Mercurial > repos > iuc > varscan_somatic

annotate varscan.py @ 8:b79bb8b09822 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
author iuc
date Thu, 28 Mar 2019 18:19:00 -0400
parents 2657ab48e16a
children 4e97191a1ff7
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2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1 #!/usr/bin/env python3
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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2 from __future__ import print_function
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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3
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4 import argparse
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5 import io
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6 import os
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7 import subprocess
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8 import sys
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9 import tempfile
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10 import time
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11 from contextlib import ExitStack
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12 from functools import partial
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13 from threading import Thread
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15 import pysam
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18 class VariantCallingError (RuntimeError):
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19 """Exception class for issues with samtools and varscan subprocesses."""
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21 def __init__(self, message=None, call='', error=''):
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22 self.message = message
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23 self.call = call.strip()
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24 self.error = error.strip()
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26 def __str__(self):
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27 if self.message is None:
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28 return ''
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29 if self.error:
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30 msg_header = '"{0}" failed with:\n{1}\n\n'.format(
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31 self.call, self.error
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32 )
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33 else:
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34 msg_header = '{0} failed.\n'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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35 'No further information about this error is available.\n\n'.format(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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36 self.call
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37 )
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38 return msg_header + self.message
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39
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41 class VarScanCaller (object):
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42 def __init__(self, ref_genome, bam_input_files,
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43 max_depth=None,
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44 min_mapqual=None, min_basequal=None,
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45 threads=1, verbose=False, quiet=True
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46 ):
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47 self.ref_genome = ref_genome
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48 self.bam_input_files = bam_input_files
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49 self.max_depth = max_depth
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50 self.min_mapqual = min_mapqual
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51 self.min_basequal = min_basequal
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52 self.threads = threads
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53 self.verbose = verbose
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54 self.quiet = quiet
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55
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56 with pysam.FastaFile(ref_genome) as ref_fa:
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57 self.ref_contigs = ref_fa.references
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58 self.ref_lengths = ref_fa.lengths
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59
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60 self.pileup_engine = ['samtools', 'mpileup']
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61 self.varcall_engine = ['varscan', 'somatic']
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62 self.requires_stdout_redirect = False
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63 self.TemporaryContigVCF = partial(
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64 tempfile.NamedTemporaryFile,
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65 mode='wb', suffix='', delete=False, dir=os.getcwd()
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66 )
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67 self.tmpfiles = []
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68
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69 def _get_pysam_pileup_args(self):
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70 param_dict = {}
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71 if self.max_depth is not None:
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72 param_dict['max_depth'] = self.max_depth
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73 if self.min_mapqual is not None:
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74 param_dict['min_mapping_quality'] = self.min_mapqual
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75 if self.min_basequal is not None:
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76 param_dict['min_base_quality'] = self.min_basequal
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77 param_dict['compute_baq'] = False
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78 param_dict['stepper'] = 'samtools'
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79 return param_dict
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80
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81 def varcall_parallel(self, normal_purity=None, tumor_purity=None,
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82 min_coverage=None,
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83 min_var_count=None,
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84 min_var_freq=None, min_hom_freq=None,
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85 p_value=None, somatic_p_value=None,
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86 threads=None, verbose=None, quiet=None
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87 ):
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88 if not threads:
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89 threads = self.threads
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90 if verbose is None:
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91 verbose = self.verbose
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92 if quiet is None:
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iuc
parents:
diff changeset
93 quiet = self.quiet
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
94 # mapping of method parameters to varcall engine command line options
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
95 varcall_engine_option_mapping = [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
96 ('--normal-purity', normal_purity),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
97 ('--tumor-purity', tumor_purity),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
98 ('--min-coverage', min_coverage),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
99 ('--min-reads2', min_var_count),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
100 ('--min-var-freq', min_var_freq),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
101 ('--min-freq-for-hom', min_hom_freq),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
102 ('--p-value', p_value),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
103 ('--somatic-p-value', somatic_p_value),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
104 ('--min-avg-qual', self.min_basequal)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
105 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
106 varcall_engine_options = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
107 for option, value in varcall_engine_option_mapping:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
108 if value is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
109 varcall_engine_options += [option, str(value)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
110 pileup_engine_options = ['-B']
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
111 if self.max_depth is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
112 pileup_engine_options += ['-d', str(self.max_depth)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
113 if self.min_mapqual is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
114 pileup_engine_options += ['-q', str(self.min_mapqual)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
115 if self.min_basequal is not None:
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iuc
parents:
diff changeset
116 pileup_engine_options += ['-Q', str(self.min_basequal)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
117
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iuc
parents:
diff changeset
118 # Create a tuple of calls to samtools mpileup and varscan for
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
119 # each contig. The contig name is stored as the third element of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
120 # that tuple.
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iuc
parents:
diff changeset
121 # The calls are stored in the reverse order of the contig list so
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
122 # that they can be popped off later in the original order
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
123 calls = [(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
124 self.pileup_engine + pileup_engine_options + [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
125 '-r', contig + ':',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
126 '-f', self.ref_genome
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iuc
parents:
diff changeset
127 ] + self.bam_input_files,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
128 self.varcall_engine + [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
129 '-', '{out}', '--output-vcf', '1', '--mpileup', '1'
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iuc
parents:
diff changeset
130 ] + varcall_engine_options,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
131 contig
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
132 ) for contig in self.ref_contigs[::-1]]
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iuc
parents:
diff changeset
133
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iuc
parents:
diff changeset
134 if verbose:
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iuc
parents:
diff changeset
135 print('Starting variant calling ..')
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iuc
parents:
diff changeset
136
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
137 # launch subprocesses and monitor their status
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iuc
parents:
diff changeset
138 subprocesses = []
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iuc
parents:
diff changeset
139 error_table = {}
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
140 tmp_io_started = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
141 tmp_io_finished = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
142 self.tmpfiles = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
143
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iuc
parents:
diff changeset
144 def enqueue_stderr_output(out, stderr_buffer):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
145 for line in iter(out.readline, b''):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
146 # Eventually we are going to print the contents of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
147 # the stderr_buffer to sys.stderr so we can
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
148 # decode things here using its encoding.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
149 # We do a 'backslashreplace' just to be on the safe side.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
150 stderr_buffer.write(line.decode(sys.stderr.encoding,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
151 'backslashreplace'))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
152 out.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
153
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
154 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
155 while subprocesses or calls:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
156 while calls and len(subprocesses) < threads:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
157 # There are still calls waiting for execution and we
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
158 # have unoccupied threads so we launch a new combined
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
159 # call to samtools mpileup and the variant caller.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
160
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
161 # pop the call arguments from our call stack
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
162 call = calls.pop()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
163 # get the name of the contig that this call is going
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
164 # to work on
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
165 contig = call[2]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
166 # Based on the contig name, generate a readable and
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
167 # file system-compatible prefix and use it to create
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
168 # a named temporary file, to which the call output
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
169 # will be redirected.
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iuc
parents:
diff changeset
170 # At the moment we create the output file we add it to
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
171 # the list of all temporary output files so that we can
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
172 # remove it eventually during cleanup.
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iuc
parents:
diff changeset
173 call_out = self.TemporaryContigVCF(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
174 prefix=''.join(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
175 c if c.isalnum() else '_' for c in contig
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iuc
parents:
diff changeset
176 ) + '_',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
177 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
178 # maintain a list of variant call outputs
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
179 # in the order the subprocesses got launched
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
180 tmp_io_started.append(call_out.name)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
181 if self.requires_stdout_redirect:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
182 # redirect stdout to the temporary file just created
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
183 stdout_p2 = call_out
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
184 stderr_p2 = subprocess.PIPE
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iuc
parents:
diff changeset
185 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
186 # variant caller wants to write output to file directly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
187 stdout_p2 = subprocess.PIPE
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
188 stderr_p2 = subprocess.STDOUT
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
189 call[1][call[1].index('{out}')] = call_out.name
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
190 call_out.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
191 # for reporting purposes, join the arguments for the
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
192 # samtools and the variant caller calls into readable
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
193 # strings
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
194 c_str = (' '.join(call[0]), ' '.join(call[1]))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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195 error_table[c_str] = [io.StringIO(), io.StringIO()]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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196 # start the subprocesses
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
197 p1 = subprocess.Popen(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
198 call[0],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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199 stdout=subprocess.PIPE, stderr=subprocess.PIPE
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
200 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
201 p2 = subprocess.Popen(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
202 call[1],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
203 stdin=p1.stdout,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
204 stdout=stdout_p2,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
205 stderr=stderr_p2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
206 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
207 # subprocess bookkeeping
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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208 subprocesses.append((c_str, p1, p2, call_out, contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
209 # make sure our newly launched call does not block
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
210 # because its buffers fill up
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iuc
parents:
diff changeset
211 p1.stdout.close()
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iuc
parents:
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212 t1 = Thread(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
213 target=enqueue_stderr_output,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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214 args=(p1.stderr, error_table[c_str][0])
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
215 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
216 t2 = Thread(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
217 target=enqueue_stderr_output,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
218 args=(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
219 p2.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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220 if self.requires_stdout_redirect else
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
221 p2.stdout,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
222 error_table[c_str][1]
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iuc
parents:
diff changeset
223 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
224 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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225 t1.daemon = t2.daemon = True
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
226 t1.start()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
227 t2.start()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
228
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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229 if verbose:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
230 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
231 'Calling variants for contig: {0}'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
232 .format(call[2])
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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diff changeset
233 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
234
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
235 # monitor all running calls to see if any of them are done
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
236 for call, p1, p2, ofo, contig in subprocesses:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
237 p1_stat = p1.poll()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
238 p2_stat = p2.poll()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
239 if p1_stat is not None or p2_stat is not None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
240 # There is an outcome for this process!
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
241 # Lets see what it is
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
242 if p1_stat or p2_stat:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
243 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
244 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
245 error_table[call][0].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
246 error_table[call][1].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
247 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
248 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
249 raise VariantCallingError(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
250 'Variant Calling for contig {0} failed.'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
251 .format(contig),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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252 call='{0} | {1}'.format(call[0], call[1])
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
253 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
254 if p1_stat == 0 and p2_stat is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
255 # VarScan is not handling the no output from
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
256 # samtools mpileup situation correctly so maybe
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
257 # that's the issue here
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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258 last_words = error_table[call][1].getvalue(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
259 ).splitlines()[-4:]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
260 if len(last_words) < 4 or any(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
261 not msg.startswith('Input stream not ready')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
262 for msg in last_words
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
263 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
264 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
265 # lets give this process a bit more time
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
266 # VarScan is waiting for input it will never
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
267 # get, stop it.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
268 p2.terminate()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
269 subprocesses.remove((call, p1, p2, ofo, contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
270 ofo.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
271 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
272 if p2_stat == 0:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
273 # Things went fine.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
274 # maintain a list of variant call outputs
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
275 # that finished successfully (in the order
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
276 # they finished)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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277 tmp_io_finished.append(ofo.name)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
278 if verbose:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
279 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
280 print('Contig {0} finished.'.format(contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
281 if not quiet:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
282 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
283 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
284 'stderr output from samtools mpileup/'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
285 'bcftools:'.upper(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
286 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
287 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
288 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
289 error_table[call][0].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
290 error_table[call][1].getvalue(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
291 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
292 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
293 # Discard the collected stderr output from
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
294 # the call, remove the call from the list of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
295 # running calls and close its output file.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
296 del error_table[call]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
297 subprocesses.remove((call, p1, p2, ofo, contig))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
298 # Closing the output file is important or we
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
299 # may hit the file system limit for open files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
300 # if there are lots of contigs.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
301 ofo.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
302 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
303 # wait a bit in between monitoring cycles
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
304 time.sleep(2)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
305 finally:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
306 for call, p1, p2, ofo, contig in subprocesses:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
307 # make sure we do not leave running subprocesses behind
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
308 for proc in (p1, p2):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
309 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
310 proc.terminate()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
311 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
312 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
313 # close currently open files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
314 ofo.close()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
315 # store the files with finished content in the order that
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
316 # the corresponding jobs were launched
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
317 self.tmpfiles = [f for f in tmp_io_started if f in tmp_io_finished]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
318 # Make sure remaining buffered stderr output of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
319 # subprocesses does not get lost.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
320 # Currently, we don't screen this output for real errors,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
321 # but simply rewrite everything.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
322 if not quiet and error_table:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
323 print()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
324 print(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
325 'stderr output from samtools mpileup/bcftools:'.upper(),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
326 file=sys.stderr
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
327 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
328 for call, errors in error_table.items():
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
329 print(' | '.join(call), ':', file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
330 print('-' * 20, file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
331 print('samtools mpileup output:', file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
332 print(errors[0].getvalue(), file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
333 print('varscan somatic output:', file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
334 print(errors[1].getvalue(), file=sys.stderr)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
335
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
336 def _add_ref_contigs_to_header(self, header):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
337 for chrom, length in zip(self.ref_contigs, self.ref_lengths):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
338 header.add_meta(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
339 'contig',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
340 items=[('ID', chrom), ('length', length)]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
341 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
342
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
343 def _add_filters_to_header(self, header):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
344 varscan_fpfilters = {
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
345 'VarCount': 'Fewer than {min_var_count2} variant-supporting reads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
346 'VarFreq': 'Variant allele frequency below {min_var_freq2}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
347 'VarAvgRL':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
348 'Average clipped length of variant-supporting reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
349 '{min_var_len}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
350 'VarReadPos': 'Relative average read position < {min_var_readpos}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
351 'VarDist3':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
352 'Average distance to effective 3\' end < {min_var_dist3}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
353 'VarMMQS':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
354 'Average mismatch quality sum for variant reads > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
355 '{max_var_mmqs}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
356 'VarMapQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
357 'Average mapping quality of variant reads < {min_var_mapqual}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
358 'VarBaseQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
359 'Average base quality of variant reads < {min_var_basequal}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
360 'Strand':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
361 'Strand representation of variant reads < {min_strandedness}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
362 'RefAvgRL':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
363 'Average clipped length of ref-supporting reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
364 '{min_ref_len}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
365 'RefReadPos':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
366 'Relative average read position < {min_ref_readpos}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
367 'RefDist3':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
368 'Average distance to effective 3\' end < {min_ref_dist3}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
369 'RefMapQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
370 'Average mapping quality of reference reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
371 '{min_ref_mapqual}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
372 'RefBaseQual':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
373 'Average base quality of ref-supporting reads < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
374 '{min_ref_basequal}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
375 'RefMMQS':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
376 'Average mismatch quality sum for ref-supporting reads > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
377 '{max_ref_mmqs}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
378 'MMQSdiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
379 'Mismatch quality sum difference (var - ref) > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
380 '{max_mmqs_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
381 'MinMMQSdiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
382 'Mismatch quality sum difference (var - ref) < '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
383 '{max_mmqs_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
384 'MapQualDiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
385 'Mapping quality difference (ref - var) > {max_mapqual_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
386 'MaxBAQdiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
387 'Average base quality difference (ref - var) > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
388 '{max_basequal_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
389 'ReadLenDiff':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
390 'Average supporting read length difference (ref - var) > '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
391 '{max_relative_len_diff}',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
392 }
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
393 for filter_id, description in varscan_fpfilters.items():
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
394 header.filters.add(filter_id, None, None, description)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
395
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
396 def _add_indel_info_flag_to_header(self, header):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
397 header.info.add(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
398 'INDEL', 0, 'Flag', 'Indicates that the variant is an INDEL'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
399 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
400
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
401 def _standardize_format_fields(self, header):
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
402 """Add standard FORMAT key declarations to a VCF header."""
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
403
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
404 format_field_specs = [
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
405 # pysam will not add quotes around single-word descriptions,
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
406 # which is a violation of the VCF specification.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
407 # To work around this we are using two words as the
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
408 # GT format description (instead of the commonly used "Genotype").
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
409 # This could be changed once pysam learns to quote correctly.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
410 ('GT', '1', 'String', 'Genotype code'),
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
411 ('GQ', '1', 'Integer', 'Genotype quality'),
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
412 ('DP', '1', 'Integer', 'Read depth'),
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
413 ('AD', 'R', 'Integer', 'Read depth for each allele'),
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
414 ('ADF', 'R', 'Integer',
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
415 'Read depth for each allele on the forward strand'),
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
416 ('ADR', 'R', 'Integer',
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
417 'Read depth for each allele on the reverse strand')
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
418 ]
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
419 # Existing FORMAT declarations cannot be overwritten.
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
420 # The only viable strategy is to mark them as removed,
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
421 # then merge the header with another one containing the
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
422 # correct declarations. This is what is implemented below.
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
423 temp_header = pysam.VariantHeader()
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
424 for spec in format_field_specs:
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
425 temp_header.formats.add(*spec)
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
426 if spec[0] in header.formats:
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
427 header.formats.remove_header(spec[0])
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
428 header.merge(temp_header)
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
429
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
430 def _compile_common_header(self, varcall_template, no_filters=False):
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
431 # read the header produced by VarScan for use as a template
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
432 with pysam.VariantFile(varcall_template, 'r') as original_data:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
433 varscan_header = original_data.header
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
434 # don't propagate non-standard and redundant FORMAT keys written
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
435 # by VarScan
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
436 varscan_header.formats.remove_header('AD')
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
437 varscan_header.formats.remove_header('FREQ')
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
438 varscan_header.formats.remove_header('RD')
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
439 varscan_header.formats.remove_header('DP4')
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
440 # build a new header containing information not written by VarScan
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
441 common_header = pysam.VariantHeader()
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
442 # copy over sample info from the VarScan template
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
443 for sample in varscan_header.samples:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
444 common_header.samples.add(sample)
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
445 # add reference information
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
446 common_header.add_meta('reference', value=self.ref_genome)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
447 # change the source information
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
448 common_header.add_meta('source', value='varscan.py')
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
449 # add contig information
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
450 self._add_ref_contigs_to_header(common_header)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
451 # declare an INDEL flag for record INFO fields
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
452 self._add_indel_info_flag_to_header(common_header)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
453 # merge in remaining information from the VarScan template
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
454 common_header.merge(varscan_header)
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
455 # add additional FILTER declarations
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
456 if not no_filters:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
457 # add filter info
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
458 self._add_filters_to_header(common_header)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
459 # generate standard FORMAT field declarations
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
460 # including a correct AD declaration to prevent VarScan's
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
461 # non-standard one from getting propagated
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
462 self._standardize_format_fields(common_header)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
463 return common_header
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
464
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
465 def _fix_record_gt_fields(self, record):
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
466 """Migrate non-standard genotype fields to standard ones."""
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
467
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
468 # The key issue to consider here is that we need to modify
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
469 # genotype field values on a per-sample basis, but htslib
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
470 # reserves memory for the values of all samples upon the first
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
471 # modification of the field in the variant record.
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
472 # => We need to calculate all values first, then fill each
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
473 # genotype field starting with the sample with the largest value.
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
474 new_gt_fields = {'AD': [], 'ADF': [], 'ADR': []}
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
475 # store the current genotype field contents for each sample
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
476 per_sample_gts = record.samples.values()
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
477 # calculate and store the new genotype field values
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
478 for gt_field in per_sample_gts:
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
479 # generate a standard AD field by combining VarScan's
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
480 # RD and non-standard AD fields
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
481 new_gt_fields['AD'].append((gt_field['RD'], gt_field['AD'][0]))
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
482 # split VarScan's DP4 field into the standard fields
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
483 # ADF and ADR
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
484 new_gt_fields['ADF'].append(
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
485 (int(gt_field['DP4'][0]), int(gt_field['DP4'][2]))
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
486 )
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
487 new_gt_fields['ADR'].append(
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
488 (int(gt_field['DP4'][1]), int(gt_field['DP4'][3]))
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
489 )
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
490 # Modify the record's genotype fields.
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
491 # For each field, modify the sample containing the largest
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
492 # value for the field first.
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
493 # Without this precaution we could trigger:
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
494 # "bcf_update_format: Assertion `!fmt->p_free' failed."
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
495 # in vcf.c of htslib resulting in a core dump.
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
496 for field in sorted(new_gt_fields):
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
497 for new_field, sample_fields in sorted(
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
498 zip(new_gt_fields[field], per_sample_gts),
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
499 key=lambda x: max(x[0]),
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
500 reverse=True
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
501 ):
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
502 sample_fields[field] = new_field
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
503 # remove redundant fields
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
504 # FREQ is easy to calculate from AD
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
505 del record.format['FREQ']
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
506 del record.format['RD']
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
507 del record.format['DP4']
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
508
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
509 def get_allele_specific_pileup_column_stats(
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
510 self, allele, pile_column, ref_fetch, use_md=True
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
511 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
512 var_reads_plus = var_reads_minus = 0
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
513 sum_mapping_qualities = 0
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
514 sum_base_qualities = 0
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
515 sum_dist_from_center = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
516 sum_dist_from_3prime = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
517 sum_clipped_length = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
518 sum_unclipped_length = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
519 sum_num_mismatches_as_fraction = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
520 sum_mismatch_qualities = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
521
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
522 for p in pile_column.pileups:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
523 # skip reads that don't support the allele we're looking for
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
524 if p.query_position is None:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
525 continue
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
526 if p.alignment.query_sequence[p.query_position] != allele:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
527 continue
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
528
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
529 if p.alignment.is_reverse:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
530 var_reads_minus += 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
531 else:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
532 var_reads_plus += 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
533 sum_mapping_qualities += p.alignment.mapping_quality
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
534 sum_base_qualities += p.alignment.query_qualities[p.query_position]
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
535 sum_clipped_length += p.alignment.query_alignment_length
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
536 unclipped_length = p.alignment.query_length
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
537 sum_unclipped_length += unclipped_length
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
538 # The following calculations are all in 1-based coordinates
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
539 # with respect to the physical 5'-end of the read sequence.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
540 if p.alignment.is_reverse:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
541 read_base_pos = unclipped_length - p.query_position
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
542 read_first_aln_pos = (
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
543 unclipped_length - p.alignment.query_alignment_end + 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
544 )
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
545 read_last_aln_pos = (
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
546 unclipped_length - p.alignment.query_alignment_start
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
547 )
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
548 else:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
549 read_base_pos = p.query_position + 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
550 read_first_aln_pos = p.alignment.query_alignment_start + 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
551 read_last_aln_pos = p.alignment.query_alignment_end
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
552 # Note: the original bam-readcount algorithm uses the less accurate
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
553 # p.alignment.query_alignment_length / 2 as the read center
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
554 read_center = (read_first_aln_pos + read_last_aln_pos) / 2
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
555 sum_dist_from_center += 1 - abs(
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
556 read_base_pos - read_center
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
557 ) / (read_center - 1)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
558 # Note: the original bam-readcount algorithm uses a more
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
559 # complicated definition of the 3'-end of a read sequence, which
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
560 # clips off runs of bases with a quality scores of exactly 2.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
561 sum_dist_from_3prime += (
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
562 read_last_aln_pos - read_base_pos
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
563 ) / (unclipped_length - 1)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
564
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
565 sum_num_mismatches = 0
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
566 if use_md:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
567 try:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
568 # see if the read has an MD tag, in which case pysam can
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
569 # calculate the reference sequence for us
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
570 aligned_pairs = p.alignment.get_aligned_pairs(
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
571 matches_only=True, with_seq=True
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
572 )
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
573 except ValueError:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
574 use_md = False
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
575 if use_md:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
576 # The ref sequence got calculated from alignment and MD tag.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
577 for qpos, rpos, ref_base in aligned_pairs:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
578 # pysam uses lowercase ref bases to indicate mismatches
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
579 if (
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
580 ref_base == 'a' or ref_base == 't' or
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
581 ref_base == 'g' or ref_base == 'c'
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
582 ):
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
583 sum_num_mismatches += 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
584 sum_mismatch_qualities += p.alignment.query_qualities[
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
585 qpos
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
586 ]
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
587 else:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
588 # We need to obtain the aligned portion of the reference
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
589 # sequence.
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
590 aligned_pairs = p.alignment.get_aligned_pairs(
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
591 matches_only=True
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
592 )
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
593 # note that ref bases can be lowercase
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
594 ref_seq = ref_fetch(
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
595 aligned_pairs[0][1], aligned_pairs[-1][1] + 1
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
596 ).upper()
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
597 ref_offset = aligned_pairs[0][1]
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
598
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
599 for qpos, rpos in p.alignment.get_aligned_pairs(
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
600 matches_only=True
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
601 ):
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
602 # see if we have a mismatch to the reference at this
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
603 # position, but note that
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
604 # - the query base may be lowercase (SAM/BAM spec)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
605 # - an '=', if present in the query seq, indicates a match
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
606 # to the reference (SAM/BAM spec)
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
607 # - there cannot be a mismatch with an N in the reference
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
608 ref_base = ref_seq[rpos - ref_offset]
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
609 read_base = p.alignment.query_sequence[qpos].upper()
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
610 if (
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
611 read_base != '=' and ref_base != 'N'
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
612 ) and (
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
613 ref_base != read_base
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
614 ):
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
615 sum_num_mismatches += 1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
616 sum_mismatch_qualities += p.alignment.query_qualities[
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
617 qpos
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
618 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
619 sum_num_mismatches_as_fraction += (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
620 sum_num_mismatches / p.alignment.query_alignment_length
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
621 )
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
622
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
623 var_reads_total = var_reads_plus + var_reads_minus
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
624 if var_reads_total == 0:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
625 # No stats without reads!
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
626 return None
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
627 avg_mapping_quality = sum_mapping_qualities / var_reads_total
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
628 avg_basequality = sum_base_qualities / var_reads_total
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
629 avg_pos_as_fraction = sum_dist_from_center / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
630 avg_num_mismatches_as_fraction = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
631 sum_num_mismatches_as_fraction / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
632 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
633 avg_sum_mismatch_qualities = sum_mismatch_qualities / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
634 avg_clipped_length = sum_clipped_length / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
635 avg_distance_to_effective_3p_end = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
636 sum_dist_from_3prime / var_reads_total
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
637 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
638
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
639 return (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
640 avg_mapping_quality,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
641 avg_basequality,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
642 var_reads_plus,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
643 var_reads_minus,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
644 avg_pos_as_fraction,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
645 avg_num_mismatches_as_fraction,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
646 avg_sum_mismatch_qualities,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
647 avg_clipped_length,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
648 avg_distance_to_effective_3p_end
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
649 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
650
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
651 def _postprocess_variant_records(self, invcf,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
652 min_var_count2, min_var_count2_lc,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
653 min_var_freq2, max_somatic_p,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
654 max_somatic_p_depth,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
655 min_ref_readpos, min_var_readpos,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
656 min_ref_dist3, min_var_dist3,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
657 min_ref_len, min_var_len,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
658 max_relative_len_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
659 min_strandedness, min_strand_reads,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
660 min_ref_basequal, min_var_basequal,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
661 max_basequal_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
662 min_ref_mapqual, min_var_mapqual,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
663 max_mapqual_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
664 max_ref_mmqs, max_var_mmqs,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
665 min_mmqs_diff, max_mmqs_diff,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
666 **args):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
667 # set FILTER field according to Varscan criteria
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
668 # multiple FILTER entries must be separated by semicolons
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
669 # No filters applied should be indicated with MISSING
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
670
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
671 # since posterior filters are always applied to just one sample,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
672 # a better place to store the info is in the FT genotype field:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
673 # can be PASS, '.' to indicate that filters have not been applied,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
674 # or a semicolon-separated list of filters that failed
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
675 # unfortunately, gemini does not support this field
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
676
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
677 with ExitStack() as io_stack:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
678 normal_reads, tumor_reads = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
679 io_stack.enter_context(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
680 pysam.Samfile(fn, 'rb')) for fn in self.bam_input_files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
681 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
682 refseq = io_stack.enter_context(pysam.FastaFile(self.ref_genome))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
683 pileup_args = self._get_pysam_pileup_args()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
684 for record in invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
685 if any(len(allele) > 1 for allele in record.alleles):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
686 # skip indel postprocessing for the moment
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
687 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
688 continue
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
689 if record.alleles[0] == 'N':
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
690 # It makes no sense to call SNPs against an unknown
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
691 # reference base
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
692 continue
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
693 # get pileup for genomic region affected by this variant
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
694 if record.info['SS'] == '2':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
695 # a somatic variant => generate pileup from tumor data
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
696 pile = tumor_reads.pileup(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
697 record.chrom, record.start, record.stop,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
698 **pileup_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
699 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
700 sample_of_interest = 'TUMOR'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
701 elif record.info['SS'] in ['1', '3']:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
702 # a germline or LOH variant => pileup from normal data
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
703 pile = normal_reads.pileup(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
704 record.chrom, record.start, record.stop,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
705 **pileup_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
706 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
707 sample_of_interest = 'NORMAL'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
708 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
709 # TO DO: figure out if there is anything interesting to do
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
710 # for SS status codes 0 (reference) and 5 (unknown)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
711 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
712 continue
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
713
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
714 # apply false-positive filtering a la varscan fpfilter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
715 # find the variant site in the pileup columns
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
716 for pile_column in pile:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
717 if pile_column.reference_pos == record.start:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
718 break
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
719 # extract required information
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
720 # overall read depth at the site
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
721 read_depth = pile_column.get_num_aligned()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
722 assert read_depth > 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
723 # no multiallelic sites in varscan
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
724 assert len(record.alleles) == 2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
725 if record.samples[sample_of_interest]['RD'] > 0:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
726 ref_stats, alt_stats = [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
727 self.get_allele_specific_pileup_column_stats(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
728 allele,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
729 pile_column,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
730 partial(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
731 pysam.FastaFile.fetch, refseq, record.chrom
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
732 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
733 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
734 for allele in record.alleles
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
735 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
736 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
737 ref_stats = None
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
738 alt_stats = self.get_allele_specific_pileup_column_stats(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
739 record.alleles[1],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
740 pile_column,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
741 partial(pysam.FastaFile.fetch, refseq, record.chrom)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
742 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
743 ref_count = 0
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
744 if ref_stats:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
745 ref_count = ref_stats[2] + ref_stats[3]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
746 if ref_stats[1] < min_ref_basequal:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
747 record.filter.add('RefBaseQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
748 if ref_count >= 2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
749 if ref_stats[0] < min_ref_mapqual:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
750 record.filter.add('RefMapQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
751 if ref_stats[4] < min_ref_readpos:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
752 record.filter.add('RefReadPos')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
753 # ref_stats[5] (avg_num_mismatches_as_fraction
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
754 # is not a filter criterion in VarScan fpfilter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
755 if ref_stats[6] > max_ref_mmqs:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
756 record.filter.add('RefMMQS')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
757 if ref_stats[7] < min_ref_len:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
758 # VarScan fpfilter does not apply this filter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
759 # for indels, but there is no reason
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
760 # not to do it.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
761 record.filter.add('RefAvgRL')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
762 if ref_stats[8] < min_ref_dist3:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
763 record.filter.add('RefDist3')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
764 if alt_stats:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
765 alt_count = alt_stats[2] + alt_stats[3]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
766 if (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
767 alt_count < min_var_count2_lc
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
768 ) or (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
769 read_depth >= max_somatic_p_depth and
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
770 alt_count < min_var_count2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
771 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
772 record.filter.add('VarCount')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
773 if alt_count / read_depth < min_var_freq2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
774 record.filter.add('VarFreq')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
775 if alt_stats[1] < min_var_basequal:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
776 record.filter.add('VarBaseQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
777 if alt_count > min_strand_reads:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
778 if (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
779 alt_stats[2] / alt_count < min_strandedness
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
780 ) or (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
781 alt_stats[3] / alt_count < min_strandedness
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
782 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
783 record.filter.add('Strand')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
784 if alt_stats[2] + alt_stats[3] >= 2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
785 if alt_stats[0] < min_var_mapqual:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
786 record.filter.add('VarMapQual')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
787 if alt_stats[4] < min_var_readpos:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
788 record.filter.add('VarReadPos')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
789 # alt_stats[5] (avg_num_mismatches_as_fraction
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
790 # is not a filter criterion in VarScan fpfilter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
791 if alt_stats[6] > max_var_mmqs:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
792 record.filter.add('VarMMQS')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
793 if alt_stats[7] < min_var_len:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
794 # VarScan fpfilter does not apply this filter
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
795 # for indels, but there is no reason
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
796 # not to do it.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
797 record.filter.add('VarAvgRL')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
798 if alt_stats[8] < min_var_dist3:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
799 record.filter.add('VarDist3')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
800 if ref_count >= 2 and alt_count >= 2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
801 if (ref_stats[0] - alt_stats[0]) > max_mapqual_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
802 record.filter.add('MapQualDiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
803 if (ref_stats[1] - alt_stats[1]) > max_basequal_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
804 record.filter.add('MaxBAQdiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
805 mmqs_diff = alt_stats[6] - ref_stats[6]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
806 if mmqs_diff < min_mmqs_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
807 record.filter.add('MinMMQSdiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
808 if mmqs_diff > max_mmqs_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
809 record.filter.add('MMQSdiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
810 if (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
811 1 - alt_stats[7] / ref_stats[7]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
812 ) > max_relative_len_diff:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
813 record.filter.add('ReadLenDiff')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
814 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
815 # No variant-supporting reads for this record!
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
816 # This can happen in rare cases because of
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
817 # samtools mpileup issues, but indicates a
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
818 # rather unreliable variant call.
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
819 record.filter.add('VarCount')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
820 record.filter.add('VarFreq')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
821 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
822
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
823 def _indel_flagged_records(self, vcf):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
824 for record in vcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
825 record.info['INDEL'] = True
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
826 yield record
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
827
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
828 def _merge_generator(self, vcf1, vcf2):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
829 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
830 record1 = next(vcf1)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
831 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
832 for record2 in vcf2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
833 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
834 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
835 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
836 record2 = next(vcf2)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
837 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
838 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
839 for record1 in vcf1:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
840 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
841 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
842 while True:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
843 if (record1.start, record1.stop) < (record2.start, record2.stop):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
844 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
845 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
846 record1 = next(vcf1)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
847 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
848 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
849 for record2 in vcf2:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
850 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
851 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
852 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
853 yield record2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
854 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
855 record2 = next(vcf2)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
856 except StopIteration:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
857 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
858 for record1 in vcf1:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
859 yield record1
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
860 return
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
861
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
862 def merge_and_postprocess(self, snps_out, indels_out=None,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
863 no_filters=False, **filter_args):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
864 temporary_data = self.tmpfiles
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
865 self.tmpfiles = []
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
866 temporary_snp_files = [f + '.snp.vcf' for f in temporary_data]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
867 temporary_indel_files = [f + '.indel.vcf' for f in temporary_data]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
868
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
869 for f in temporary_data:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
870 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
871 os.remove(f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
872 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
873 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
874
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
875 def filter_minimal(data, **kwargs):
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
876 for record in data:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
877 if record.alleles[0] != 'N' or len(record.alleles[1]) > 1:
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
878 # Yield everything except SNPs called against an unknown
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
879 # reference base
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
880 yield record
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
881
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
882 if no_filters:
8
b79bb8b09822 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit bd1034af3217cd9fc654d7187bf674a89465755b
iuc
parents: 7
diff changeset
883 apply_filters = filter_minimal
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
884 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
885 apply_filters = self._postprocess_variant_records
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
886
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
887 output_header = self._compile_common_header(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
888 temporary_snp_files[0],
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
889 no_filters
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
890 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
891 if indels_out is None:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
892 with open(snps_out, 'w') as o:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
893 o.write(str(output_header).format(**filter_args))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
894 for snp_f, indel_f in zip(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
895 temporary_snp_files, temporary_indel_files
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
896 ):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
897 with pysam.VariantFile(snp_f, 'r') as snp_invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
898 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
899 # to avoid Warnings from htslib about missing contig
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
900 # info
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
901 self._add_ref_contigs_to_header(snp_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
902 self._add_filters_to_header(snp_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
903 self._add_indel_info_flag_to_header(snp_invcf.header)
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
904 self._standardize_format_fields(snp_invcf.header)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
905 with pysam.VariantFile(indel_f, 'r') as indel_invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
906 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
907 # to avoid Warnings from htslib about missing
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
908 # contig info
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
909 self._add_ref_contigs_to_header(indel_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
910 self._add_filters_to_header(indel_invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
911 self._add_indel_info_flag_to_header(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
912 indel_invcf.header
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
913 )
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
914 self._standardize_format_fields(indel_invcf.header)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
915 for record in apply_filters(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
916 self._merge_generator(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
917 snp_invcf,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
918 self._indel_flagged_records(indel_invcf)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
919 ),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
920 **filter_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
921 ):
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
922 self._fix_record_gt_fields(record)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
923 o.write(str(record))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
924 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
925 os.remove(snp_f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
926 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
927 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
928 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
929 os.remove(indel_f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
930 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
931 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
932
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
933 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
934 with open(snps_out, 'w') as o:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
935 o.write(str(output_header).format(**filter_args))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
936 for f in temporary_snp_files:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
937 with pysam.VariantFile(f, 'r') as invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
938 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
939 # to avoid Warnings from htslib about missing
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
940 # contig info and errors because of undeclared
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
941 # filters
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
942 self._add_ref_contigs_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
943 self._add_filters_to_header(invcf.header)
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
944 self._standardize_format_fields(invcf.header)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
945 for record in apply_filters(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
946 invcf, **filter_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
947 ):
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
948 self._fix_record_gt_fields(record)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
949 o.write(str(record))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
950 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
951 os.remove(f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
952 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
953 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
954 with open(indels_out, 'w') as o:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
955 o.write(str(output_header))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
956 for f in temporary_indel_files:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
957 with pysam.VariantFile(f, 'r') as invcf:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
958 # fix the input header on the fly
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
959 # to avoid Warnings from htslib about missing
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
960 # contig info and errors because of undeclared
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
961 # filters
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
962 self._add_ref_contigs_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
963 self._add_filters_to_header(invcf.header)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
964 self._add_indel_info_flag_to_header(invcf.header)
6
2c66c4025db2 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
965 self._standardize_format_fields(invcf.header)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
966 for record in apply_filters(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
967 self._indel_flagged_records(invcf), **filter_args
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
968 ):
7
2657ab48e16a planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
969 self._fix_record_gt_fields(record)
2
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
970 o.write(str(record))
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
971 try:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
972 os.remove(f)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
973 except Exception:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
974 pass
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
975
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
976
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
977 def varscan_call(ref_genome, normal, tumor, output_path, **args):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
978 """Preparse arguments and orchestrate calling and postprocessing."""
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
979
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
980 if args.pop('split_output'):
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
981 if '%T' in output_path:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
982 out = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
983 output_path.replace('%T', 'snp'),
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
984 output_path.replace('%T', 'indel')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
985 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
986 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
987 out = (
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
988 output_path + '.snp',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
989 output_path + '.indel'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
990 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
991 else:
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
992 out = (output_path, None)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
993
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
994 instance_args = {
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
995 k: args.pop(k) for k in [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
996 'max_depth',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
997 'min_mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
998 'min_basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
999 'threads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1000 'verbose',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1001 'quiet'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1002 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1003 }
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1004 varscan_somatic_args = {
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1005 k: args.pop(k) for k in [
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1006 'normal_purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1007 'tumor_purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1008 'min_coverage',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1009 'min_var_count',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1010 'min_var_freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1011 'min_hom_freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1012 'somatic_p_value',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1013 'p_value'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1014 ]
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1015 }
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1016
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1017 v = VarScanCaller(ref_genome, [normal, tumor], **instance_args)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1018 v.varcall_parallel(**varscan_somatic_args)
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iuc
parents:
diff changeset
1019 v.merge_and_postprocess(*out, **args)
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1020
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1021
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1022 if __name__ == '__main__':
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1023 p = argparse.ArgumentParser()
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1024 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1025 'ref_genome',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1026 metavar='reference_genome',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1027 help='the reference genome (in fasta format)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1028 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1029 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1030 '--normal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1031 metavar='BAM_file', required=True,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1032 help='the BAM input file of aligned reads from the normal sample'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1033 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1034 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1035 '--tumor',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1036 metavar='BAM_file', required=True,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1037 help='the BAM input file of aligned reads from the tumor sample'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1038 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1039 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1040 '-o', '--ofile', required=True,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1041 metavar='OFILE', dest='output_path',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1042 help='Name of the variant output file. With --split-output, the name '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1043 'may use the %%T replacement token or will be used as the '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1044 'basename for the two output files to be generated (see '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1045 '-s|--split-output below).'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1046 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1047 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1048 '-s', '--split-output',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1049 dest='split_output', action='store_true', default=False,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1050 help='indicate that separate output files for SNPs and indels '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1051 'should be generated (original VarScan behavior). If specified, '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1052 '%%T in the --ofile file name will be replaced with "snp" and '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1053 '"indel" to generate the names of the SNP and indel output '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1054 'files, respectively. If %%T is not found in the file name, it '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1055 'will get interpreted as a basename to which ".snp"/".indel" '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1056 'will be appended.'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1057 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1058 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1059 '-t', '--threads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1060 type=int, default=1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1061 help='level of parallelism'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1062 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1063 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1064 '-v', '--verbose',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1065 action='store_true',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1066 help='be verbose about progress'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1067 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1068 p.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1069 '-q', '--quiet',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1070 action='store_true',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1071 help='suppress output from wrapped tools'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1072 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1073 call_group = p.add_argument_group('Variant calling parameters')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1074 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1075 '--normal-purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1076 dest='normal_purity', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1077 default=1.0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1078 help='Estimated purity of the normal sample (default: 1.0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1079 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1080 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1081 '--tumor-purity',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1082 dest='tumor_purity', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1083 default=1.0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1084 help='Estimated purity of the tumor sample (default: 1.0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1085 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1086 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1087 '--max-pileup-depth',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1088 dest='max_depth', type=int, default=8000,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1089 help='Maximum depth of generated pileups (samtools mpileup -d option; '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1090 'default: 8000)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1091 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1092 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1093 '--min-basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1094 dest='min_basequal', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1095 default=13,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1096 help='Minimum base quality at the variant position to use a read '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1097 '(default: 13)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1098 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1099 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1100 '--min-mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1101 dest='min_mapqual', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1102 default=0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1103 help='Minimum mapping quality required to use a read '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1104 '(default: 0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1105 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1106 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1107 '--min-coverage',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1108 dest='min_coverage', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1109 default=8,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1110 help='Minimum site coverage required in the normal and in the tumor '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1111 'sample to call a variant (default: 8)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1112 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1113 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1114 '--min-var-count',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1115 dest='min_var_count', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1116 default=2,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1117 help='Minimum number of variant-supporting reads required to call a '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1118 'variant (default: 2)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1119 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1120 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1121 '--min-var-freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1122 dest='min_var_freq', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1123 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1124 help='Minimum variant allele frequency for calling (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1125 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1126 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1127 '--min-hom-freq',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1128 dest='min_hom_freq', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1129 default=0.75,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1130 help='Minimum variant allele frequency for homozygous call '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1131 '(default: 0.75)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1132 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1133 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1134 '--p-value',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1135 dest='p_value', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1136 default=0.99,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1137 help='P-value threshold for heterozygous call (default: 0.99)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1138 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1139 call_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1140 '--somatic-p-value',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1141 dest='somatic_p_value', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1142 default=0.05,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1143 help='P-value threshold for somatic call (default: 0.05)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1144 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1145 filter_group = p.add_argument_group('Posterior variant filter parameters')
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1146 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1147 '--no-filters',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1148 dest='no_filters', action='store_true',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1149 help='Disable all posterior variant filters. '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1150 'If specified, all following options will be ignored'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1151 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1152 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1153 '--min-var-count2',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1154 dest='min_var_count2', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1155 default=4,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1156 help='Minimum number of variant-supporting reads (default: 4)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1157 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1158 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1159 '--min-var-count2-lc',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1160 dest='min_var_count2_lc', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1161 default=2,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1162 help='Minimum number of variant-supporting reads when depth below '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1163 '--somatic-p-depth (default: 2)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1164 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1165 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1166 '--min-var-freq2',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1167 dest='min_var_freq2', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1168 default=0.05,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1169 help='Minimum variant allele frequency (default: 0.05)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1170 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1171 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1172 '--max-somatic-p',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1173 dest='max_somatic_p', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1174 default=0.05,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1175 help='Maximum somatic p-value (default: 0.05)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1176 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1177 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1178 '--max-somatic-p-depth',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1179 dest='max_somatic_p_depth', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1180 default=10,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1181 help='Depth required to run --max-somatic-p filter (default: 10)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1182 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1183 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1184 '--min-ref-readpos',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1185 dest='min_ref_readpos', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1186 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1187 help='Minimum average relative distance of site from the ends of '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1188 'ref-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1189 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1190 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1191 '--min-var-readpos',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1192 dest='min_var_readpos', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1193 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1194 help='Minimum average relative distance of site from the ends of '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1195 'variant-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1196 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1197 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1198 '--min-ref-dist3',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1199 dest='min_ref_dist3', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1200 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1201 help='Minimum average relative distance of site from the effective '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1202 '3\'end of ref-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1203 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1204 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1205 '--min-var-dist3',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1206 dest='min_var_dist3', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1207 default=0.1,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1208 help='Minimum average relative distance of site from the effective '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1209 '3\'end of variant-supporting reads (default: 0.1)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1210 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1211 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1212 '--min-ref-len',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1213 dest='min_ref_len', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1214 default=90,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1215 help='Minimum average trimmed length of reads supporting the ref '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1216 'allele (default: 90)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1217 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1218 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1219 '--min-var-len',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1220 dest='min_var_len', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1221 default=90,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1222 help='Minimum average trimmed length of reads supporting the variant '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1223 'allele (default: 90)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1224 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1225 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1226 '--max-len-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1227 dest='max_relative_len_diff', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1228 default=0.25,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1229 help='Maximum average relative read length difference (ref - var; '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1230 'default: 0.25)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1231 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1232 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1233 '--min-strandedness',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1234 dest='min_strandedness', type=float,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1235 default=0.01,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1236 help='Minimum fraction of variant reads from each strand '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1237 '(default: 0.01)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1238 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1239 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1240 '--min-strand-reads',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1241 dest='min_strand_reads', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1242 default=5,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1243 help='Minimum allele depth required to run --min-strandedness filter '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1244 '(default: 5)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1245 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1246 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1247 '--min-ref-basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1248 dest='min_ref_basequal', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1249 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1250 help='Minimum average base quality for the ref allele (default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1251 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1252 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1253 '--min-var-basequal',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1254 dest='min_var_basequal', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1255 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1256 help='Minimum average base quality for the variant allele '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1257 '(default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1258 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1259 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1260 '--max-basequal-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1261 dest='max_basequal_diff', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1262 default=50,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1263 help='Maximum average base quality diff (ref - var; default: 50)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1264 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1265 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1266 '--min-ref-mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1267 dest='min_ref_mapqual', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1268 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1269 help='Minimum average mapping quality of reads supporting the ref '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1270 'allele (default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1271 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1272 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1273 '--min-var-mapqual',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1274 dest='min_var_mapqual', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1275 default=15,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1276 help='Minimum average mapping quality of reads supporting the variant '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1277 'allele (default: 15)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1278 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1279 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1280 '--max-mapqual-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1281 dest='max_mapqual_diff', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1282 default=50,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1283 help='Maximum average mapping quality difference (ref - var; '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1284 'default: 50)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1285 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1286 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1287 '--max-ref-mmqs',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1288 dest='max_ref_mmqs', type=int,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1289 default=100,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1290 help='Maximum mismatch quality sum of reads supporting the ref '
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1291 'allele (default: 100)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1292 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1293 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1294 '--max-var-mmqs',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1295 dest='max_var_mmqs', type=int,
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1296 default=100,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1297 help='Maximum mismatch quality sum of reads supporting the variant '
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1298 'allele (default: 100)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1299 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1300 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1301 '--min-mmqs-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1302 dest='min_mmqs_diff', type=int,
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1303 default=0,
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1304 help='Minimum mismatch quality sum difference (var - ref; default: 0)'
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1305 )
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1306 filter_group.add_argument(
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1307 '--max-mmqs-diff',
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1308 dest='max_mmqs_diff', type=int,
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1309 default=50,
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1310 help='Maximum mismatch quality sum difference (var - ref; default: 50)'
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1311 )
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1312 args = vars(p.parse_args())
2fe9ebb98aad planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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1313 varscan_call(**args)