Mercurial > repos > mheinzl > variant_analyzer2

annotate mut2read.py @ 87:49b4a9ca7400 draft

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planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
author mheinzl
date Sat, 22 Apr 2023 10:04:18 +0000
parents e46d5e377760
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1 #!/usr/bin/env python
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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2
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3 """mut2read.py
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5 Author -- Gundula Povysil
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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6 Contact -- povysil@bioinf.jku.at
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7
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8 Takes a tabular file with mutations and a BAM file as input and prints
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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9 all tags of reads that carry the mutation to a user specified output file.
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10 Creates fastq file of reads of tags with mutation.
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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12 ======= ========== ================= ================================
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13 Version Date Author Description
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14 0.2.1 2019-10-27 Gundula Povysil -
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15 ======= ========== ================= ================================
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16
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17 USAGE: python mut2read.py DCS_Mutations.tabular DCS.bam Aligned_Families.tabular Interesting_Reads.fastq tag_count_dict.json
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18 """
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20 import argparse
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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21 import json
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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22 import os
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23 import re
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24 import sys
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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25
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26 import numpy as np
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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27 import pysam
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28 from cyvcf2 import VCF
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31 def make_argparser():
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32 parser = argparse.ArgumentParser(description='Takes a vcf file with mutations and a BAM file as input and prints all tags of reads that carry the mutation to a user specified output file and creates a fastq file of reads of tags with mutation.')
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33 parser.add_argument('--mutFile',
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34 help='VCF file with DCS mutations.')
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35 parser.add_argument('--bamFile',
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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36 help='BAM file with aligned DCS reads.')
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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37 parser.add_argument('--familiesFile',
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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38 help='TABULAR file with aligned families.')
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39 parser.add_argument('--outputFastq',
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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40 help='Output FASTQ file of reads with mutations.')
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41 parser.add_argument('--outputJson',
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42 help='Output JSON file to store collected data.')
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43 parser.add_argument('--refalttiers', action="store_true",
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44 help='Store also information about the reference allele.')
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45 return parser
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48 def mut2read(argv):
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49 parser = make_argparser()
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50 args = parser.parse_args(argv[1:])
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52 file1 = args.mutFile
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53 file2 = args.bamFile
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54 file3 = args.familiesFile
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55 outfile = args.outputFastq
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56 json_file = args.outputJson
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57 refalttiers = args.refalttiers
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59 if os.path.isfile(file1) is False:
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60 sys.exit("Error: Could not find '{}'".format(file1))
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62 if os.path.isfile(file2) is False:
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63 sys.exit("Error: Could not find '{}'".format(file2))
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65 if os.path.isfile(file3) is False:
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66 sys.exit("Error: Could not find '{}'".format(file3))
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68 # read dcs bam file
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69 # pysam.index(file2)
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70 bam = pysam.AlignmentFile(file2, "rb")
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72 # get tags
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73 tag_dict = {}
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74 cvrg_dict = {}
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75 tag_dict_ref = {}
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76
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77 for variant in VCF(file1):
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78 chrom = variant.CHROM
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79 stop_pos = variant.start
11a2a34f8a2b planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
parents: 0
diff changeset
80 ref = variant.REF
43
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mheinzl
parents: 11
diff changeset
81 if len(variant.ALT) == 0:
d21960b45a6b planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
parents: 11
diff changeset
82 continue
d21960b45a6b planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
parents: 11
diff changeset
83 else:
d21960b45a6b planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
parents: 11
diff changeset
84 alt = variant.ALT[0]
78
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
85 alt = alt.upper()
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
86 ref = ref.upper()
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
87 if "N" in alt: # skip indels with N in alt allele --> it is not an indel but just a mismatch at the position where the N is (checked this in IGV)
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
88 continue
7
ded0dc6a20d3 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
parents: 6
diff changeset
89 chrom_stop_pos = str(chrom) + "#" + str(stop_pos) + "#" + ref + "#" + alt
0
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
parents:
diff changeset
90 dcs_len = []
78
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
91 for pileupcolumn in bam.pileup(chrom, stop_pos - 1, stop_pos + 1, max_depth=100000000):
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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92 if pileupcolumn.reference_pos == stop_pos:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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93 count_alt = 0
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mheinzl
parents: 75
diff changeset
94 count_ref = 0
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mheinzl
parents: 75
diff changeset
95 count_indel = 0
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
96 count_n = 0
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mheinzl
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diff changeset
97 count_other = 0
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mheinzl
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98 count_lowq = 0
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mheinzl
parents: 75
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99 for pileupread in pileupcolumn.pileups:
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mheinzl
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100 if not pileupread.is_refskip:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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101 if pileupread.is_del:
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mheinzl
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102 p = pileupread.query_position_or_next
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mheinzl
parents: 75
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103 e = p + len(alt) - 1
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104 else:
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mheinzl
parents: 75
diff changeset
105 p = pileupread.query_position
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
106 e = p + len(alt)
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
107 s = p
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
108 split_cigar = re.split('(\d+)', pileupread.alignment.cigarstring)
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
109 if len(ref) < len(alt):
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
110 if "I" in split_cigar:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
111 all_insertions = [inser_i for inser_i, ins in enumerate(split_cigar) if ins == "I"]
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
112 for ai in all_insertions: # if multiple insertions in DCS
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
113 ins_index = [int(ci) for ci in split_cigar[:ai - 1] if ci.isdigit()]
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
114 ins_count = split_cigar[ai - 1] # nr of insertions should match with alt allele
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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diff changeset
115 if "I" in split_cigar and sum(ins_index) == p + 1 and len(alt) - 1 == int(ins_count): # if position in read matches and length of insertion
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
116 nuc = pileupread.alignment.query_sequence[s:e]
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
117 break
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diff changeset
118 else:
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mheinzl
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diff changeset
119 nuc = pileupread.alignment.query_sequence[s]
0
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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120 else:
78
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diff changeset
121 nuc = pileupread.alignment.query_sequence[s]
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diff changeset
122 elif len(ref) > len(alt):
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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123 ref_positions = pileupread.alignment.get_reference_positions(full_length=True)[s:p + len(ref)]
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124 if "D" in split_cigar:
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125 all_deletions = [del_i for del_i, dele in enumerate(split_cigar) if dele == "D"]
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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126 for di, ai in enumerate(all_deletions): # if multiple insertions in DCS
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127 if di > 0: # more than 1 deletion, don't count previous deletion to position
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128 all_deletions_mod = split_cigar[:ai - 1]
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129 prev_del_idx = [all_deletions_mod.index("D") - 1, all_deletions_mod.index("D")]
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diff changeset
130 split_cigar_no_prev = [ad for i, ad in enumerate(all_deletions_mod) if i not in prev_del_idx]
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131 del_index = [int(ci) for ci in split_cigar_no_prev[:ai - 1] if ci.isdigit()]
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132 else: # first deletion in read, sum all previous (mis)matches and insertions to position
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133 del_index = [int(ci) for ci in split_cigar[:ai - 1] if ci.isdigit()]
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134 del_count = split_cigar[ai - 1] # nr of deletions should match with ref allele
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135 if "D" in split_cigar and sum(del_index) == p + 1 and len(ref) - 1 == int(del_count):
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
136 nuc = pileupread.alignment.query_sequence[s:e]
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137 if nuc == "":
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138 nuc = str(alt)
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diff changeset
139 break
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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140 else:
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diff changeset
141 nuc = pileupread.alignment.query_sequence[s:s + len(ref)]
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142 elif len(ref_positions) < len(ref): # DCS has reference but the position is at the very end of the DCS and therefore not the full reference positions are there
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diff changeset
143 nuc = pileupread.alignment.get_reference_sequence()[s:s + len(ref)]
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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144 if nuc.upper() == ref[:len(nuc)]:
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mheinzl
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145 nuc = str(ref)
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146 else:
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diff changeset
147 nuc = pileupread.alignment.query_sequence[s:s + len(ref)]
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148 else: # SNV: query position is None if is_del or is_refskip is set.
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diff changeset
149 nuc = pileupread.alignment.query_sequence[s]
0
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diff changeset
150
78
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151 nuc = nuc.upper()
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diff changeset
152 tag = pileupread.alignment.query_name
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mheinzl
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153 if "_" in tag:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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154 tag = re.split('_', tag)[0]
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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155
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
156 if nuc == alt:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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157 count_alt += 1
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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158 if tag in tag_dict:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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159 tag_dict[tag][chrom_stop_pos] = alt
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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160 else:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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161 tag_dict[tag] = {}
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
162 tag_dict[tag][chrom_stop_pos] = alt
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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163 elif nuc == ref:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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164 count_ref += 1
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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165 if tag in tag_dict_ref:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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166 tag_dict_ref[tag][chrom_stop_pos] = ref
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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167 else:
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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168 tag_dict_ref[tag] = {}
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
169 tag_dict_ref[tag][chrom_stop_pos] = ref
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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170 elif nuc == "N":
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mheinzl
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171 count_n += 1
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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172 elif nuc == "lowQ":
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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173 count_lowq += 1
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
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174 else:
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mheinzl
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diff changeset
175 count_other += 1
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
176 dcs_len.append(len(pileupread.alignment.query_sequence))
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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177
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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178 dcs_median = np.median(np.array(dcs_len))
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
179 cvrg_dict[chrom_stop_pos] = (count_ref, count_alt, dcs_median)
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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180 print("coverage at pos %s = %s, ref = %s, alt = %s, other bases = %s, N = %s, indel = %s, low quality = %s, median length of DCS = %s\n" %
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 75
diff changeset
181 (pileupcolumn.pos, count_ref + count_alt, count_ref, count_alt, count_other, count_n,
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
182 count_indel, count_lowq, dcs_median))
0
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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diff changeset
183 bam.close()
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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184
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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diff changeset
185 with open(json_file, "w") as f:
78
fdfe9a919ff7 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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186 json.dump((tag_dict, cvrg_dict, tag_dict_ref), f)
0
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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187
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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diff changeset
188 # create fastq from aligned reads
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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189 with open(outfile, 'w') as out:
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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190 with open(file3, 'r') as families:
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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191 for line in families:
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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diff changeset
192 line = line.rstrip('\n')
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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diff changeset
193 splits = line.split('\t')
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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194 tag = splits[0]
84
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mheinzl
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diff changeset
195 if refalttiers is True:
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
196 if tag in tag_dict or tag in tag_dict_ref:
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
197 str1 = splits[4]
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
198 curr_seq = str1.replace("-", "")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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diff changeset
199 str2 = splits[5]
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
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diff changeset
200 curr_qual = str2.replace(" ", "")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
201 out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
202 out.write(curr_seq + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
203 out.write("+" + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
204 out.write(curr_qual + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
205 else:
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
206 if tag in tag_dict:
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
207 str1 = splits[4]
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
208 curr_seq = str1.replace("-", "")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
209 str2 = splits[5]
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
210 curr_qual = str2.replace(" ", "")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
211 out.write("@" + splits[0] + "." + splits[1] + "." + splits[2] + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
212 out.write(curr_seq + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
parents: 78
diff changeset
213 out.write("+" + "\n")
e46d5e377760 planemo upload for repository https://github.com/Single-Molecule-Genetics/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8-dirty
mheinzl
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diff changeset
214 out.write(curr_qual + "\n")
0
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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215
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216
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
mheinzl
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diff changeset
217 if __name__ == '__main__':
e5953c54cfb5 planemo upload for repository https://github.com/gpovysil/VariantAnalyzerGalaxy/tree/master/tools/variant_analyzer commit ee4a8e6cf290e6c8a4d55f9cd2839d60ab3b11c8
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diff changeset
218 sys.exit(mut2read(sys.argv))