Mercurial > repos > davidvanzessen > demultiplex_emc

comparison demultiplex.py @ 0:36c79869620b draft

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author davidvanzessen
date Fri, 09 Nov 2018 05:37:11 -0500
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children b6d63b9efb8f
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-1:000000000000 0:36c79869620b
1 import argparse
2 import csv
3 import logging
4 import os
5 import sys
6 from collections import defaultdict
7 from collections import namedtuple
8
9 from Bio import SeqIO
10 from Bio.Alphabet import generic_dna
11 from Bio.Seq import Seq
12 from Bio.SeqRecord import SeqRecord
13
14
15 def sniff_format(file_path):
16 """
17 Try to guess the file format (fastq/fasta) by looking at the first character of the first line.
18 Should be '@' for fastq and '>' for fasta.
19 """
20 with open(file_path, 'rU') as file_handle:
21 for line in file_handle:
22 if line.startswith("@"):
23 return "fastq"
24 if line.startswith(">"):
25 return "fasta"
26 break
27 return None
28
29
30 def search_barcode_in_first_half(sequence, barcode):
31 if type(sequence) is Seq:
32 sequence = str(sequence)
33 elif type(sequence) is SeqRecord:
34 sequence = str(sequence.seq)
35 return sequence.find(barcode, 0, int(len(sequence) / 2))
36
37
38 def search_barcode_in_second_half(sequence, barcode):
39 if type(sequence) is Seq:
40 sequence = str(sequence)
41 elif type(sequence) is SeqRecord:
42 sequence = str(sequence.seq)
43 return sequence.find(barcode, int(len(sequence) / 2))
44
45
46 def search_barcodes_in_sequence(barcode_datas, sequence):
47 for barcode_data in barcode_datas:
48 barcode_search_position = search_barcode_in_first_half(sequence, barcode_data.barcode)
49 if barcode_search_position != -1:
50 return barcode_search_position, barcode_data, False
51 barcode_search_position = search_barcode_in_second_half(sequence, barcode_data.barcode_reverse)
52 if barcode_search_position != -1:
53 return barcode_search_position, barcode_data, True
54
55 barcode_search_position = search_barcode_in_first_half(sequence, barcode_data.barcode_reverse)
56 if barcode_search_position != -1:
57 return barcode_search_position, barcode_data, True
58
59 barcode_search_position = search_barcode_in_second_half(sequence, barcode_data.barcode)
60 if barcode_search_position != -1:
61 return barcode_search_position, barcode_data, False
62
63 return -1, None, None
64
65
66 def main():
67 parser = argparse.ArgumentParser()
68 parser.add_argument("-i", "--input", help="The input file")
69 parser.add_argument("-f", "--format", help="The format of the input file (fastq/fasta)", default="auto", choices=["fasta", "fastq", "auto"])
70 parser.add_argument("-o", "--output-dir", help="The output dir")
71 parser.add_argument("-m", "--mapping-file", help="A tab seperated file containing two columns, ID and barcode (no header)")
72
73 args = parser.parse_args()
74
75 input_file_path = args.input
76 basename_input_file_path = os.path.basename(input_file_path)
77 input_basename_no_ext, input_extension = os.path.splitext(basename_input_file_path)
78
79 input_format = args.format
80
81 logging.basicConfig(stream=sys.stdout, level=logging.INFO)
82
83 if input_format == "auto":
84 if input_extension in [".fasta", ".fa"]:
85 input_format = "fasta"
86 elif input_extension in [".fastq", ".fq"]:
87 input_format = "fastq"
88 else:
89 logging.info("Can't auto detect input format based on extension: {0}".format(input_extension))
90 logging.info("Sniffing format...")
91 input_format = sniff_format(input_file_path)
92 if not input_format:
93 logging.error("Can't auto detect input format")
94 sys.exit(1)
95 logging.info("Sniffed '{0}' as format.".format(input_format))
96
97 output_dir = args.output_dir
98 if not os.path.exists(output_dir):
99 os.makedirs(output_dir)
100
101 with open(args.mapping_file, newline="") as handle:
102 ID_barcode_mapping = list(csv.DictReader(handle, fieldnames=['ID', 'barcode'], delimiter="\t"))
103
104 logging.info("Input: {0}".format(input_file_path))
105 logging.info("Format: {0}".format(input_format))
106 logging.info("Output: {0}".format(output_dir))
107 logging.info("Mapping: {0} ({1} mappings)".format(args.mapping_file, len(ID_barcode_mapping)))
108
109 BarcodeData = namedtuple("BarcodeData", [
110 "ID",
111 "barcode",
112 "barcode_reverse",
113 "output_file_path",
114 "output_file_handle"
115 ])
116
117 barcode_data_dict = defaultdict(list)
118 ID_file_handle_dict = {}
119
120 for ID_barcode in ID_barcode_mapping:
121 ID = ID_barcode["ID"]
122 barcode = ID_barcode["barcode"]
123
124 output_file_path = os.path.join(
125 output_dir,
126 "{0}_{1}.{2}".format(input_basename_no_ext, ID, input_format)
127 )
128
129 if ID not in ID_file_handle_dict:
130 ID_file_handle = open(output_file_path, 'w')
131 ID_file_handle_dict[ID] = ID_file_handle
132
133 ID_file_handle = ID_file_handle_dict[ID]
134
135 barcode_data_dict[ID] += [BarcodeData(
136 ID=ID,
137 barcode=barcode,
138 barcode_reverse=str(Seq(barcode, generic_dna).reverse_complement()),
139 output_file_path=output_file_path,
140 output_file_handle=ID_file_handle
141 )]
142
143 discarded_output_file_path = os.path.join(
144 output_dir,
145 "{0}_{1}.{2}".format(basename_input_file_path, "discarded", input_format)
146 )
147
148 total_sequences = 0
149 sequences_assigned_by_id = defaultdict(int)
150
151 with open(input_file_path, 'rU') as input_file_handle, open(discarded_output_file_path, 'w') as discarded_output_handle:
152 for record in SeqIO.parse(input_file_handle, input_format):
153 total_sequences += 1
154 for ID, barcode_datas in barcode_data_dict.items():
155 barcode_position, barcode_data, reverse = search_barcodes_in_sequence(barcode_datas, record)
156 if barcode_position == -1:
157 continue
158 barcode = barcode_data.barcode if not reverse else barcode_data.barcode_reverse
159 sequences_assigned_by_id[barcode_data.ID] += 1
160 logging.debug(str(record.seq))
161 logging.debug(" " * barcode_position + barcode)
162 SeqIO.write(record, ID_file_handle_dict[ID], input_format)
163 break
164 else: # no match # TODO fuzzy match ?
165 SeqIO.write(record, discarded_output_handle, input_format)
166 if total_sequences % 10000 == 0:
167 assigned_sequences = sum(sequences_assigned_by_id.values())
168 logging.info("Processed {0} sequences, assigned {1} ({2}%)".format(
169 total_sequences,
170 assigned_sequences,
171 round(assigned_sequences / total_sequences * 100)
172 ))
173
174 for file_handle in ID_file_handle_dict.values():
175 file_handle.close()
176
177 assigned_sequences = sum(sequences_assigned_by_id.values())
178 logging.info("Processed {0} sequences, assigned {1} ({2}%)".format(
179 total_sequences,
180 assigned_sequences,
181 round(assigned_sequences / total_sequences * 100)
182 ))
183
184
185 if __name__ == "__main__":
186 main()
187