Mercurial > repos > artbio > small_rna_maps

annotate small_rna_maps.py @ 4:a6b9a081064b draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit b58cb36616bf351278e57ec1949e9ebf3c3cdff1
author artbio
date Fri, 25 Aug 2017 12:22:03 -0400
parents ed8b0142538d
children 12c14642e6ac
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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diff changeset
1 import argparse
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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2 from collections import defaultdict
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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4 import numpy
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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6 import pysam
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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9 def Parser():
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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10 the_parser = argparse.ArgumentParser()
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artbio
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11 the_parser.add_argument('--inputs', dest='inputs', required=True,
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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12 nargs='+', help='list of input BAM files')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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13 the_parser.add_argument('--sample_names', dest='sample_names',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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14 required=True, nargs='+',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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15 help='list of sample names')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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16 the_parser.add_argument('--outputs', nargs='+', action='store',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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17 help='list of two output paths (only two)')
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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18 the_parser.add_argument('-M', '--plot_methods', nargs='+', action='store',
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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19 help='list of 2 plot methods (only two) among:\
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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20 Counts, Max, Mean, Median, Coverage and Size')
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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21 args = the_parser.parse_args()
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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22 return args
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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25 class Map:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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26
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artbio
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27 def __init__(self, bam_file, sample):
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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28 self.sample_name = sample
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 self.bam_object = pysam.AlignmentFile(bam_file, 'rb')
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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30 self.chromosomes = dict(zip(self.bam_object.references,
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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31 self.bam_object.lengths))
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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32 self.map_dict = self.create_map(self.bam_object)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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34 def create_map(self, bam_object):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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35 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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36 Returns a map_dictionary {(chromosome,read_position,polarity):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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37 [read_length, ...]}
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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38 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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39 map_dictionary = defaultdict(list)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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40 # get empty value for start and end of each chromosome
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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41 for chrom in self.chromosomes:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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42 map_dictionary[(chrom, 1, 'F')] = []
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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43 map_dictionary[(chrom, self.chromosomes[chrom], 'F')] = []
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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44 for chrom in self.chromosomes:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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45 for read in bam_object.fetch(chrom):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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46 positions = read.positions # a list of covered positions
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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47 if read.is_reverse:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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48 map_dictionary[(chrom, positions[-1]+1,
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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49 'R')].append(read.query_alignment_length)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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50 else:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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51 map_dictionary[(chrom, positions[0]+1,
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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52 'F')].append(read.query_alignment_length)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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53 return map_dictionary
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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54
3
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artbio
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55 def compute_readcount(self, map_dictionary, out):
2
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artbio
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56 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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57 takes a map_dictionary as input and writes
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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58 a readmap_dictionary {(chromosome,read_position,polarity):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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59 number_of_reads}
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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60 in an open file handler out
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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61 '''
2
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62 readmap_dictionary = dict()
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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63 for key in map_dictionary:
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artbio
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64 readmap_dictionary[key] = len(map_dictionary[key])
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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65 self.write_table(readmap_dictionary, out)
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66
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67 def compute_max(self, map_dictionary, out):
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68 '''
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
artbio
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69 takes a map_dictionary as input and writes
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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70 a max_dictionary {(chromosome,read_position,polarity):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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71 max_of_number_of_read_at_any_position}
2
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72 Not clear this function is still required
0
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73 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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74 merge_keylist = [(i[0], 0) for i in map_dictionary.keys()]
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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75 max_dictionary = dict(merge_keylist)
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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76 for key in map_dictionary:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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77 if len(map_dictionary[key]) > max_dictionary[key[0]]:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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78 max_dictionary[key[0]] = len(map_dictionary[key])
2
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79 self.write_table(max_dictionary, out)
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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80
2
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81 def compute_mean(self, map_dictionary, out):
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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82 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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83 takes a map_dictionary as input and returns
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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84 a mean_dictionary {(chromosome,read_position,polarity):
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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85 mean_value_of_reads}
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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86 '''
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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87 mean_dictionary = dict()
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diff changeset
88 for key in map_dictionary:
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artbio
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diff changeset
89 if len(map_dictionary[key]) == 0:
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artbio
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diff changeset
90 mean_dictionary[key] = 0
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91 else:
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artbio
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diff changeset
92 mean_dictionary[key] = round(numpy.mean(map_dictionary[key]),
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93 1)
2
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94 self.write_table(mean_dictionary, out)
0
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95
2
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96 def compute_median(self, map_dictionary, out):
0
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97 '''
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diff changeset
98 takes a map_dictionary as input and returns
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99 a mean_dictionary {(chromosome,read_position,polarity):
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100 mean_value_of_reads}
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101 '''
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artbio
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102 median_dictionary = dict()
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103 for key in map_dictionary:
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104 if len(map_dictionary[key]) == 0:
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artbio
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105 median_dictionary[key] = 0
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106 else:
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artbio
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107 median_dictionary[key] = numpy.median(map_dictionary[key])
2
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108 self.write_table(median_dictionary, out)
0
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109
2
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diff changeset
110 def compute_coverage(self, map_dictionary, out, quality=10):
0
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artbio
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111 '''
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artbio
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diff changeset
112 takes a map_dictionary as input and returns
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artbio
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113 a coverage_dictionary {(chromosome,read_position,polarity):
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114 coverage}
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artbio
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115 '''
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artbio
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diff changeset
116 coverage_dictionary = dict()
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artbio
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117 for chrom in self.chromosomes:
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artbio
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diff changeset
118 coverage_dictionary[(chrom, 1, 'F')] = 0
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artbio
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diff changeset
119 coverage_dictionary[(chrom, self.chromosomes[chrom], 'F')] = 0
4
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120 for read in self.bam_object.fetch(chrom):
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121 positions = read.positions # a list of covered positions
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artbio
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122 for pos in positions:
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123 if not map_dictionary[(chrom, pos+1, 'F')]:
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diff changeset
124 map_dictionary[(chrom, pos+1, 'F')] = []
0
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125 for key in map_dictionary:
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diff changeset
126 coverage = self.bam_object.count_coverage(
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127 reference=key[0],
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128 start=key[1]-1,
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129 end=key[1],
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130 quality_threshold=quality)
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diff changeset
131 """ Add the 4 coverage values """
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132 coverage = [sum(x) for x in zip(*coverage)]
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133 coverage_dictionary[key] = coverage[0]
2
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diff changeset
134 self.write_table(coverage_dictionary, out)
0
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135
2
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diff changeset
136 def compute_size(self, map_dictionary, out):
0
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137 '''
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artbio
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diff changeset
138 Takes a map_dictionary and returns a dictionary of sizes:
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artbio
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139 {chrom: {polarity: {size: nbre of reads}}}
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diff changeset
140 '''
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artbio
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diff changeset
141 size_dictionary = defaultdict(lambda: defaultdict(
1
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diff changeset
142 lambda: defaultdict(int)))
0
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143 # to track empty chromosomes
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144 for chrom in self.chromosomes:
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145 if self.bam_object.count(chrom) == 0:
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artbio
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diff changeset
146 size_dictionary[chrom]['F'][10] = 0
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147 for key in map_dictionary:
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148 for size in map_dictionary[key]:
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artbio
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149 size_dictionary[key[0]][key[2]][size] += 1
2
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diff changeset
150 self.write_size_table(size_dictionary, out)
0
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151
2
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152 def write_table(self, mapdict, out):
0
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diff changeset
153 '''
2
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diff changeset
154 Generic writer
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diff changeset
155 Dataset, Chromosome, Chrom_length, Coordinate, Polarity,
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diff changeset
156 <some mapped value>
0
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diff changeset
157 out is an *open* file handler
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158 '''
2
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159 for key in sorted(mapdict):
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160 line = [self.sample_name, key[0], self.chromosomes[key[0]],
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diff changeset
161 key[1], key[2], mapdict[key]]
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diff changeset
162 line = [str(i) for i in line]
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diff changeset
163 out.write('\t'.join(line) + '\n')
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164
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165 def write_size_table(self, sizedic, out):
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166 '''
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diff changeset
167 Generic writer of summary values
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diff changeset
168 Dataset, Chromosome, Chrom_length, <some category>, <some value>
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diff changeset
169 out is an *open* file handler
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170 '''
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diff changeset
171 for chrom in sorted(sizedic):
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diff changeset
172 sizes = sizedic[chrom]['F'].keys()
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diff changeset
173 sizes.extend(sizedic[chrom]['R'].keys())
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artbio
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diff changeset
174 for polarity in sorted(sizedic[chrom]):
0
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175 for size in range(min(sizes), max(sizes)+1):
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176 try:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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177 line = [self.sample_name, chrom, polarity, size,
2
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178 sizedic[chrom][polarity][size]]
0
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179 except KeyError:
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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180 line = [self.sample_name, chrom, polarity, size, 0]
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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181 line = [str(i) for i in line]
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182 out.write('\t'.join(line) + '\n')
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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183
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184
2
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185 def main(inputs, samples, methods, outputs):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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186 for method, output in zip(methods, outputs):
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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187 F = open(output, 'w')
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188 if method == 'Size':
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189 header = ["Dataset", "Chromosome", "Polarity", method, "Count"]
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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190 else:
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191 header = ["Dataset", "Chromosome", "Chrom_length", "Coordinate",
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192 "Polarity", method]
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193 F.write('\t'.join(header) + '\n')
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194 for input, sample in zip(inputs, samples):
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195 mapobj = Map(input, sample)
3
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196 token = {"Counts": mapobj.compute_readcount,
2
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197 "Max": mapobj.compute_max,
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198 "Mean": mapobj.compute_mean,
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199 "Median": mapobj.compute_median,
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200 "Coverage": mapobj.compute_coverage,
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201 "Size": mapobj.compute_size}
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202 token[method](mapobj.map_dict, F)
0
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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203 F.close()
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204
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205
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206 if __name__ == "__main__":
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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207 args = Parser()
6d48150495e3 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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208 # if identical sample names
2
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209 if len(set(args.sample_names)) != len(args.sample_names):
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210 args.sample_names = [name + '_' + str(i) for
507383cce5a8 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/small_rna_maps commit edbb53cb13b52bf8e71c562fa8acc2c3be2fb270
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211 i, name in enumerate(args.sample_names)]
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212 main(args.inputs, args.sample_names, args.plot_methods, args.outputs)