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annotate small_rna_maps.py @ 0:0a06985c0894 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
author artbio
date Tue, 22 Aug 2017 12:06:58 -0400
parents
children 615fa2171a34
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0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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diff changeset
1 import argparse
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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2 from collections import defaultdict
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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3
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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4 import numpy
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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5
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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6 import pysam
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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7
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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8
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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9 def Parser():
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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10 the_parser = argparse.ArgumentParser()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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11 the_parser.add_argument('--inputs', dest='inputs', required=True,
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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12 nargs='+', help='list of input BAM files')
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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13 the_parser.add_argument('--sample_names', dest='sample_names',
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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14 required=True, nargs='+',
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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15 help='list of sample names')
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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16 the_parser.add_argument('--outputs', nargs='+', action='store',
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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17 help='list of two output paths (only two)')
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18 the_parser.add_argument('-M', '--plot_methods', nargs='+', action='store',
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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19 help='list of 2 plot methods (only two) among:\
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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20 Counts, Max, Mean, Median, Coverage and Size')
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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21 args = the_parser.parse_args()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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22 return args
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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25 class Map:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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artbio
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27 def __init__(self, bam_file, sample):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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28 self.sample_name = sample
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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29 self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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30 self.chromosomes = dict(zip(self.bam_object.references,
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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31 self.bam_object.lengths))
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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32 self.map_dict = self.create_map(self.bam_object)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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33
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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34 def create_map(self, bam_object):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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35 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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36 Returns a map_dictionary {(chromosome,read_position,polarity):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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37 [read_length, ...]}
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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38 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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39 map_dictionary = defaultdict(list)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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40 # get empty value for start and end of each chromosome
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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41 for chrom in self.chromosomes:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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42 map_dictionary[(chrom, 1, 'F')] = []
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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43 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
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44 for chrom in self.chromosomes:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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45 for read in bam_object.fetch(chrom):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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46 positions = read.positions # a list of covered positions
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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47 for pos in positions:
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48 if not map_dictionary[(chrom, pos+1, 'F')]:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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49 map_dictionary[(chrom, pos+1, 'F')] = []
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50 if read.is_reverse:
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51 map_dictionary[(chrom, positions[-1]+1,
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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52 'R')].append(read.query_alignment_length)
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53 else:
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54 map_dictionary[(chrom, positions[0]+1,
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55 'F')].append(read.query_alignment_length)
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artbio
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56 return map_dictionary
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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57
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58 def compute_readcount(self, map_dictionary, out):
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59 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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60 takes a map_dictionary as input and writes
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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61 a readmap_dictionary {(chromosome,read_position,polarity):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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62 number_of_reads}
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63 in an open file handler out
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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64 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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65 readmap_dictionary = dict()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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66 for key in map_dictionary:
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67 readmap_dictionary[key] = len(map_dictionary[key])
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68 self.write_table(readmap_dictionary, out)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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69
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70 def compute_max(self, map_dictionary, out):
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71 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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72 takes a map_dictionary as input and writes
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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73 a max_dictionary {(chromosome,read_position,polarity):
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74 max_of_number_of_read_at_any_position}
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75 Not clear this function is still required
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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76 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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77 merge_keylist = [(i[0], 0) for i in map_dictionary.keys()]
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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78 max_dictionary = dict(merge_keylist)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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79 for key in map_dictionary:
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artbio
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80 if len(map_dictionary[key]) > max_dictionary[key[0]]:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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81 max_dictionary[key[0]] = len(map_dictionary[key])
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artbio
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82 self.write_table(max_dictionary, out)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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83
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84 def compute_mean(self, map_dictionary, out):
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85 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
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86 takes a map_dictionary as input and returns
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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87 a mean_dictionary {(chromosome,read_position,polarity):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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88 mean_value_of_reads}
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
89 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
90 mean_dictionary = dict()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
91 for key in map_dictionary:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
92 if len(map_dictionary[key]) == 0:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
93 mean_dictionary[key] = 0
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
94 else:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
95 mean_dictionary[key] = round(numpy.mean(map_dictionary[key]),
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
96 1)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
97 self.write_table(mean_dictionary, out)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
98
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artbio
parents:
diff changeset
99 def compute_median(self, map_dictionary, out):
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artbio
parents:
diff changeset
100 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
101 takes a map_dictionary as input and returns
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
102 a mean_dictionary {(chromosome,read_position,polarity):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
103 mean_value_of_reads}
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
104 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
105 median_dictionary = dict()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
106 for key in map_dictionary:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
107 if len(map_dictionary[key]) == 0:
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artbio
parents:
diff changeset
108 median_dictionary[key] = 0
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
109 else:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
110 median_dictionary[key] = numpy.median(map_dictionary[key])
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
111 self.write_table(median_dictionary, out)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
112
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artbio
parents:
diff changeset
113 def compute_coverage(self, map_dictionary, out, quality=10):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
114 '''
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artbio
parents:
diff changeset
115 takes a map_dictionary as input and returns
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
116 a coverage_dictionary {(chromosome,read_position,polarity):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
117 coverage}
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
118 '''
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artbio
parents:
diff changeset
119 coverage_dictionary = dict()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
120 for chrom in self.chromosomes:
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artbio
parents:
diff changeset
121 coverage_dictionary[(chrom, 1, 'F')] = 0
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
122 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
123 for key in map_dictionary:
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artbio
parents:
diff changeset
124 coverage = self.bam_object.count_coverage(
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
125 reference=key[0],
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artbio
parents:
diff changeset
126 start=key[1]-1,
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artbio
parents:
diff changeset
127 end=key[1],
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
128 quality_threshold=quality)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
129 """ Add the 4 coverage values """
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
130 coverage = [sum(x) for x in zip(*coverage)]
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artbio
parents:
diff changeset
131 coverage_dictionary[key] = coverage[0]
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
132 self.write_table(coverage_dictionary, out)
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
133
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artbio
parents:
diff changeset
134 def compute_size(self, map_dictionary, out):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
135 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
136 Takes a map_dictionary and returns a dictionary of sizes:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
137 {chrom: {polarity: {size: nbre of reads}}}
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
138 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
139 size_dictionary = defaultdict(lambda: defaultdict(
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
140 lambda: defaultdict(int)))
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
141 # to track empty chromosomes
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
142 for chrom in self.chromosomes:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
143 if self.bam_object.count(chrom) == 0:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
144 size_dictionary[chrom]['F'][10] = 0
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
145 for key in map_dictionary:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
146 for size in map_dictionary[key]:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
147 size_dictionary[key[0]][key[2]][size] += 1
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
148 self.write_size_table(size_dictionary, out)
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artbio
parents:
diff changeset
149
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artbio
parents:
diff changeset
150 def write_table(self, mapdict, out):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
151 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
152 Generic writer
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
153 Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
154 <some mapped value>
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
155 out is an *open* file handler
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
156 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
157 for key in sorted(mapdict):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
158 line = [self.sample_name, key[0], self.chromosomes[key[0]],
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
159 key[1], key[2], mapdict[key]]
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
160 line = [str(i) for i in line]
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
161 out.write('\t'.join(line) + '\n')
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
162
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artbio
parents:
diff changeset
163 def write_size_table(self, sizedic, out):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
164 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
165 Generic writer of summary values
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
166 Dataset, Chromosome, Chrom_length, <some category>, <some value>
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
167 out is an *open* file handler
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
168 '''
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
169 for chrom in sorted(sizedic):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
170 sizes = sizedic[chrom]['F'].keys()
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
171 sizes.extend(sizedic[chrom]['R'].keys())
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
172 for polarity in sorted(sizedic[chrom]):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
173 for size in range(min(sizes), max(sizes)+1):
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
174 try:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
175 line = [self.sample_name, chrom, polarity, size,
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
176 sizedic[chrom][polarity][size]]
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
177 except KeyError:
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
diff changeset
178 line = [self.sample_name, chrom, polarity, size, 0]
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
artbio
parents:
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179 line = [str(i) for i in line]
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180 out.write('\t'.join(line) + '\n')
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181
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182
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183 def main(inputs, samples, methods, outputs):
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184 for method, output in zip(methods, outputs):
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185 F = open(output, 'w')
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186 if method == 'Size':
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187 header = ["Dataset", "Chromosome", "Polarity", method, "Count"]
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188 else:
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189 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
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190 "Polarity", method]
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191 F.write('\t'.join(header) + '\n')
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192 for input, sample in zip(inputs, samples):
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193 mapobj = Map(input, sample)
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194 token = {"Counts": mapobj.compute_readcount,
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195 "Max": mapobj.compute_max,
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196 "Mean": mapobj.compute_mean,
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197 "Median": mapobj.compute_median,
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198 "Coverage": mapobj.compute_coverage,
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199 "Size": mapobj.compute_size}
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200 token[method](mapobj.map_dict, F)
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201 F.close()
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202
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203
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204 if __name__ == "__main__":
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205 args = Parser()
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206 # if identical sample names
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207 if len(set(args.sample_names)) != len(args.sample_names):
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208 args.sample_names = [name + '_' + str(i) for
0a06985c0894 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit 7b2ceb05489c27ddb769c38fdec56274108a6fa1
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209 i, name in enumerate(args.sample_names)]
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210 main(args.inputs, args.sample_names, args.plot_methods, args.outputs)