Mercurial > repos > iuc > varscan_copynumber

annotate varscan.py @ 7:192bd5b78300 draft

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planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
author iuc
date Mon, 21 Jan 2019 12:06:22 -0500
parents 0cb031c7f464
children c24910ad5441
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4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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3
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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4 import argparse
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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5 import io
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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6 import os
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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7 import subprocess
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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8 import sys
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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9 import tempfile
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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10 import time
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
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11 from contextlib import ExitStack
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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12 from functools import partial
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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13 from threading import Thread
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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14
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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15 import pysam
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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18 class VariantCallingError (RuntimeError):
4ce3441c407c 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."""
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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20
4ce3441c407c 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=''):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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22 self.message = message
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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23 self.call = call.strip()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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24 self.error = error.strip()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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26 def __str__(self):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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27 if self.message is None:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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28 return ''
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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29 if self.error:
4ce3441c407c 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(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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31 self.call, self.error
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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32 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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33 else:
4ce3441c407c 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'
4ce3441c407c 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(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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36 self.call
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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37 )
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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39
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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41 class VarScanCaller (object):
4ce3441c407c 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,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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43 max_depth=None,
4ce3441c407c 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,
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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46 ):
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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52 self.threads = threads
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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53 self.verbose = verbose
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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54 self.quiet = quiet
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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55
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56 with pysam.FastaFile(ref_genome) as ref_fa:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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']
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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61 self.varcall_engine = ['varscan', 'somatic']
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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62 self.requires_stdout_redirect = False
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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63 self.TemporaryContigVCF = partial(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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64 tempfile.NamedTemporaryFile,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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65 mode='wb', suffix='', delete=False, dir=os.getcwd()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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66 )
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67 self.tmpfiles = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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68
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69 def _get_pysam_pileup_args(self):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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77 param_dict['compute_baq'] = False
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78 param_dict['stepper'] = 'samtools'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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79 return param_dict
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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85 p_value=None, somatic_p_value=None,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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86 threads=None, verbose=None, quiet=None
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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87 ):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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88 if not threads:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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89 threads = self.threads
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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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:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
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93 quiet = self.quiet
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
95 varcall_engine_option_mapping = [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
96 ('--normal-purity', normal_purity),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
97 ('--tumor-purity', tumor_purity),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
98 ('--min-coverage', min_coverage),
4ce3441c407c 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),
4ce3441c407c 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),
4ce3441c407c 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),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
102 ('--p-value', p_value),
4ce3441c407c 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),
4ce3441c407c 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)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
105 ]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
106 varcall_engine_options = []
4ce3441c407c 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:
4ce3441c407c 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:
4ce3441c407c 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)]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
110 pileup_engine_options = ['-B']
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
111 if self.max_depth is not None:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
112 pileup_engine_options += ['-d', str(self.max_depth)]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
113 if self.min_mapqual is not None:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
114 pileup_engine_options += ['-q', str(self.min_mapqual)]
4ce3441c407c 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:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
116 pileup_engine_options += ['-Q', str(self.min_basequal)]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
117
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
118 # Create a tuple of calls to samtools mpileup and varscan for
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
120 # that tuple.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
121 # The calls are stored in the reverse order of the contig list so
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
123 calls = [(
4ce3441c407c 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 + [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
125 '-r', contig + ':',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
126 '-f', self.ref_genome
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
127 ] + self.bam_input_files,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
128 self.varcall_engine + [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
129 '-', '{out}', '--output-vcf', '1', '--mpileup', '1'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
130 ] + varcall_engine_options,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
131 contig
4ce3441c407c 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]]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
133
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
134 if verbose:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
135 print('Starting variant calling ..')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
136
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
138 subprocesses = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
139 error_table = {}
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
140 tmp_io_started = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
141 tmp_io_finished = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
142 self.tmpfiles = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
143
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
144 def enqueue_stderr_output(out, stderr_buffer):
4ce3441c407c 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''):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
146 # Eventually we are going to print the contents of
4ce3441c407c 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
4ce3441c407c 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.
4ce3441c407c 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.
4ce3441c407c 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,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
151 'backslashreplace'))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
152 out.close()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
153
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
154 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
155 while subprocesses or calls:
4ce3441c407c 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:
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
160
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
162 call = calls.pop()
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
164 # to work on
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
165 contig = call[2]
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
168 # a named temporary file, to which the call output
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
169 # will be redirected.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
170 # At the moment we create the output file we add it to
4ce3441c407c 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
4ce3441c407c 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.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
173 call_out = self.TemporaryContigVCF(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
174 prefix=''.join(
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
176 ) + '_',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
177 )
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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)
4ce3441c407c 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:
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
183 stdout_p2 = call_out
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
184 stderr_p2 = subprocess.PIPE
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
185 else:
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
187 stdout_p2 = subprocess.PIPE
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
188 stderr_p2 = subprocess.STDOUT
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
190 call_out.close()
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
193 # strings
4ce3441c407c 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]))
4ce3441c407c 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()]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
196 # start the subprocesses
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
197 p1 = subprocess.Popen(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
198 call[0],
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
199 stdout=subprocess.PIPE, stderr=subprocess.PIPE
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
200 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
201 p2 = subprocess.Popen(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
202 call[1],
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
203 stdin=p1.stdout,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
204 stdout=stdout_p2,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
205 stderr=stderr_p2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
206 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
207 # subprocess bookkeeping
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
208 subprocesses.append((c_str, p1, p2, call_out, contig))
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
211 p1.stdout.close()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
212 t1 = Thread(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
213 target=enqueue_stderr_output,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
214 args=(p1.stderr, error_table[c_str][0])
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
215 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
216 t2 = Thread(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
217 target=enqueue_stderr_output,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
218 args=(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
219 p2.stderr
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
220 if self.requires_stdout_redirect else
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
221 p2.stdout,
4ce3441c407c 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]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
223 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
224 )
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
226 t1.start()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
227 t2.start()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
228
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
229 if verbose:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
230 print(
4ce3441c407c 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}'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
232 .format(call[2])
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
233 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
234
4ce3441c407c 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
4ce3441c407c 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:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
237 p1_stat = p1.poll()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
238 p2_stat = p2.poll()
4ce3441c407c 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:
4ce3441c407c 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!
4ce3441c407c 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
4ce3441c407c 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:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
243 print()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
244 print(
4ce3441c407c 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(),
4ce3441c407c 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(),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
247 file=sys.stderr
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
248 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
249 raise VariantCallingError(
4ce3441c407c 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.'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
251 .format(contig),
4ce3441c407c 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])
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
253 )
4ce3441c407c 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:
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
258 last_words = error_table[call][1].getvalue(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
259 ).splitlines()[-4:]
4ce3441c407c 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(
4ce3441c407c 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')
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
263 ):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
264 break
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
267 # get, stop it.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
268 p2.terminate()
4ce3441c407c 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))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
270 ofo.close()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
271 break
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
272 if p2_stat == 0:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
273 # Things went fine.
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
276 # they finished)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
277 tmp_io_finished.append(ofo.name)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
278 if verbose:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
279 print()
4ce3441c407c 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))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
281 if not quiet:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
282 print()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
283 print(
4ce3441c407c 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/'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
285 'bcftools:'.upper(),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
286 file=sys.stderr
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
287 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
288 print(
4ce3441c407c 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(),
4ce3441c407c 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(),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
291 file=sys.stderr
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
292 )
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
296 del error_table[call]
4ce3441c407c 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))
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
301 ofo.close()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
302 break
4ce3441c407c 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
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
304 time.sleep(2)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
305 finally:
4ce3441c407c 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:
4ce3441c407c 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
4ce3441c407c 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):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
309 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
310 proc.terminate()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
311 except Exception:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
312 pass
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
313 # close currently open files
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
314 ofo.close()
4ce3441c407c 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
4ce3441c407c 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
4ce3441c407c 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]
4ce3441c407c 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
4ce3441c407c 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.
4ce3441c407c 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,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
321 # but simply rewrite everything.
4ce3441c407c 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:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
323 print()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
324 print(
4ce3441c407c 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(),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
326 file=sys.stderr
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
327 )
4ce3441c407c 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():
4ce3441c407c 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)
4ce3441c407c 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)
4ce3441c407c 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)
4ce3441c407c 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)
4ce3441c407c 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)
4ce3441c407c 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)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
335
4ce3441c407c 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):
4ce3441c407c 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):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
338 header.add_meta(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
339 'contig',
4ce3441c407c 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)]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
341 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
342
4ce3441c407c 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):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
344 varscan_fpfilters = {
4ce3441c407c 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',
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
347 'VarAvgRL':
4ce3441c407c 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 < '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
349 '{min_var_len}',
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
351 'VarDist3':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
353 'VarMMQS':
4ce3441c407c 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 > '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
355 '{max_var_mmqs}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
356 'VarMapQual':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
358 'VarBaseQual':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
360 'Strand':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
362 'RefAvgRL':
4ce3441c407c 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 < '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
364 '{min_ref_len}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
365 'RefReadPos':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
367 'RefDist3':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
369 'RefMapQual':
4ce3441c407c 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 < '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
371 '{min_ref_mapqual}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
372 'RefBaseQual':
4ce3441c407c 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 < '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
374 '{min_ref_basequal}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
375 'RefMMQS':
4ce3441c407c 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 > '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
377 '{max_ref_mmqs}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
378 'MMQSdiff':
4ce3441c407c 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) > '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
380 '{max_mmqs_diff}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
381 'MinMMQSdiff':
4ce3441c407c 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) < '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
383 '{max_mmqs_diff}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
384 'MapQualDiff':
4ce3441c407c 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}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
386 'MaxBAQdiff':
4ce3441c407c 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) > '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
388 '{max_basequal_diff}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
389 'ReadLenDiff':
4ce3441c407c 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) > '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
391 '{max_relative_len_diff}',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
392 }
4ce3441c407c 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():
4ce3441c407c 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)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
395
4ce3441c407c 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):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
397 header.info.add(
4ce3441c407c 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'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
399 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
400
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
401 def _standardize_format_fields(self, header):
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
402 """Add standard FORMAT key declarations to a VCF header."""
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
403
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
404 format_field_specs = [
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
405 ('GT', '1', 'String', 'Genotype'),
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
406 ('GQ', '1', 'Integer', 'Genotype quality'),
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
407 ('DP', '1', 'Integer', 'Read depth'),
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
408 ('AD', 'R', 'Integer', 'Read depth for each allele'),
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
409 ('ADF', 'R', 'Integer',
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
410 'Read depth for each allele on the forward strand'),
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
411 ('ADR', 'R', 'Integer',
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
412 'Read depth for each allele on the reverse strand')
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
413 ]
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
414 # Existing FORMAT declarations cannot be overwritten.
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
415 # The only viable strategy is to mark them as removed,
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
416 # then merge the header with another one containing the
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
417 # correct declarations. This is what is implemented below.
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
418 temp_header = pysam.VariantHeader()
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
419 for spec in format_field_specs:
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
420 temp_header.formats.add(*spec)
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
421 if spec[0] in header.formats:
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
422 header.formats.remove_header(spec[0])
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
423 header.merge(temp_header)
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
424
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
425 def _compile_common_header(self, varcall_template, no_filters=False):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
426 # fix the header generated by VarScan
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
427 # by adding reference and contig information
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
428 common_header = pysam.VariantHeader()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
429 common_header.add_meta('reference', value=self.ref_genome)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
430 self._add_ref_contigs_to_header(common_header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
431 if not no_filters:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
432 # add filter info
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
433 self._add_filters_to_header(common_header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
434 # change the source information
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
435 common_header.add_meta('source', value='varscan.py')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
436 # declare an INDEL flag for record INFO fields
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
437 self._add_indel_info_flag_to_header(common_header)
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
438 # generate standard FORMAT field declarations
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
439 # including a correct AD declaration to prevent VarScan's
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
440 # non-standard one from getting propagated
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
441 self._standardize_format_fields(common_header)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
442 # take the remaining metadata from the template header produced by
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
443 # VarScan
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
444 with pysam.VariantFile(varcall_template, 'r') as original_data:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
445 varscan_header = original_data.header
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
446 # don't propagate non-standard and redundant FORMAT keys written
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
447 # by VarScan
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
448 varscan_header.formats.remove_header('AD')
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
449 varscan_header.formats.remove_header('FREQ')
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
450 varscan_header.formats.remove_header('RD')
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
451 varscan_header.formats.remove_header('DP4')
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
452 for sample in varscan_header.samples:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
453 common_header.samples.add(sample)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
454 common_header.merge(varscan_header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
455 return common_header
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
456
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
457 def _fix_record_gt_fields(self, record):
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
458 """Migrate non-standard genotype fields to standard ones."""
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
459
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
460 # The key issue to consider here is that we need to modify
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
461 # genotype field values on a per-sample basis, but htslib
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
462 # reserves memory for the values of all samples upon the first
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
463 # modification of the field in the variant record.
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
464 # => We need to calculate all values first, then fill each
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
465 # genotype field starting with the sample with the largest value.
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
466 new_gt_fields = {'AD': [], 'ADF': [], 'ADR': []}
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
467 # store the current genotype field contents for each sample
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
468 per_sample_gts = record.samples.values()
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
469 # calculate and store the new genotype field values
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
470 for gt_field in per_sample_gts:
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
471 # generate a standard AD field by combining VarScan's
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
472 # RD and non-standard AD fields
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
473 new_gt_fields['AD'].append((gt_field['RD'], gt_field['AD'][0]))
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
474 # split VarScan's DP4 field into the standard fields
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
475 # ADF and ADR
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
476 new_gt_fields['ADF'].append(
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
477 (int(gt_field['DP4'][0]), int(gt_field['DP4'][2]))
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
478 )
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
479 new_gt_fields['ADR'].append(
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
480 (int(gt_field['DP4'][1]), int(gt_field['DP4'][3]))
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
481 )
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
482 # Modify the record's genotype fields.
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
483 # For each field, modify the sample containing the largest
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
484 # value for the field first.
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
485 # Without this precaution we could trigger:
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
486 # "bcf_update_format: Assertion `!fmt->p_free' failed."
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
487 # in vcf.c of htslib resulting in a core dump.
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
488 for field in sorted(new_gt_fields):
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
489 for new_field, sample_fields in sorted(
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
490 zip(new_gt_fields[field], per_sample_gts),
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
491 key=lambda x: max(x[0]),
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
492 reverse=True
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
493 ):
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
494 sample_fields[field] = new_field
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
495 # remove redundant fields
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
496 # FREQ is easy to calculate from AD
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
497 del record.format['FREQ']
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
498 del record.format['RD']
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
499 del record.format['DP4']
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
500
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
501 def pileup_masker(self, mask):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
502 def apply_mask_on_pileup(piled_items):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
503 for item, status in zip(piled_items, mask):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
504 if status:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
505 yield item
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
506 return apply_mask_on_pileup
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
507
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
508 def get_allele_specific_pileup_column_stats(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
509 self, allele, pile_column, ref_fetch
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
510 ):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
511 # number of reads supporting the given allele on
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
512 # forward and reverse strand, and in total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
513 var_reads_plus = var_reads_minus = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
514 var_supp_read_mask = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
515 for base in pile_column.get_query_sequences():
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
516 if base == allele:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
517 # allele supporting read on + strand
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
518 var_reads_plus += 1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
519 var_supp_read_mask.append(True)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
520 elif base.upper() == allele:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
521 # allele supporting read on - strand
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
522 var_reads_minus += 1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
523 var_supp_read_mask.append(True)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
524 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
525 var_supp_read_mask.append(False)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
526 var_reads_total = var_reads_plus + var_reads_minus
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
527
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
528 if var_reads_total == 0:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
529 # No stats without reads!
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
530 return None
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
531
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
532 var_supp_only = self.pileup_masker(var_supp_read_mask)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
533
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
534 # average mapping quality of the reads supporting the
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
535 # given allele
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
536 avg_mapping_quality = sum(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
537 mq for mq in var_supp_only(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
538 pile_column.get_mapping_qualities()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
539 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
540 ) / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
541
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
542 # for the remaining stats we need access to complete
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
543 # read information
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
544 piled_reads = [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
545 p for p in var_supp_only(pile_column.pileups)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
546 ]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
547 assert len(piled_reads) == var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
548 sum_avg_base_qualities = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
549 sum_dist_from_center = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
550 sum_dist_from_3prime = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
551 sum_clipped_length = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
552 sum_unclipped_length = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
553 sum_num_mismatches_as_fraction = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
554 sum_mismatch_qualities = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
555
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
556 for p in piled_reads:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
557 sum_avg_base_qualities += sum(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
558 p.alignment.query_qualities
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
559 ) / p.alignment.infer_query_length()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
560 sum_clipped_length += p.alignment.query_alignment_length
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
561 unclipped_length = p.alignment.infer_read_length()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
562 sum_unclipped_length += unclipped_length
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
563 read_center = p.alignment.query_alignment_length / 2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
564 sum_dist_from_center += 1 - abs(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
565 p.query_position - read_center
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
566 ) / read_center
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
567 if p.alignment.is_reverse:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
568 sum_dist_from_3prime += p.query_position / unclipped_length
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
569 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
570 sum_dist_from_3prime += 1 - p.query_position / unclipped_length
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
571
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
572 sum_num_mismatches = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
573 for qpos, rpos in p.alignment.get_aligned_pairs():
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
574 if qpos is not None and rpos is not None:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
575 if p.alignment.query_sequence[qpos] != ref_fetch(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
576 rpos, rpos + 1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
577 ).upper(): # ref bases can be lowercase!
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
578 sum_num_mismatches += 1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
579 sum_mismatch_qualities += p.alignment.query_qualities[
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
580 qpos
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
581 ]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
582 sum_num_mismatches_as_fraction += (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
583 sum_num_mismatches / p.alignment.query_alignment_length
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
584 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
585 avg_basequality = sum_avg_base_qualities / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
586 avg_pos_as_fraction = sum_dist_from_center / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
587 avg_num_mismatches_as_fraction = (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
588 sum_num_mismatches_as_fraction / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
589 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
590 avg_sum_mismatch_qualities = sum_mismatch_qualities / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
591 avg_clipped_length = sum_clipped_length / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
592 avg_distance_to_effective_3p_end = (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
593 sum_dist_from_3prime / var_reads_total
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
594 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
595
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
596 return (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
597 avg_mapping_quality,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
598 avg_basequality,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
599 var_reads_plus,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
600 var_reads_minus,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
601 avg_pos_as_fraction,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
602 avg_num_mismatches_as_fraction,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
603 avg_sum_mismatch_qualities,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
604 avg_clipped_length,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
605 avg_distance_to_effective_3p_end
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
606 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
607
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
608 def _postprocess_variant_records(self, invcf,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
609 min_var_count2, min_var_count2_lc,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
610 min_var_freq2, max_somatic_p,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
611 max_somatic_p_depth,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
612 min_ref_readpos, min_var_readpos,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
613 min_ref_dist3, min_var_dist3,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
614 min_ref_len, min_var_len,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
615 max_relative_len_diff,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
616 min_strandedness, min_strand_reads,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
617 min_ref_basequal, min_var_basequal,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
618 max_basequal_diff,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
619 min_ref_mapqual, min_var_mapqual,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
620 max_mapqual_diff,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
621 max_ref_mmqs, max_var_mmqs,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
622 min_mmqs_diff, max_mmqs_diff,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
623 **args):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
624 # set FILTER field according to Varscan criteria
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
625 # multiple FILTER entries must be separated by semicolons
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
626 # No filters applied should be indicated with MISSING
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
627
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
628 # since posterior filters are always applied to just one sample,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
629 # a better place to store the info is in the FT genotype field:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
630 # can be PASS, '.' to indicate that filters have not been applied,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
631 # or a semicolon-separated list of filters that failed
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
632 # unfortunately, gemini does not support this field
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
633
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
634 with ExitStack() as io_stack:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
635 normal_reads, tumor_reads = (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
636 io_stack.enter_context(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
637 pysam.Samfile(fn, 'rb')) for fn in self.bam_input_files
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
638 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
639 refseq = io_stack.enter_context(pysam.FastaFile(self.ref_genome))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
640 pileup_args = self._get_pysam_pileup_args()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
641 for record in invcf:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
642 if any(len(allele) > 1 for allele in record.alleles):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
643 # skip indel postprocessing for the moment
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
644 yield record
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
645 continue
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
646 # get pileup for genomic region affected by this variant
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
647 if record.info['SS'] == '2':
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
648 # a somatic variant => generate pileup from tumor data
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
649 pile = tumor_reads.pileup(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
650 record.chrom, record.start, record.stop,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
651 **pileup_args
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
652 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
653 sample_of_interest = 'TUMOR'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
654 elif record.info['SS'] in ['1', '3']:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
655 # a germline or LOH variant => pileup from normal data
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
656 pile = normal_reads.pileup(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
657 record.chrom, record.start, record.stop,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
658 **pileup_args
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
659 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
660 sample_of_interest = 'NORMAL'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
661 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
662 # TO DO: figure out if there is anything interesting to do
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
663 # for SS status codes 0 (reference) and 5 (unknown)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
664 yield record
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
665 continue
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
666
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
667 # apply false-positive filtering a la varscan fpfilter
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
668 # find the variant site in the pileup columns
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
669 for pile_column in pile:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
670 if pile_column.reference_pos == record.start:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
671 break
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
672 # extract required information
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
673 # overall read depth at the site
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
674 read_depth = pile_column.get_num_aligned()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
675 assert read_depth > 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
676 # no multiallelic sites in varscan
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
677 assert len(record.alleles) == 2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
678 if record.samples[sample_of_interest]['RD'] > 0:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
679 ref_stats, alt_stats = [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
680 self.get_allele_specific_pileup_column_stats(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
681 allele,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
682 pile_column,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
683 partial(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
684 pysam.FastaFile.fetch, refseq, record.chrom
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
685 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
686 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
687 for allele in record.alleles
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
688 ]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
689 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
690 ref_stats = None
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
691 alt_stats = self.get_allele_specific_pileup_column_stats(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
692 record.alleles[1],
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
693 pile_column,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
694 partial(pysam.FastaFile.fetch, refseq, record.chrom)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
695 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
696 ref_count = 0
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
697 if ref_stats:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
698 ref_count = ref_stats[2] + ref_stats[3]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
699 if ref_stats[1] < min_ref_basequal:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
700 record.filter.add('RefBaseQual')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
701 if ref_count >= 2:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
702 if ref_stats[0] < min_ref_mapqual:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
703 record.filter.add('RefMapQual')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
704 if ref_stats[4] < min_ref_readpos:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
705 record.filter.add('RefReadPos')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
706 # ref_stats[5] (avg_num_mismatches_as_fraction
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
707 # is not a filter criterion in VarScan fpfilter
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
708 if ref_stats[6] > max_ref_mmqs:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
709 record.filter.add('RefMMQS')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
710 if ref_stats[7] < min_ref_len:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
711 # VarScan fpfilter does not apply this filter
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
712 # for indels, but there is no reason
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
713 # not to do it.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
714 record.filter.add('RefAvgRL')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
715 if ref_stats[8] < min_ref_dist3:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
716 record.filter.add('RefDist3')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
717 if alt_stats:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
718 alt_count = alt_stats[2] + alt_stats[3]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
719 if (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
720 alt_count < min_var_count2_lc
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
721 ) or (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
722 read_depth >= max_somatic_p_depth and
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
723 alt_count < min_var_count2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
724 ):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
725 record.filter.add('VarCount')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
726 if alt_count / read_depth < min_var_freq2:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
727 record.filter.add('VarFreq')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
728 if alt_stats[1] < min_var_basequal:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
729 record.filter.add('VarBaseQual')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
730 if alt_count > min_strand_reads:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
731 if (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
732 alt_stats[2] / alt_count < min_strandedness
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
733 ) or (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
734 alt_stats[3] / alt_count < min_strandedness
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
735 ):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
736 record.filter.add('Strand')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
737 if alt_stats[2] + alt_stats[3] >= 2:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
738 if alt_stats[0] < min_var_mapqual:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
739 record.filter.add('VarMapQual')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
740 if alt_stats[4] < min_var_readpos:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
741 record.filter.add('VarReadPos')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
742 # alt_stats[5] (avg_num_mismatches_as_fraction
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
743 # is not a filter criterion in VarScan fpfilter
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
744 if alt_stats[6] > max_var_mmqs:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
745 record.filter.add('VarMMQS')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
746 if alt_stats[7] < min_var_len:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
747 # VarScan fpfilter does not apply this filter
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
748 # for indels, but there is no reason
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
749 # not to do it.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
750 record.filter.add('VarAvgRL')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
751 if alt_stats[8] < min_var_dist3:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
752 record.filter.add('VarDist3')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
753 if ref_count >= 2 and alt_count >= 2:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
754 if (ref_stats[0] - alt_stats[0]) > max_mapqual_diff:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
755 record.filter.add('MapQualDiff')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
756 if (ref_stats[1] - alt_stats[1]) > max_basequal_diff:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
757 record.filter.add('MaxBAQdiff')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
758 mmqs_diff = alt_stats[6] - ref_stats[6]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
759 if mmqs_diff < min_mmqs_diff:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
760 record.filter.add('MinMMQSdiff')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
761 if mmqs_diff > max_mmqs_diff:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
762 record.filter.add('MMQSdiff')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
763 if (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
764 1 - alt_stats[7] / ref_stats[7]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
765 ) > max_relative_len_diff:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
766 record.filter.add('ReadLenDiff')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
767 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
768 # No variant-supporting reads for this record!
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
769 # This can happen in rare cases because of
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
770 # samtools mpileup issues, but indicates a
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
771 # rather unreliable variant call.
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
772 record.filter.add('VarCount')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
773 record.filter.add('VarFreq')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
774 yield record
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
775
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
776 def _indel_flagged_records(self, vcf):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
777 for record in vcf:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
778 record.info['INDEL'] = True
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
779 yield record
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
780
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
781 def _merge_generator(self, vcf1, vcf2):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
782 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
783 record1 = next(vcf1)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
784 except StopIteration:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
785 for record2 in vcf2:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
786 yield record2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
787 return
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
788 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
789 record2 = next(vcf2)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
790 except StopIteration:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
791 yield record1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
792 for record1 in vcf1:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
793 yield record1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
794 return
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
795 while True:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
796 if (record1.start, record1.stop) < (record2.start, record2.stop):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
797 yield record1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
798 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
799 record1 = next(vcf1)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
800 except StopIteration:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
801 yield record2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
802 for record2 in vcf2:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
803 yield record2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
804 return
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
805 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
806 yield record2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
807 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
808 record2 = next(vcf2)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
809 except StopIteration:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
810 yield record1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
811 for record1 in vcf1:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
812 yield record1
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
813 return
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
814
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
815 def merge_and_postprocess(self, snps_out, indels_out=None,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
816 no_filters=False, **filter_args):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
817 temporary_data = self.tmpfiles
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
818 self.tmpfiles = []
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
819 temporary_snp_files = [f + '.snp.vcf' for f in temporary_data]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
820 temporary_indel_files = [f + '.indel.vcf' for f in temporary_data]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
821
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
822 for f in temporary_data:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
823 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
824 os.remove(f)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
825 except Exception:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
826 pass
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
827
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
828 def noop_gen(data, **kwargs):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
829 for d in data:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
830 yield d
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
831
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
832 if no_filters:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
833 apply_filters = noop_gen
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
834 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
835 apply_filters = self._postprocess_variant_records
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
836
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
837 output_header = self._compile_common_header(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
838 temporary_snp_files[0],
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
839 no_filters
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
840 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
841 if indels_out is None:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
842 with open(snps_out, 'w') as o:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
843 o.write(str(output_header).format(**filter_args))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
844 for snp_f, indel_f in zip(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
845 temporary_snp_files, temporary_indel_files
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
846 ):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
847 with pysam.VariantFile(snp_f, 'r') as snp_invcf:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
848 # fix the input header on the fly
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
849 # to avoid Warnings from htslib about missing contig
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
850 # info
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
851 self._add_ref_contigs_to_header(snp_invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
852 self._add_filters_to_header(snp_invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
853 self._add_indel_info_flag_to_header(snp_invcf.header)
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
854 self._standardize_format_fields(snp_invcf.header)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
855 with pysam.VariantFile(indel_f, 'r') as indel_invcf:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
856 # fix the input header on the fly
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
857 # to avoid Warnings from htslib about missing
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
858 # contig info
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
859 self._add_ref_contigs_to_header(indel_invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
860 self._add_filters_to_header(indel_invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
861 self._add_indel_info_flag_to_header(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
862 indel_invcf.header
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
863 )
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
864 self._standardize_format_fields(indel_invcf.header)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
865 for record in apply_filters(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
866 self._merge_generator(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
867 snp_invcf,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
868 self._indel_flagged_records(indel_invcf)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
869 ),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
870 **filter_args
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
871 ):
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
872 self._fix_record_gt_fields(record)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
873 o.write(str(record))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
874 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
875 os.remove(snp_f)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
876 except Exception:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
877 pass
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
878 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
879 os.remove(indel_f)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
880 except Exception:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
881 pass
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
882
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
883 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
884 with open(snps_out, 'w') as o:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
885 o.write(str(output_header).format(**filter_args))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
886 for f in temporary_snp_files:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
887 with pysam.VariantFile(f, 'r') as invcf:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
888 # fix the input header on the fly
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
889 # to avoid Warnings from htslib about missing
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
890 # contig info and errors because of undeclared
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
891 # filters
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
892 self._add_ref_contigs_to_header(invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
893 self._add_filters_to_header(invcf.header)
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
894 self._standardize_format_fields(invcf.header)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
895 for record in apply_filters(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
896 invcf, **filter_args
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
897 ):
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
898 self._fix_record_gt_fields(record)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
899 o.write(str(record))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
900 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
901 os.remove(f)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
902 except Exception:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
903 pass
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
904 with open(indels_out, 'w') as o:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
905 o.write(str(output_header))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
906 for f in temporary_indel_files:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
907 with pysam.VariantFile(f, 'r') as invcf:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
908 # fix the input header on the fly
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
909 # to avoid Warnings from htslib about missing
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
910 # contig info and errors because of undeclared
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
911 # filters
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
912 self._add_ref_contigs_to_header(invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
913 self._add_filters_to_header(invcf.header)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
914 self._add_indel_info_flag_to_header(invcf.header)
6
0cb031c7f464 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 4b7660df2384d8c8c6b5a6f02a00d13211e6ff6c
iuc
parents: 2
diff changeset
915 self._standardize_format_fields(invcf.header)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
916 for record in apply_filters(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
917 self._indel_flagged_records(invcf), **filter_args
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
918 ):
7
192bd5b78300 planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit f5e4d8903b6d69b0507f6a8fc4c2533fc7a15dfa
iuc
parents: 6
diff changeset
919 self._fix_record_gt_fields(record)
2
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
920 o.write(str(record))
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
921 try:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
922 os.remove(f)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
923 except Exception:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
924 pass
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
925
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
926
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
927 def varscan_call(ref_genome, normal, tumor, output_path, **args):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
928 """Preparse arguments and orchestrate calling and postprocessing."""
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
929
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
930 if args.pop('split_output'):
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
931 if '%T' in output_path:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
932 out = (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
933 output_path.replace('%T', 'snp'),
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
934 output_path.replace('%T', 'indel')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
935 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
936 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
937 out = (
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
938 output_path + '.snp',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
939 output_path + '.indel'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
940 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
941 else:
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
942 out = (output_path, None)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
943
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
944 instance_args = {
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
945 k: args.pop(k) for k in [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
946 'max_depth',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
947 'min_mapqual',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
948 'min_basequal',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
949 'threads',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
950 'verbose',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
951 'quiet'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
952 ]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
953 }
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
954 varscan_somatic_args = {
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
955 k: args.pop(k) for k in [
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
956 'normal_purity',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
957 'tumor_purity',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
958 'min_coverage',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
959 'min_var_count',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
960 'min_var_freq',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
961 'min_hom_freq',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
962 'somatic_p_value',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
963 'p_value'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
964 ]
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
965 }
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
966
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
967 v = VarScanCaller(ref_genome, [normal, tumor], **instance_args)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
968 v.varcall_parallel(**varscan_somatic_args)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
969 v.merge_and_postprocess(*out, **args)
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
970
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
971
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
972 if __name__ == '__main__':
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
973 p = argparse.ArgumentParser()
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
974 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
975 'ref_genome',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
976 metavar='reference_genome',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
977 help='the reference genome (in fasta format)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
978 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
979 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
980 '--normal',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
981 metavar='BAM_file', required=True,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
982 help='the BAM input file of aligned reads from the normal sample'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
983 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
984 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
985 '--tumor',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
986 metavar='BAM_file', required=True,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
987 help='the BAM input file of aligned reads from the tumor sample'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
988 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
989 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
990 '-o', '--ofile', required=True,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
991 metavar='OFILE', dest='output_path',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
992 help='Name of the variant output file. With --split-output, the name '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
993 'may use the %%T replacement token or will be used as the '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
994 'basename for the two output files to be generated (see '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
995 '-s|--split-output below).'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
996 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
997 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
998 '-s', '--split-output',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
999 dest='split_output', action='store_true', default=False,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1000 help='indicate that separate output files for SNPs and indels '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1001 'should be generated (original VarScan behavior). If specified, '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1002 '%%T in the --ofile file name will be replaced with "snp" and '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1003 '"indel" to generate the names of the SNP and indel output '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1004 'files, respectively. If %%T is not found in the file name, it '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1005 'will get interpreted as a basename to which ".snp"/".indel" '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1006 'will be appended.'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1007 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1008 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1009 '-t', '--threads',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1010 type=int, default=1,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1011 help='level of parallelism'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1012 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1013 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1014 '-v', '--verbose',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1015 action='store_true',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1016 help='be verbose about progress'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1017 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1018 p.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1019 '-q', '--quiet',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1020 action='store_true',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1021 help='suppress output from wrapped tools'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1022 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1023 call_group = p.add_argument_group('Variant calling parameters')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1024 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1025 '--normal-purity',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1026 dest='normal_purity', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1027 default=1.0,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1028 help='Estimated purity of the normal sample (default: 1.0)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1029 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1030 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1031 '--tumor-purity',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1032 dest='tumor_purity', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1033 default=1.0,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1034 help='Estimated purity of the tumor sample (default: 1.0)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1035 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1036 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1037 '--max-pileup-depth',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1038 dest='max_depth', type=int, default=8000,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1039 help='Maximum depth of generated pileups (samtools mpileup -d option; '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1040 'default: 8000)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1041 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1042 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1043 '--min-basequal',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1044 dest='min_basequal', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1045 default=13,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1046 help='Minimum base quality at the variant position to use a read '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1047 '(default: 13)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1048 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1049 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1050 '--min-mapqual',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1051 dest='min_mapqual', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1052 default=0,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1053 help='Minimum mapping quality required to use a read '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1054 '(default: 0)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1055 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1056 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1057 '--min-coverage',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1058 dest='min_coverage', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1059 default=8,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1060 help='Minimum site coverage required in the normal and in the tumor '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1061 'sample to call a variant (default: 8)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1062 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1063 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1064 '--min-var-count',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1065 dest='min_var_count', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1066 default=2,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1067 help='Minimum number of variant-supporting reads required to call a '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1068 'variant (default: 2)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1069 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1070 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1071 '--min-var-freq',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1072 dest='min_var_freq', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1073 default=0.1,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1074 help='Minimum variant allele frequency for calling (default: 0.1)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1075 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1076 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1077 '--min-hom-freq',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1078 dest='min_hom_freq', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1079 default=0.75,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1080 help='Minimum variant allele frequency for homozygous call '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1081 '(default: 0.75)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1082 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1083 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1084 '--p-value',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1085 dest='p_value', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1086 default=0.99,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1087 help='P-value threshold for heterozygous call (default: 0.99)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1088 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1089 call_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1090 '--somatic-p-value',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1091 dest='somatic_p_value', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1092 default=0.05,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1093 help='P-value threshold for somatic call (default: 0.05)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1094 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1095 filter_group = p.add_argument_group('Posterior variant filter parameters')
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1096 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1097 '--no-filters',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1098 dest='no_filters', action='store_true',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1099 help='Disable all posterior variant filters. '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1100 'If specified, all following options will be ignored'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1101 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1102 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1103 '--min-var-count2',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1104 dest='min_var_count2', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1105 default=4,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1106 help='Minimum number of variant-supporting reads (default: 4)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1107 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1108 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1109 '--min-var-count2-lc',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1110 dest='min_var_count2_lc', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1111 default=2,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1112 help='Minimum number of variant-supporting reads when depth below '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1113 '--somatic-p-depth (default: 2)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1114 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1115 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1116 '--min-var-freq2',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1117 dest='min_var_freq2', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1118 default=0.05,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1119 help='Minimum variant allele frequency (default: 0.05)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1120 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1121 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1122 '--max-somatic-p',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1123 dest='max_somatic_p', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1124 default=0.05,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1125 help='Maximum somatic p-value (default: 0.05)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1126 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1127 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1128 '--max-somatic-p-depth',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1129 dest='max_somatic_p_depth', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1130 default=10,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1131 help='Depth required to run --max-somatic-p filter (default: 10)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1132 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1133 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1134 '--min-ref-readpos',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1135 dest='min_ref_readpos', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1136 default=0.1,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1137 help='Minimum average relative distance of site from the ends of '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1138 'ref-supporting reads (default: 0.1)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1139 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1140 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1141 '--min-var-readpos',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1142 dest='min_var_readpos', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1143 default=0.1,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1144 help='Minimum average relative distance of site from the ends of '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1145 'variant-supporting reads (default: 0.1)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1146 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1147 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1148 '--min-ref-dist3',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1149 dest='min_ref_dist3', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1150 default=0.1,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1151 help='Minimum average relative distance of site from the effective '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1152 '3\'end of ref-supporting reads (default: 0.1)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1153 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1154 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1155 '--min-var-dist3',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1156 dest='min_var_dist3', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1157 default=0.1,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1158 help='Minimum average relative distance of site from the effective '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1159 '3\'end of variant-supporting reads (default: 0.1)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1160 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1161 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1162 '--min-ref-len',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1163 dest='min_ref_len', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1164 default=90,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1165 help='Minimum average trimmed length of reads supporting the ref '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1166 'allele (default: 90)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1167 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1168 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1169 '--min-var-len',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1170 dest='min_var_len', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1171 default=90,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1172 help='Minimum average trimmed length of reads supporting the variant '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1173 'allele (default: 90)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1174 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1175 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1176 '--max-len-diff',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1177 dest='max_relative_len_diff', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1178 default=0.25,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1179 help='Maximum average relative read length difference (ref - var; '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1180 'default: 0.25)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1181 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1182 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1183 '--min-strandedness',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1184 dest='min_strandedness', type=float,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1185 default=0.01,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1186 help='Minimum fraction of variant reads from each strand '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1187 '(default: 0.01)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1188 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1189 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1190 '--min-strand-reads',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1191 dest='min_strand_reads', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1192 default=5,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1193 help='Minimum allele depth required to run --min-strandedness filter '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1194 '(default: 5)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1195 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1196 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1197 '--min-ref-basequal',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1198 dest='min_ref_basequal', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1199 default=15,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1200 help='Minimum average base quality for the ref allele (default: 15)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1201 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1202 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1203 '--min-var-basequal',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1204 dest='min_var_basequal', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1205 default=15,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1206 help='Minimum average base quality for the variant allele '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1207 '(default: 15)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1208 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1209 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1210 '--max-basequal-diff',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1211 dest='max_basequal_diff', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1212 default=50,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1213 help='Maximum average base quality diff (ref - var; default: 50)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1214 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1215 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1216 '--min-ref-mapqual',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1217 dest='min_ref_mapqual', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1218 default=15,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1219 help='Minimum average mapping quality of reads supporting the ref '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1220 'allele (default: 15)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1221 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1222 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1223 '--min-var-mapqual',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1224 dest='min_var_mapqual', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1225 default=15,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1226 help='Minimum average mapping quality of reads supporting the variant '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1227 'allele (default: 15)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1228 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1229 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1230 '--max-mapqual-diff',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1231 dest='max_mapqual_diff', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1232 default=50,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1233 help='Maximum average mapping quality difference (ref - var; '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1234 'default: 50)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1235 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1236 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1237 '--max-ref-mmqs',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1238 dest='max_ref_mmqs', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1239 default=100,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1240 help='Maximum mismatch quality sum of reads supporting the ref '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1241 'allele (default: 100)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1242 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1243 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1244 '--max-var-mmqs',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1245 dest='max_var_mmqs', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1246 default=100,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1247 help='Maximum mismatch quality sum of reads supporting the variant '
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1248 'allele (default: 100)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1249 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1250 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1251 '--min-mmqs-diff',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1252 dest='min_mmqs_diff', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1253 default=0,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1254 help='Minimum mismatch quality sum difference (var - ref; default: 0)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1255 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1256 filter_group.add_argument(
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1257 '--max-mmqs-diff',
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1258 dest='max_mmqs_diff', type=int,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1259 default=50,
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1260 help='Maximum mismatch quality sum difference (var - ref; default: 50)'
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1261 )
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1262 args = vars(p.parse_args())
4ce3441c407c planemo upload for repository https://github.com/galaxyproject/iuc/tree/master/tools/varscan commit 30867f1f022bed18ba1c3b8dc9c54226890b3a9c
iuc
parents:
diff changeset
1263 varscan_call(**args)