_MAX_ALLELES = 2

44
45
46
47
48
# Default maximum number of noisy markers allowed per sample.
# This value can be overridden by the -x command line option.
_DEF_MAX_NOISY = 2


49
50
51
def find_alleles(samples_in, outfile, reportfile, min_reads, min_allele_pct,
                 max_noise_pct, max_alleles, max_noisy, stuttermark_column,
                 seqformat, library):
jhoogenboom's avatar
jhoogenboom committed
52
53
    if seqformat is not None and library is not None:
        library = parse_library(library)
54

jhoogenboom's avatar
jhoogenboom committed
55
    outfile.write("\t".join(["sample", "marker", "total", "allele"]) + "\n")
56
57
    allelelist = {}
    get_sample_data(
58
        samples_in,
59
60
61
        lambda tag, data: find_alleles_sample(
            data if stuttermark_column is None
                 else {key: data[key] for key in allelelist[tag]},
jhoogenboom's avatar
jhoogenboom committed
62
            outfile, reportfile, tag, min_reads, min_allele_pct, max_noise_pct,
63
64
65
            max_alleles, max_noisy, seqformat, library),
        allelelist,
        stuttermark_column)
66
67
68
#find_alleles


jhoogenboom's avatar
jhoogenboom committed
69
70
71
def find_alleles_sample(data, outfile, reportfile, tag, min_reads,
                        min_allele_pct, max_noise_pct, max_alleles, max_noisy,
                        seqformat, library):
jhoogenboom's avatar
jhoogenboom committed
72
73
74
75
    top_noise = {}
    top_allele = {}
    alleles = {}
    for marker, allele in data:
76
        reads = sum(data[marker, allele])
jhoogenboom's avatar
jhoogenboom committed
77

78
79
80
81
82
83
        if marker not in alleles:
            alleles[marker] = {allele: reads}
            top_allele[marker] = reads
            top_noise[marker] = ["-", 0]
        else:
            if reads > top_allele[marker]:
jhoogenboom's avatar
jhoogenboom committed
84
                # New highest allele!
85
86
87
88
89
90
91
92
93
94
                top_allele[marker] = reads
                for allelex in alleles[marker].keys():
                    if (alleles[marker][allelex] <
                            top_allele[marker] * (min_allele_pct/100.)):
                        if alleles[marker][allelex] > top_noise[marker][1]:
                            top_noise[marker] = [
                                allelex, alleles[marker][allelex]]
                        del alleles[marker][allelex]
                alleles[marker][allele] = reads
            elif reads >= top_allele[marker]*(min_allele_pct/100.):
jhoogenboom's avatar
jhoogenboom committed
95
96
                # New secundary allele!
                alleles[marker][allele] = reads
97
            elif reads >= top_noise[marker][1]:
jhoogenboom's avatar
jhoogenboom committed
98
                # New highest noise!
99
                top_noise[marker] = [allele, reads]
jhoogenboom's avatar
jhoogenboom committed
100

101
102
    # Find and eliminate noisy markers in this sample first.
    noisy_markers = 0
jhoogenboom's avatar
jhoogenboom committed
103
    for marker in alleles:
104
        if top_allele[marker] < min_reads:
jhoogenboom's avatar
jhoogenboom committed
105
106
107
108
            reportfile.write(
                "Sample %s is not suitable for marker %s:\n"
                "highest allele has only %i reads\n\n" %
                    (tag, marker, top_allele[marker]))
109
110
            alleles[marker] = {}
            continue
jhoogenboom's avatar
jhoogenboom committed
111
112
113
        if len(alleles[marker]) > max_alleles:
            allele_order = sorted(alleles[marker],
                                  key=lambda x: -alleles[marker][x])
114
115
            top_noise[marker] = [allele_order[max_alleles],
                alleles[marker][allele_order[max_alleles]]]
jhoogenboom's avatar
jhoogenboom committed
116
117
            alleles[marker] = {x: alleles[marker][x]
                               for x in allele_order[:max_alleles]}
118
        if top_noise[marker][1] > top_allele[marker]*(max_noise_pct/100.):
jhoogenboom's avatar
jhoogenboom committed
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
            reportfile.write(
                "Sample %s is not suitable for marker %s:\n"
                "highest non-allele is %.1f%% of the highest allele\n" %
                (tag, marker, 100.*top_noise[marker][1]/top_allele[marker]))
            for allele in sorted(alleles[marker],
                                 key=lambda x: -alleles[marker][x]):
                seq = allele if seqformat is None \
                    else ensure_sequence_format(allele, seqformat,
                        library=library, marker=marker)
                reportfile.write("%i\tALLELE\t%s\n" %
                    (alleles[marker][allele], seq))
            seq = top_noise[marker][0] if seqformat is None \
                else ensure_sequence_format(top_noise[marker][0],
                    seqformat, library=library, marker=marker)
            reportfile.write("%i\tNOISE\t%s\n\n" % (top_noise[marker][1], seq))
134
135
136
137
138
            noisy_markers += 1
            alleles[marker] = {}

    # Drop this sample completely if it has too many noisy markers.
    if noisy_markers > max_noisy:
jhoogenboom's avatar
jhoogenboom committed
139
        reportfile.write("Sample %s appears to be contaminated!\n\n" % tag)
140
141
142
143
144
145
        return

    # The sample is OK, write out its alleles.
    for marker in alleles:
        for allele in sorted(alleles[marker],
                             key=lambda x: -alleles[marker][x]):
jhoogenboom's avatar
jhoogenboom committed
146
147
            seq = allele if seqformat is None else ensure_sequence_format(
                allele, seqformat, library=library, marker=marker)
jhoogenboom's avatar
jhoogenboom committed
148
149
            outfile.write("\t".join(
                [tag, marker, str(alleles[marker][allele]), seq]) + "\n")
150
#find_alleles_sample
jhoogenboom's avatar
jhoogenboom committed
151
152
153


def add_arguments(parser):
154
    add_input_output_args(parser, False, False, True)
jhoogenboom's avatar
jhoogenboom committed
155
156
157
    filtergroup = parser.add_argument_group("filtering options")
    filtergroup.add_argument('-m', '--min-allele-pct', metavar="PCT",
        type=float, default=_DEF_MIN_ALLELE_PCT,
jhoogenboom's avatar
jhoogenboom committed
158
        help="call heterozygous if the second allele is at least this "
jhoogenboom's avatar
jhoogenboom committed
159
160
             "percentage of the highest allele of a marker "
             "(default: %(default)s)")
jhoogenboom's avatar
jhoogenboom committed
161
162
    filtergroup.add_argument('-M', '--max-noise-pct', metavar="PCT",
        type=float, default=_DEF_MAX_NOISE_PCT,
163
164
        help="a sample is considered contaminated/unsuitable for a marker if "
             "the highest non-allelic sequence is at least this percentage of "
jhoogenboom's avatar
jhoogenboom committed
165
             "the highest allele of that marker (default: %(default)s)")
jhoogenboom's avatar
jhoogenboom committed
166
167
168
    filtergroup.add_argument('-n', '--min-reads', metavar="N",
        type=pos_int_arg, default=_DEF_MIN_READS,
        help="require at least this number of reads for the highest allele "
jhoogenboom's avatar
jhoogenboom committed
169
             "of each marker (default: %(default)s)")
jhoogenboom's avatar
jhoogenboom committed
170
171
    filtergroup.add_argument('-a', '--max-alleles', metavar="N",
        type=pos_int_arg, default=_DEF_MAX_ALLELES,
172
173
        help="allow no more than this number of alleles per marker (default: "
             "%(default)s)")
jhoogenboom's avatar
jhoogenboom committed
174
175
    filtergroup.add_argument('-x', '--max-noisy', metavar="N",
        type=pos_int_arg, default=_DEF_MAX_NOISY,
176
177
        help="entirely reject a sample if more than this number of markers "
             "have a high non-allelic sequence (default: %(default)s)")
jhoogenboom's avatar
jhoogenboom committed
178
    filtergroup.add_argument('-c', '--stuttermark-column', metavar="COLNAME",
jhoogenboom's avatar
jhoogenboom committed
179
180
181
        help="name of column with Stuttermark output; if specified, sequences "
             "for which the value in this column does not start with ALLELE "
             "are ignored")
jhoogenboom's avatar
jhoogenboom committed
182
    add_sequence_format_args(parser)
jhoogenboom's avatar
jhoogenboom committed
183
184
185
186
#add_arguments


def run(args):
187
188
    files = get_input_output_files(args)
    if not files:
jhoogenboom's avatar
jhoogenboom committed
189
190
        raise ValueError("please specify an input file, or pipe in the output "
                         "of another program")
191

192
193
194
195
    find_alleles(files[0], files[1], args.report, args.min_reads,
                 args.min_allele_pct, args.max_noise_pct, args.max_alleles,
                 args.max_noisy, args.stuttermark_column, args.sequence_format,
                 args.library)
jhoogenboom's avatar
jhoogenboom committed
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
#run


def main():
    """
    Main entry point.
    """
    parser = argparse.ArgumentParser(
        description=__doc__)
    try:
        add_arguments(parser)
        run(parser.parse_args())
    except OSError as error:
        parser.error(error)
#main


if __name__ == "__main__":
    main()