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annotate mircounts.py @ 7:65befdc9925a draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit 3514091150570410ce32cbdfda26fd6e5591fef1
author artbio
date Sat, 14 Oct 2017 18:53:02 -0400
parents da1aa7de2b19
children 2a08a6eb471c
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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1 #!/usr/bin/env python
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
artbio
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2 import argparse
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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4 import pysam
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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7 def Parser():
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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8 parser = argparse.ArgumentParser(description='miRNAs counts and coverages')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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9 parser.add_argument('-a', '--alignment', metavar='FILE', type=str,
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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10 dest='alignment_file', help='Alignment bam file')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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11 parser.add_argument('--gff', metavar='FILE', type=str, dest='gff_file',
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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12 help='GFF3 describing both pre-miRNAs\
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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13 and mature miRNAs')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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14 parser.add_argument('-q', '--quality_threshold', type=int,
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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15 dest='quality_threshold',
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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16 help='Quality threshold for coverage (default=10)',
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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17 default=10)
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18 parser.add_argument('-p', '--pre_mirs', type=str, dest='pre_mirs',
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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19 help='pre-miRNAs count file path', metavar='FILE')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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20 parser.add_argument('-m', '--mirs', type=str, dest='mirs',
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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21 help='mature miRNA count file path', metavar='FILE')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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22 parser.add_argument('--lattice', metavar='FILE', type=str, dest='lattice',
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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23 help='Output file for the lattice dataframe.')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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24 args = parser.parse_args()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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25 return args
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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28 def get_pre_mir_counts(bamfile):
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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29 """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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30 Takes a AlignmentFile object and returns a dictionary of counts for reads
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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31 aligning with pre_mirs (as keys)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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32 """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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33 count = dict()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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34 for ref_name in bamfile.references:
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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35 count[ref_name] = bamfile.count(reference=ref_name)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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36 return count
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37
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38
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39 def get_pre_mir_coverage(bamfile, quality=10):
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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40 """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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41 Takes a AlignmentFile object and returns a dictionary of lists
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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42 of coverage along the coordinates of pre_mirs (as keys)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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43 """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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44 coverage = dict()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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45 for ref_name, ref_len in zip(bamfile.references, bamfile.lengths):
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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46 coverage[ref_name] = bamfile.count_coverage(reference=ref_name,
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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47 start=0, end=ref_len,
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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48 quality_threshold=quality)
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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49 """ Add the 4 coverage values """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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50 coverage[ref_name] = [sum(x) for x in
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51 zip(*coverage[ref_name])]
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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52 return coverage
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53
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54
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55 def get_mir_counts(bamfile, gff_file):
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56 """
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57 Takes a AlignmentFile and a gff file and computes for
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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58 each 'miRNA' region of the gff the number of reads that hit it
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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59 returns a dict[mir_name] = count
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60 """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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61 counts = dict()
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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62 for line in open(gff_file, 'r'):
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63 if line[0] != '#':
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64 gff_fields = line[:-1].split("\t")
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65 if gff_fields[2] == 'miRNA':
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66 mir_name = gff_fields[0]
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67 premir_name = gff_fields[8].split('=')[-1]
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68 mir_start = int(gff_fields[3])
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69 mir_end = int(gff_fields[4])
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70 # GFF is 1-based, pysam is 0-based.
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71 counts[mir_name] = bamfile.count(reference=premir_name,
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72 start=mir_start-1,
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73 end=mir_end-1)
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74 return counts
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75
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76
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77 def write_dataframe_coverage(countdict, outfile):
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78 """
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79 Takes a dict[pre_mir reference name] = [coverage list]
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80 and writes a dataframe with columns:
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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81 <gene_type name>, offset, normoffset, counts and normcounts
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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82 in the outfile
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83 """
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84 F = open(outfile, 'w')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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85 F.write('Mir_hairpin\tOffset\tNorm_offset\tCount\tNorm_count\n')
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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86 for ref in sorted(countdict):
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87 """
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88 For each reference name in mirs,
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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89 write the coverage of each of its positions
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90 """
da29af78a960 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit d4d8106d66b65679a1a685ab94bfcf99cdb7b959
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91 maximum = max(countdict[ref])
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92 reference_length = len(countdict[ref])
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93 for pos, c in enumerate(countdict[ref]):
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94 """ Compute and write value for each reference position"""
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95 F.write('%s\t%s\t%s\t%s\t%s\n' % (ref, str(pos + 1),
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96 str(float(pos+1)/reference_length), str(float(c)),
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97 str(float(c)/maximum) if maximum != 0 else '0'))
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98 F.close()
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99
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100
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101 def write_counts(countdict, outfile):
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102 """
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103 Takes a dict[<gene_type name>]=count and
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104 writes a count table
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105 """
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106 F = open(outfile, 'w')
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107 for gene in sorted(countdict):
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108 F.write('%s\t%s\n' % (gene, str(countdict[gene])))
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109 F.close()
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110
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111
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112 def main():
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113 args = Parser()
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114 bamfile = pysam.AlignmentFile(args.alignment_file, 'rb', check_sq=False)
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115 if args.pre_mirs:
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116 pre_mirs = get_pre_mir_counts(bamfile)
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117 write_counts(pre_mirs, args.pre_mirs)
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118 if args.lattice:
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119 pre_mirs_coverage = get_pre_mir_coverage(bamfile,
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120 args.quality_threshold)
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121 write_dataframe_coverage(pre_mirs_coverage, args.lattice)
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122 if args.mirs:
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123 mirs = get_mir_counts(bamfile, args.gff_file)
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124 write_counts(mirs, args.mirs)
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125
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126
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127 if __name__ == '__main__':
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128 main()