Mercurial > repos > iuc > varscan_mpileup

annotate varscan.py @ 3:ee62c46d9cbe draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 79f2f0e89e74348cf18602e83762a0cb26131f17
author iuc
date Tue, 04 Dec 2018 05:51:02 -0500
parents d062703d6f13
children ab2f908f0b08
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d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
1 #!/usr/bin/env python3
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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2 from __future__ import print_function
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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3
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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4 import argparse
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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5 import io
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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6 import os
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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7 import subprocess
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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8 import sys
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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9 import tempfile
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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10 import time
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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11 from contextlib import ExitStack
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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12 from functools import partial
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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13 from threading import Thread
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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14
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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15 import pysam
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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17
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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18 class VariantCallingError (RuntimeError):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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19 """Exception class for issues with samtools and varscan subprocesses."""
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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21 def __init__(self, message=None, call='', error=''):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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22 self.message = message
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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23 self.call = call.strip()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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 ''
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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29 if self.error:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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30 msg_header = '"{0}" failed with:\n{1}\n\n'.format(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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31 self.call, self.error
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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32 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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33 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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34 msg_header = '{0} failed.\n'
d062703d6f13 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(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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36 self.call
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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37 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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38 return msg_header + self.message
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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39
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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40
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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41 class VarScanCaller (object):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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42 def __init__(self, ref_genome, bam_input_files,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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43 max_depth=None,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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44 min_mapqual=None, min_basequal=None,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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45 threads=1, verbose=False, quiet=True
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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46 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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47 self.ref_genome = ref_genome
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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48 self.bam_input_files = bam_input_files
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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49 self.max_depth = max_depth
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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50 self.min_mapqual = min_mapqual
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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51 self.min_basequal = min_basequal
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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52 self.threads = threads
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
95 varcall_engine_option_mapping = [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
96 ('--normal-purity', normal_purity),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
97 ('--tumor-purity', tumor_purity),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
98 ('--min-coverage', min_coverage),
d062703d6f13 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),
d062703d6f13 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),
d062703d6f13 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),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
102 ('--p-value', p_value),
d062703d6f13 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),
d062703d6f13 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)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
105 ]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
106 varcall_engine_options = []
d062703d6f13 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:
d062703d6f13 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:
d062703d6f13 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)]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
110 pileup_engine_options = ['-B']
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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111 if self.max_depth is not None:
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iuc
parents:
diff changeset
112 pileup_engine_options += ['-d', str(self.max_depth)]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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113 if self.min_mapqual is not None:
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iuc
parents:
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114 pileup_engine_options += ['-q', str(self.min_mapqual)]
d062703d6f13 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:
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116 pileup_engine_options += ['-Q', str(self.min_basequal)]
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iuc
parents:
diff changeset
117
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iuc
parents:
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118 # Create a tuple of calls to samtools mpileup and varscan for
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
123 calls = [(
d062703d6f13 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 + [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
125 '-r', contig + ':',
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iuc
parents:
diff changeset
126 '-f', self.ref_genome
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iuc
parents:
diff changeset
127 ] + self.bam_input_files,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
128 self.varcall_engine + [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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diff changeset
129 '-', '{out}', '--output-vcf', '1', '--mpileup', '1'
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iuc
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diff changeset
130 ] + varcall_engine_options,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
131 contig
d062703d6f13 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
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diff changeset
133
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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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
138 subprocesses = []
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
139 error_table = {}
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
140 tmp_io_started = []
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
141 tmp_io_finished = []
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
142 self.tmpfiles = []
d062703d6f13 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):
d062703d6f13 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''):
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iuc
parents:
diff changeset
146 # Eventually we are going to print the contents of
d062703d6f13 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
d062703d6f13 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.
d062703d6f13 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.
d062703d6f13 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,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
151 'backslashreplace'))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
152 out.close()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
153
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
154 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
155 while subprocesses or calls:
d062703d6f13 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:
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
160
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
162 call = calls.pop()
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
164 # to work on
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
165 contig = call[2]
d062703d6f13 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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
168 # a named temporary file, to which the call output
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
173 call_out = self.TemporaryContigVCF(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
174 prefix=''.join(
d062703d6f13 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 ) + '_',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
177 )
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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)
d062703d6f13 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:
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
183 stdout_p2 = call_out
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
184 stderr_p2 = subprocess.PIPE
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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parents:
diff changeset
185 else:
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
187 stdout_p2 = subprocess.PIPE
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
188 stderr_p2 = subprocess.STDOUT
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
190 call_out.close()
d062703d6f13 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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
193 # strings
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
194 c_str = (' '.join(call[0]), ' '.join(call[1]))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
195 error_table[c_str] = [io.StringIO(), io.StringIO()]
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
197 p1 = subprocess.Popen(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
198 call[0],
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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200 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
201 p2 = subprocess.Popen(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
202 call[1],
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
203 stdin=p1.stdout,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
204 stdout=stdout_p2,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
205 stderr=stderr_p2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
206 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
207 # subprocess bookkeeping
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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208 subprocesses.append((c_str, p1, p2, call_out, contig))
d062703d6f13 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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
211 p1.stdout.close()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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212 t1 = Thread(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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213 target=enqueue_stderr_output,
d062703d6f13 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])
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
215 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
216 t2 = Thread(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
217 target=enqueue_stderr_output,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
218 args=(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
219 p2.stderr
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
221 p2.stdout,
d062703d6f13 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]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
223 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
224 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
225 t1.daemon = t2.daemon = True
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
226 t1.start()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
227 t2.start()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
228
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
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229 if verbose:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
230 print(
d062703d6f13 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}'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
232 .format(call[2])
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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parents:
diff changeset
233 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
234
d062703d6f13 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
d062703d6f13 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:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
237 p1_stat = p1.poll()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
238 p2_stat = p2.poll()
d062703d6f13 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:
d062703d6f13 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!
d062703d6f13 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
d062703d6f13 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:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
243 print()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
244 print(
d062703d6f13 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(),
d062703d6f13 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(),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
247 file=sys.stderr
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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diff changeset
248 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
249 raise VariantCallingError(
d062703d6f13 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.'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
251 .format(contig),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
252 call='{0} | {1}'.format(call[0], call[1])
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
253 )
d062703d6f13 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:
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
259 ).splitlines()[-4:]
d062703d6f13 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(
d062703d6f13 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')
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
263 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
264 break
d062703d6f13 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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
267 # get, stop it.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
268 p2.terminate()
d062703d6f13 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))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
270 ofo.close()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
271 break
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
272 if p2_stat == 0:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
273 # Things went fine.
d062703d6f13 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
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
276 # they finished)
d062703d6f13 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)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
278 if verbose:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
279 print()
d062703d6f13 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))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
281 if not quiet:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
282 print()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
283 print(
d062703d6f13 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/'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
285 'bcftools:'.upper(),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
286 file=sys.stderr
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
287 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
288 print(
d062703d6f13 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(),
d062703d6f13 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(),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
291 file=sys.stderr
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
292 )
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
296 del error_table[call]
d062703d6f13 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))
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
301 ofo.close()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
302 break
d062703d6f13 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
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
304 time.sleep(2)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
305 finally:
d062703d6f13 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:
d062703d6f13 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
d062703d6f13 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):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
309 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
310 proc.terminate()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
311 except Exception:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
312 pass
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
313 # close currently open files
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
314 ofo.close()
d062703d6f13 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
d062703d6f13 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
d062703d6f13 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]
d062703d6f13 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
d062703d6f13 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.
d062703d6f13 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,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
321 # but simply rewrite everything.
d062703d6f13 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:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
323 print()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
324 print(
d062703d6f13 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(),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
326 file=sys.stderr
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
327 )
d062703d6f13 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():
d062703d6f13 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)
d062703d6f13 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)
d062703d6f13 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)
d062703d6f13 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)
d062703d6f13 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)
d062703d6f13 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)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
335
d062703d6f13 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):
d062703d6f13 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):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
338 header.add_meta(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
339 'contig',
d062703d6f13 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)]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
341 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
342
d062703d6f13 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):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
344 varscan_fpfilters = {
d062703d6f13 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',
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
347 'VarAvgRL':
d062703d6f13 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 < '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
349 '{min_var_len}',
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
351 'VarDist3':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
353 'VarMMQS':
d062703d6f13 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 > '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
355 '{max_var_mmqs}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
356 'VarMapQual':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
358 'VarBaseQual':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
360 'Strand':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
362 'RefAvgRL':
d062703d6f13 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 < '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
364 '{min_ref_len}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
365 'RefReadPos':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
367 'RefDist3':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
369 'RefMapQual':
d062703d6f13 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 < '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
371 '{min_ref_mapqual}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
372 'RefBaseQual':
d062703d6f13 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 < '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
374 '{min_ref_basequal}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
375 'RefMMQS':
d062703d6f13 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 > '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
377 '{max_ref_mmqs}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
378 'MMQSdiff':
d062703d6f13 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) > '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
380 '{max_mmqs_diff}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
381 'MinMMQSdiff':
d062703d6f13 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) < '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
383 '{max_mmqs_diff}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
384 'MapQualDiff':
d062703d6f13 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}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
386 'MaxBAQdiff':
d062703d6f13 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) > '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
388 '{max_basequal_diff}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
389 'ReadLenDiff':
d062703d6f13 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) > '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
391 '{max_relative_len_diff}',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
392 }
d062703d6f13 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():
d062703d6f13 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)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
395
d062703d6f13 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):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
397 header.info.add(
d062703d6f13 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'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
399 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
400
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
401 def _compile_common_header(self, varcall_template, no_filters=False):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
402 # fix the header generated by VarScan
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
403 # by adding reference and contig information
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
404 common_header = pysam.VariantHeader()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
405 common_header.add_meta('reference', value=self.ref_genome)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
406 self._add_ref_contigs_to_header(common_header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
407 if not no_filters:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
408 # add filter info
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
409 self._add_filters_to_header(common_header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
410 # change the source information
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
411 common_header.add_meta('source', value='varscan.py')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
412 # declare an INDEL flag for record INFO fields
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
413 self._add_indel_info_flag_to_header(common_header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
414 # take the remaining metadata from the template header produced by
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
415 # VarScan
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
416 with pysam.VariantFile(varcall_template, 'r') as original_data:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
417 varscan_header = original_data.header
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
418 for sample in varscan_header.samples:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
419 common_header.samples.add(sample)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
420 common_header.merge(varscan_header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
421 return common_header
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
422
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
423 def pileup_masker(self, mask):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
424 def apply_mask_on_pileup(piled_items):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
425 for item, status in zip(piled_items, mask):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
426 if status:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
427 yield item
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
428 return apply_mask_on_pileup
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
429
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
430 def get_allele_specific_pileup_column_stats(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
431 self, allele, pile_column, ref_fetch
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
432 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
433 # number of reads supporting the given allele on
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
434 # forward and reverse strand, and in total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
435 var_reads_plus = var_reads_minus = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
436 var_supp_read_mask = []
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
437 for base in pile_column.get_query_sequences():
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
438 if base == allele:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
439 # allele supporting read on + strand
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
440 var_reads_plus += 1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
441 var_supp_read_mask.append(True)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
442 elif base.upper() == allele:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
443 # allele supporting read on - strand
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
444 var_reads_minus += 1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
445 var_supp_read_mask.append(True)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
446 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
447 var_supp_read_mask.append(False)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
448 var_reads_total = var_reads_plus + var_reads_minus
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
449
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
450 if var_reads_total == 0:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
451 # No stats without reads!
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
452 return None
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
453
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
454 var_supp_only = self.pileup_masker(var_supp_read_mask)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
455
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
456 # average mapping quality of the reads supporting the
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
457 # given allele
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
458 avg_mapping_quality = sum(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
459 mq for mq in var_supp_only(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
460 pile_column.get_mapping_qualities()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
461 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
462 ) / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
463
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
464 # for the remaining stats we need access to complete
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
465 # read information
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
466 piled_reads = [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
467 p for p in var_supp_only(pile_column.pileups)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
468 ]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
469 assert len(piled_reads) == var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
470 sum_avg_base_qualities = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
471 sum_dist_from_center = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
472 sum_dist_from_3prime = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
473 sum_clipped_length = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
474 sum_unclipped_length = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
475 sum_num_mismatches_as_fraction = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
476 sum_mismatch_qualities = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
477
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
478 for p in piled_reads:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
479 sum_avg_base_qualities += sum(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
480 p.alignment.query_qualities
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
481 ) / p.alignment.infer_query_length()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
482 sum_clipped_length += p.alignment.query_alignment_length
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
483 unclipped_length = p.alignment.infer_read_length()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
484 sum_unclipped_length += unclipped_length
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
485 read_center = p.alignment.query_alignment_length / 2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
486 sum_dist_from_center += 1 - abs(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
487 p.query_position - read_center
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
488 ) / read_center
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
489 if p.alignment.is_reverse:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
490 sum_dist_from_3prime += p.query_position / unclipped_length
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
491 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
492 sum_dist_from_3prime += 1 - p.query_position / unclipped_length
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
493
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
494 sum_num_mismatches = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
495 for qpos, rpos in p.alignment.get_aligned_pairs():
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
496 if qpos is not None and rpos is not None:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
497 if p.alignment.query_sequence[qpos] != ref_fetch(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
498 rpos, rpos + 1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
499 ).upper(): # ref bases can be lowercase!
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
500 sum_num_mismatches += 1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
501 sum_mismatch_qualities += p.alignment.query_qualities[
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
502 qpos
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
503 ]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
504 sum_num_mismatches_as_fraction += (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
505 sum_num_mismatches / p.alignment.query_alignment_length
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
506 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
507 avg_basequality = sum_avg_base_qualities / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
508 avg_pos_as_fraction = sum_dist_from_center / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
509 avg_num_mismatches_as_fraction = (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
510 sum_num_mismatches_as_fraction / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
511 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
512 avg_sum_mismatch_qualities = sum_mismatch_qualities / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
513 avg_clipped_length = sum_clipped_length / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
514 avg_distance_to_effective_3p_end = (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
515 sum_dist_from_3prime / var_reads_total
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
516 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
517
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
518 return (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
519 avg_mapping_quality,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
520 avg_basequality,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
521 var_reads_plus,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
522 var_reads_minus,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
523 avg_pos_as_fraction,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
524 avg_num_mismatches_as_fraction,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
525 avg_sum_mismatch_qualities,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
526 avg_clipped_length,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
527 avg_distance_to_effective_3p_end
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
528 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
529
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
530 def _postprocess_variant_records(self, invcf,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
531 min_var_count2, min_var_count2_lc,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
532 min_var_freq2, max_somatic_p,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
533 max_somatic_p_depth,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
534 min_ref_readpos, min_var_readpos,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
535 min_ref_dist3, min_var_dist3,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
536 min_ref_len, min_var_len,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
537 max_relative_len_diff,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
538 min_strandedness, min_strand_reads,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
539 min_ref_basequal, min_var_basequal,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
540 max_basequal_diff,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
541 min_ref_mapqual, min_var_mapqual,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
542 max_mapqual_diff,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
543 max_ref_mmqs, max_var_mmqs,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
544 min_mmqs_diff, max_mmqs_diff,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
545 **args):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
546 # set FILTER field according to Varscan criteria
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
547 # multiple FILTER entries must be separated by semicolons
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
548 # No filters applied should be indicated with MISSING
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
549
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
550 # since posterior filters are always applied to just one sample,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
551 # a better place to store the info is in the FT genotype field:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
552 # can be PASS, '.' to indicate that filters have not been applied,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
553 # or a semicolon-separated list of filters that failed
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
554 # unfortunately, gemini does not support this field
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
555
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
556 with ExitStack() as io_stack:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
557 normal_reads, tumor_reads = (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
558 io_stack.enter_context(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
559 pysam.Samfile(fn, 'rb')) for fn in self.bam_input_files
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
560 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
561 refseq = io_stack.enter_context(pysam.FastaFile(self.ref_genome))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
562 pileup_args = self._get_pysam_pileup_args()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
563 for record in invcf:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
564 if any(len(allele) > 1 for allele in record.alleles):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
565 # skip indel postprocessing for the moment
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
566 yield record
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
567 continue
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
568 # get pileup for genomic region affected by this variant
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
569 if record.info['SS'] == '2':
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
570 # a somatic variant => generate pileup from tumor data
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
571 pile = tumor_reads.pileup(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
572 record.chrom, record.start, record.stop,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
573 **pileup_args
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
574 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
575 sample_of_interest = 'TUMOR'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
576 elif record.info['SS'] in ['1', '3']:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
577 # a germline or LOH variant => pileup from normal data
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
578 pile = normal_reads.pileup(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
579 record.chrom, record.start, record.stop,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
580 **pileup_args
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
581 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
582 sample_of_interest = 'NORMAL'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
583 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
584 # TO DO: figure out if there is anything interesting to do
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
585 # for SS status codes 0 (reference) and 5 (unknown)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
586 yield record
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
587 continue
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
588
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
589 # apply false-positive filtering a la varscan fpfilter
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
590 # find the variant site in the pileup columns
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
591 for pile_column in pile:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
592 if pile_column.reference_pos == record.start:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
593 break
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
594 # extract required information
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
595 # overall read depth at the site
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
596 read_depth = pile_column.get_num_aligned()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
597 assert read_depth > 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
598 # no multiallelic sites in varscan
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
599 assert len(record.alleles) == 2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
600 if record.samples[sample_of_interest]['RD'] > 0:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
601 ref_stats, alt_stats = [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
602 self.get_allele_specific_pileup_column_stats(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
603 allele,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
604 pile_column,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
605 partial(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
606 pysam.FastaFile.fetch, refseq, record.chrom
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
607 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
608 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
609 for allele in record.alleles
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
610 ]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
611 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
612 ref_stats = None
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
613 alt_stats = self.get_allele_specific_pileup_column_stats(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
614 record.alleles[1],
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
615 pile_column,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
616 partial(pysam.FastaFile.fetch, refseq, record.chrom)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
617 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
618 ref_count = 0
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
619 if ref_stats:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
620 ref_count = ref_stats[2] + ref_stats[3]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
621 if ref_stats[1] < min_ref_basequal:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
622 record.filter.add('RefBaseQual')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
623 if ref_count >= 2:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
624 if ref_stats[0] < min_ref_mapqual:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
625 record.filter.add('RefMapQual')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
626 if ref_stats[4] < min_ref_readpos:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
627 record.filter.add('RefReadPos')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
628 # ref_stats[5] (avg_num_mismatches_as_fraction
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
629 # is not a filter criterion in VarScan fpfilter
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
630 if ref_stats[6] > max_ref_mmqs:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
631 record.filter.add('RefMMQS')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
632 if ref_stats[7] < min_ref_len:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
633 # VarScan fpfilter does not apply this filter
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
634 # for indels, but there is no reason
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
635 # not to do it.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
636 record.filter.add('RefAvgRL')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
637 if ref_stats[8] < min_ref_dist3:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
638 record.filter.add('RefDist3')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
639 if alt_stats:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
640 alt_count = alt_stats[2] + alt_stats[3]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
641 if (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
642 alt_count < min_var_count2_lc
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
643 ) or (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
644 read_depth >= max_somatic_p_depth and
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
645 alt_count < min_var_count2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
646 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
647 record.filter.add('VarCount')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
648 if alt_count / read_depth < min_var_freq2:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
649 record.filter.add('VarFreq')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
650 if alt_stats[1] < min_var_basequal:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
651 record.filter.add('VarBaseQual')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
652 if alt_count > min_strand_reads:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
653 if (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
654 alt_stats[2] / alt_count < min_strandedness
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
655 ) or (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
656 alt_stats[3] / alt_count < min_strandedness
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
657 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
658 record.filter.add('Strand')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
659 if alt_stats[2] + alt_stats[3] >= 2:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
660 if alt_stats[0] < min_var_mapqual:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
661 record.filter.add('VarMapQual')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
662 if alt_stats[4] < min_var_readpos:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
663 record.filter.add('VarReadPos')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
664 # alt_stats[5] (avg_num_mismatches_as_fraction
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
665 # is not a filter criterion in VarScan fpfilter
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
666 if alt_stats[6] > max_var_mmqs:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
667 record.filter.add('VarMMQS')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
668 if alt_stats[7] < min_var_len:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
669 # VarScan fpfilter does not apply this filter
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
670 # for indels, but there is no reason
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
671 # not to do it.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
672 record.filter.add('VarAvgRL')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
673 if alt_stats[8] < min_var_dist3:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
674 record.filter.add('VarDist3')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
675 if ref_count >= 2 and alt_count >= 2:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
676 if (ref_stats[0] - alt_stats[0]) > max_mapqual_diff:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
677 record.filter.add('MapQualDiff')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
678 if (ref_stats[1] - alt_stats[1]) > max_basequal_diff:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
679 record.filter.add('MaxBAQdiff')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
680 mmqs_diff = alt_stats[6] - ref_stats[6]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
681 if mmqs_diff < min_mmqs_diff:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
682 record.filter.add('MinMMQSdiff')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
683 if mmqs_diff > max_mmqs_diff:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
684 record.filter.add('MMQSdiff')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
685 if (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
686 1 - alt_stats[7] / ref_stats[7]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
687 ) > max_relative_len_diff:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
688 record.filter.add('ReadLenDiff')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
689 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
690 # No variant-supporting reads for this record!
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
691 # This can happen in rare cases because of
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
692 # samtools mpileup issues, but indicates a
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
693 # rather unreliable variant call.
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
694 record.filter.add('VarCount')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
695 record.filter.add('VarFreq')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
696 yield record
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
697
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
698 def _indel_flagged_records(self, vcf):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
699 for record in vcf:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
700 record.info['INDEL'] = True
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
701 yield record
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
702
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
703 def _merge_generator(self, vcf1, vcf2):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
704 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
705 record1 = next(vcf1)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
706 except StopIteration:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
707 for record2 in vcf2:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
708 yield record2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
709 return
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
710 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
711 record2 = next(vcf2)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
712 except StopIteration:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
713 yield record1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
714 for record1 in vcf1:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
715 yield record1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
716 return
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
717 while True:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
718 if (record1.start, record1.stop) < (record2.start, record2.stop):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
719 yield record1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
720 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
721 record1 = next(vcf1)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
722 except StopIteration:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
723 yield record2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
724 for record2 in vcf2:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
725 yield record2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
726 return
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
727 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
728 yield record2
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
729 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
730 record2 = next(vcf2)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
731 except StopIteration:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
732 yield record1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
733 for record1 in vcf1:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
734 yield record1
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
735 return
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
736
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
737 def merge_and_postprocess(self, snps_out, indels_out=None,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
738 no_filters=False, **filter_args):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
739 temporary_data = self.tmpfiles
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
740 self.tmpfiles = []
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
741 temporary_snp_files = [f + '.snp.vcf' for f in temporary_data]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
742 temporary_indel_files = [f + '.indel.vcf' for f in temporary_data]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
743
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
744 for f in temporary_data:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
745 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
746 os.remove(f)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
747 except Exception:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
748 pass
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
749
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
750 def noop_gen(data, **kwargs):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
751 for d in data:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
752 yield d
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
753
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
754 if no_filters:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
755 apply_filters = noop_gen
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
756 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
757 apply_filters = self._postprocess_variant_records
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
758
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
759 output_header = self._compile_common_header(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
760 temporary_snp_files[0],
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
761 no_filters
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
762 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
763 if indels_out is None:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
764 with open(snps_out, 'w') as o:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
765 o.write(str(output_header).format(**filter_args))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
766 for snp_f, indel_f in zip(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
767 temporary_snp_files, temporary_indel_files
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
768 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
769 with pysam.VariantFile(snp_f, 'r') as snp_invcf:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
770 # fix the input header on the fly
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
771 # to avoid Warnings from htslib about missing contig
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
772 # info
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
773 self._add_ref_contigs_to_header(snp_invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
774 self._add_filters_to_header(snp_invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
775 self._add_indel_info_flag_to_header(snp_invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
776 with pysam.VariantFile(indel_f, 'r') as indel_invcf:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
777 # fix the input header on the fly
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
778 # to avoid Warnings from htslib about missing
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
779 # contig info
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
780 self._add_ref_contigs_to_header(indel_invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
781 self._add_filters_to_header(indel_invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
782 self._add_indel_info_flag_to_header(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
783 indel_invcf.header
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
784 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
785 for record in apply_filters(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
786 self._merge_generator(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
787 snp_invcf,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
788 self._indel_flagged_records(indel_invcf)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
789 ),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
790 **filter_args
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
791 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
792 o.write(str(record))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
793 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
794 os.remove(snp_f)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
795 except Exception:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
796 pass
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
797 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
798 os.remove(indel_f)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
799 except Exception:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
800 pass
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
801
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
802 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
803 with open(snps_out, 'w') as o:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
804 o.write(str(output_header).format(**filter_args))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
805 for f in temporary_snp_files:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
806 with pysam.VariantFile(f, 'r') as invcf:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
807 # fix the input header on the fly
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
808 # to avoid Warnings from htslib about missing
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
809 # contig info and errors because of undeclared
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
810 # filters
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
811 self._add_ref_contigs_to_header(invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
812 self._add_filters_to_header(invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
813 for record in apply_filters(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
814 invcf, **filter_args
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
815 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
816 o.write(str(record))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
817 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
818 os.remove(f)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
819 except Exception:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
820 pass
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
821 with open(indels_out, 'w') as o:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
822 o.write(str(output_header))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
823 for f in temporary_indel_files:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
824 with pysam.VariantFile(f, 'r') as invcf:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
825 # fix the input header on the fly
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
826 # to avoid Warnings from htslib about missing
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
827 # contig info and errors because of undeclared
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
828 # filters
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
829 self._add_ref_contigs_to_header(invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
830 self._add_filters_to_header(invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
831 self._add_indel_info_flag_to_header(invcf.header)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
832 for record in apply_filters(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
833 self._indel_flagged_records(invcf), **filter_args
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
834 ):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
835 o.write(str(record))
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
836 try:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
837 os.remove(f)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
838 except Exception:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
839 pass
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
840
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
841
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
842 def varscan_call(ref_genome, normal, tumor, output_path, **args):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
843 """Preparse arguments and orchestrate calling and postprocessing."""
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
844
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
845 if args.pop('split_output'):
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
846 if '%T' in output_path:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
847 out = (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
848 output_path.replace('%T', 'snp'),
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
849 output_path.replace('%T', 'indel')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
850 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
851 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
852 out = (
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
853 output_path + '.snp',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
854 output_path + '.indel'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
855 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
856 else:
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
857 out = (output_path, None)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
858
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
859 instance_args = {
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
860 k: args.pop(k) for k in [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
861 'max_depth',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
862 'min_mapqual',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
863 'min_basequal',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
864 'threads',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
865 'verbose',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
866 'quiet'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
867 ]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
868 }
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
869 varscan_somatic_args = {
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
870 k: args.pop(k) for k in [
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
871 'normal_purity',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
872 'tumor_purity',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
873 'min_coverage',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
874 'min_var_count',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
875 'min_var_freq',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
876 'min_hom_freq',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
877 'somatic_p_value',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
878 'p_value'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
879 ]
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
880 }
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
881
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
882 v = VarScanCaller(ref_genome, [normal, tumor], **instance_args)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
883 v.varcall_parallel(**varscan_somatic_args)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
884 v.merge_and_postprocess(*out, **args)
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
885
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
886
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
887 if __name__ == '__main__':
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
888 p = argparse.ArgumentParser()
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
889 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
890 'ref_genome',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
891 metavar='reference_genome',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
892 help='the reference genome (in fasta format)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
893 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
894 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
895 '--normal',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
896 metavar='BAM_file', required=True,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
897 help='the BAM input file of aligned reads from the normal sample'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
898 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
899 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
900 '--tumor',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
901 metavar='BAM_file', required=True,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
902 help='the BAM input file of aligned reads from the tumor sample'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
903 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
904 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
905 '-o', '--ofile', required=True,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
906 metavar='OFILE', dest='output_path',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
907 help='Name of the variant output file. With --split-output, the name '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
908 'may use the %%T replacement token or will be used as the '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
909 'basename for the two output files to be generated (see '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
910 '-s|--split-output below).'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
911 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
912 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
913 '-s', '--split-output',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
914 dest='split_output', action='store_true', default=False,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
915 help='indicate that separate output files for SNPs and indels '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
916 'should be generated (original VarScan behavior). If specified, '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
917 '%%T in the --ofile file name will be replaced with "snp" and '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
918 '"indel" to generate the names of the SNP and indel output '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
919 'files, respectively. If %%T is not found in the file name, it '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
920 'will get interpreted as a basename to which ".snp"/".indel" '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
921 'will be appended.'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
922 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
923 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
924 '-t', '--threads',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
925 type=int, default=1,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
926 help='level of parallelism'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
927 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
928 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
929 '-v', '--verbose',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
930 action='store_true',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
931 help='be verbose about progress'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
932 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
933 p.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
934 '-q', '--quiet',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
935 action='store_true',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
936 help='suppress output from wrapped tools'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
937 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
938 call_group = p.add_argument_group('Variant calling parameters')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
939 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
940 '--normal-purity',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
941 dest='normal_purity', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
942 default=1.0,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
943 help='Estimated purity of the normal sample (default: 1.0)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
944 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
945 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
946 '--tumor-purity',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
947 dest='tumor_purity', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
948 default=1.0,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
949 help='Estimated purity of the tumor sample (default: 1.0)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
950 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
951 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
952 '--max-pileup-depth',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
953 dest='max_depth', type=int, default=8000,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
954 help='Maximum depth of generated pileups (samtools mpileup -d option; '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
955 'default: 8000)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
956 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
957 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
958 '--min-basequal',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
959 dest='min_basequal', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
960 default=13,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
961 help='Minimum base quality at the variant position to use a read '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
962 '(default: 13)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
963 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
964 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
965 '--min-mapqual',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
966 dest='min_mapqual', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
967 default=0,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
968 help='Minimum mapping quality required to use a read '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
969 '(default: 0)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
970 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
971 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
972 '--min-coverage',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
973 dest='min_coverage', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
974 default=8,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
975 help='Minimum site coverage required in the normal and in the tumor '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
976 'sample to call a variant (default: 8)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
977 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
978 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
979 '--min-var-count',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
980 dest='min_var_count', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
981 default=2,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
982 help='Minimum number of variant-supporting reads required to call a '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
983 'variant (default: 2)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
984 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
985 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
986 '--min-var-freq',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
987 dest='min_var_freq', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
988 default=0.1,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
989 help='Minimum variant allele frequency for calling (default: 0.1)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
990 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
991 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
992 '--min-hom-freq',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
993 dest='min_hom_freq', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
994 default=0.75,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
995 help='Minimum variant allele frequency for homozygous call '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
996 '(default: 0.75)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
997 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
998 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
999 '--p-value',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1000 dest='p_value', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1001 default=0.99,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1002 help='P-value threshold for heterozygous call (default: 0.99)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1003 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1004 call_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1005 '--somatic-p-value',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1006 dest='somatic_p_value', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1007 default=0.05,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1008 help='P-value threshold for somatic call (default: 0.05)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1009 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1010 filter_group = p.add_argument_group('Posterior variant filter parameters')
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1011 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1012 '--no-filters',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1013 dest='no_filters', action='store_true',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1014 help='Disable all posterior variant filters. '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1015 'If specified, all following options will be ignored'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1016 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1017 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1018 '--min-var-count2',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1019 dest='min_var_count2', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1020 default=4,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1021 help='Minimum number of variant-supporting reads (default: 4)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1022 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1023 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1024 '--min-var-count2-lc',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1025 dest='min_var_count2_lc', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1026 default=2,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1027 help='Minimum number of variant-supporting reads when depth below '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1028 '--somatic-p-depth (default: 2)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1029 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1030 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1031 '--min-var-freq2',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1032 dest='min_var_freq2', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1033 default=0.05,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1034 help='Minimum variant allele frequency (default: 0.05)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1035 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1036 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1037 '--max-somatic-p',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1038 dest='max_somatic_p', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1039 default=0.05,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1040 help='Maximum somatic p-value (default: 0.05)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1041 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1042 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1043 '--max-somatic-p-depth',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1044 dest='max_somatic_p_depth', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1045 default=10,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1046 help='Depth required to run --max-somatic-p filter (default: 10)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1047 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1048 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1049 '--min-ref-readpos',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1050 dest='min_ref_readpos', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1051 default=0.1,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1052 help='Minimum average relative distance of site from the ends of '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1053 'ref-supporting reads (default: 0.1)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1054 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1055 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1056 '--min-var-readpos',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1057 dest='min_var_readpos', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1058 default=0.1,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1059 help='Minimum average relative distance of site from the ends of '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1060 'variant-supporting reads (default: 0.1)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1061 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1062 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1063 '--min-ref-dist3',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1064 dest='min_ref_dist3', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1065 default=0.1,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1066 help='Minimum average relative distance of site from the effective '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1067 '3\'end of ref-supporting reads (default: 0.1)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1068 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1069 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1070 '--min-var-dist3',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1071 dest='min_var_dist3', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1072 default=0.1,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1073 help='Minimum average relative distance of site from the effective '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1074 '3\'end of variant-supporting reads (default: 0.1)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1075 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1076 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1077 '--min-ref-len',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1078 dest='min_ref_len', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1079 default=90,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1080 help='Minimum average trimmed length of reads supporting the ref '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1081 'allele (default: 90)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1082 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1083 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1084 '--min-var-len',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1085 dest='min_var_len', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1086 default=90,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1087 help='Minimum average trimmed length of reads supporting the variant '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1088 'allele (default: 90)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1089 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1090 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1091 '--max-len-diff',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1092 dest='max_relative_len_diff', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1093 default=0.25,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1094 help='Maximum average relative read length difference (ref - var; '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1095 'default: 0.25)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1096 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1097 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1098 '--min-strandedness',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1099 dest='min_strandedness', type=float,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1100 default=0.01,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1101 help='Minimum fraction of variant reads from each strand '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1102 '(default: 0.01)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1103 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1104 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1105 '--min-strand-reads',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1106 dest='min_strand_reads', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1107 default=5,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1108 help='Minimum allele depth required to run --min-strandedness filter '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1109 '(default: 5)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1110 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1111 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1112 '--min-ref-basequal',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1113 dest='min_ref_basequal', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1114 default=15,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1115 help='Minimum average base quality for the ref allele (default: 15)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1116 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1117 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1118 '--min-var-basequal',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1119 dest='min_var_basequal', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1120 default=15,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1121 help='Minimum average base quality for the variant allele '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1122 '(default: 15)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1123 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1124 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1125 '--max-basequal-diff',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1126 dest='max_basequal_diff', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1127 default=50,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1128 help='Maximum average base quality diff (ref - var; default: 50)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1129 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1130 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1131 '--min-ref-mapqual',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1132 dest='min_ref_mapqual', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1133 default=15,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1134 help='Minimum average mapping quality of reads supporting the ref '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1135 'allele (default: 15)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1136 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1137 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1138 '--min-var-mapqual',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1139 dest='min_var_mapqual', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1140 default=15,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1141 help='Minimum average mapping quality of reads supporting the variant '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1142 'allele (default: 15)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1143 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1144 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1145 '--max-mapqual-diff',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1146 dest='max_mapqual_diff', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1147 default=50,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1148 help='Maximum average mapping quality difference (ref - var; '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1149 'default: 50)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1150 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1151 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1152 '--max-ref-mmqs',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1153 dest='max_ref_mmqs', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1154 default=100,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1155 help='Maximum mismatch quality sum of reads supporting the ref '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1156 'allele (default: 100)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1157 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1158 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1159 '--max-var-mmqs',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1160 dest='max_var_mmqs', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1161 default=100,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1162 help='Maximum mismatch quality sum of reads supporting the variant '
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1163 'allele (default: 100)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1164 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1165 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1166 '--min-mmqs-diff',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1167 dest='min_mmqs_diff', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1168 default=0,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1169 help='Minimum mismatch quality sum difference (var - ref; default: 0)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1170 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1171 filter_group.add_argument(
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1172 '--max-mmqs-diff',
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1173 dest='max_mmqs_diff', type=int,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1174 default=50,
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1175 help='Maximum mismatch quality sum difference (var - ref; default: 50)'
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1176 )
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1177 args = vars(p.parse_args())
d062703d6f13 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1178 varscan_call(**args)