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1 """
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2 genetrack.py
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3
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4 Input: either ssccidx or gff format of reads
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5 .ssccidx format: tab-separated chromosome (chr##), index, + reads, - reads
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6 .gff format: standard gff, score interpreted as number of reads
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7
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8 Output: Called peaks in either gff or txt format
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9 .txt format: tab-separated chromosome, strand, start, end, read count
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10 .gff format: standard gff, score is read count
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11 """
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12 import argparse
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13 import csv
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14 import os
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15 import genetrack_util
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16
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17
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18 if __name__ == '__main__':
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19 parser = argparse.ArgumentParser()
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20 parser.add_argument('--input_format', dest='input_format', help='Input format.')
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21 parser.add_argument('--input', dest='inputs', action='append', nargs=2, help="Input datasets")
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22 parser.add_argument('--sigma', dest='sigma', type=int, default=5, help='Sigma.')
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23 parser.add_argument('--exclusion', dest='exclusion', type=int, default=20, help='Exclusion zone.')
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24 parser.add_argument('--up_width', dest='up_width', type=int, default=10, help='Upstream width of called peaks.')
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25 parser.add_argument('--down_width', dest='down_width', type=int, default=10, help='Downstream width of called peaks.')
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26 parser.add_argument('--filter', dest='filter', type=int, default=3, help='Absolute read filter.')
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27 parser.add_argument('--chunk_size', dest='chunk_size', type=int, default=10, help='Size, in millions of base pairs.')
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28 args = parser.parse_args()
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29
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30 os.mkdir('output')
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31 for (dataset_path, hid) in args.inputs:
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32 if args.input_format == 'gff':
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33 # Make sure the reads for each chromosome are sorted by index.
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34 input_path = genetrack_util.sort_chromosome_reads_by_index(dataset_path)
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35 else:
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36 # We're processing ssccidx data.
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37 input_path = dataset_path
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38 output_name = 's%se%su%sd%sF%s_on_data_%s' % (str(args.sigma),
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39 str(args.exclusion),
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40 str(args.up_width),
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41 str(args.down_width),
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42 str(args.filter),
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43 str(hid))
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44 output_path = os.path.join('output', output_name)
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45 reader = csv.reader(open(input_path, 'rU'), delimiter='\t')
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46 writer = csv.writer(open(output_path, 'wt'), delimiter='\t')
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47 chunk_size = args.chunk_size * 10 ** 6
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48 width = args.sigma * 5
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49 manager = genetrack_util.ChromosomeManager(reader)
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50 while not manager.done:
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51 cname = manager.chromosome_name()
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52 # Should we process this chromosome?
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53 data = manager.load_chromosome()
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54 if not data:
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55 continue
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56 keys = genetrack_util.make_keys(data)
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57 lo, hi = genetrack_util.get_range(data)
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58 for chunk in genetrack_util.get_chunks(lo, hi, size=chunk_size, overlap=width):
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59 (slice_start, slice_end), process_bounds = chunk
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60 window = genetrack_util.get_window(data, slice_start, slice_end, keys)
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61 genetrack_util.process_chromosome(cname,
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62 window,
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63 writer,
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64 process_bounds,
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65 args.width,
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66 args.sigma,
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67 args.up_width,
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68 args.down_width,
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69 args.exclusion,
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70 args.filter)
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