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1 from typing import (
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2 Callable,
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3 List,
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4 Optional,
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5 Tuple,
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6 Iterable,
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7 Union,
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8 )
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9
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10 from pysam.libcutils import _pysam_dispatch
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11
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12
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13 class SamtoolsError(Exception):
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14 '''exception raised in case of an error incurred in the samtools
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15 library.'''
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16
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17 def __init__(self, value):
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18 self.value = value
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19
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20 def __str__(self):
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21 return repr(self.value)
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22
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23
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24 class PysamDispatcher(object):
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25 '''The dispatcher emulates the samtools/bctools command line.
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26
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27 Captures stdout and stderr.
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28
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29 Raises a :class:`pysam.SamtoolsError` exception in case samtools
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30 exits with an error code other than 0.
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31
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32 Some command line options are associated with parsers. For
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33 example, the samtools command "pileup -c" creates a tab-separated
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34 table on standard output. In order to associate parsers with
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35 options, an optional list of parsers can be supplied. The list
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36 will be processed in order checking for the presence of each
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37 option.
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38
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39 If no parser is given or no appropriate parser is found, the
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40 stdout output of samtools/bcftools commands will be returned.
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41
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42 '''
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43
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44 dispatch = None
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45 parsers = None
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46 collection = None
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47
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48 def __init__(
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49 self,
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50 collection: str,
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51 dispatch: str,
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52 parsers: Optional[Iterable[Tuple[str, Callable[[Union[str, List[str]]], Union[str, List[str]]]]]] = None,
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53 ):
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54 self.collection = collection
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55 self.dispatch = dispatch
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56 self.parsers = parsers
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57 self.stderr = []
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58
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59 def __call__(self, *args: str, **kwargs) -> Union[str, List[str]]:
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60 '''
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61 execute a samtools command.
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62
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63 Keyword arguments:
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64 catch_stdout -- redirect stdout from the samtools command and
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65 return as variable (default True)
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66 save_stdout -- redirect stdout to a filename.
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67 raw -- ignore any parsers associated with this samtools command.
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68 split_lines -- return stdout (if catch_stdout is True and stderr
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69 as a list of strings.
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70 '''
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71 retval, stderr, stdout = _pysam_dispatch(
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72 self.collection,
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73 self.dispatch,
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74 args,
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75 catch_stdout=kwargs.get("catch_stdout", True),
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76 save_stdout=kwargs.get("save_stdout", None))
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77
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78 if kwargs.get("split_lines", False):
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79 stdout = stdout.splitlines()
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80 if stderr:
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81 stderr = stderr.splitlines()
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82
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83 if retval:
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84 raise SamtoolsError(
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85 "%s returned with error %i: "
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86 "stdout=%s, stderr=%s" %
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87 (self.collection,
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88 retval,
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89 stdout,
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90 stderr))
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91
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92 self.stderr = stderr
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93
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94 # call parser for stdout:
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95 if not kwargs.get("raw") and stdout and self.parsers:
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96 for options, parser in self.parsers:
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97 for option in options:
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98 if option not in args:
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99 break
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100 else:
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101 return parser(stdout)
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102
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103 return stdout
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104
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105 def get_messages(self):
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106 return self.stderr
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107
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108 def usage(self):
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109 '''return the samtools usage information for this command'''
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110 retval, stderr, stdout = _pysam_dispatch(
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111 self.collection,
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112 self.dispatch,
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113 is_usage=True,
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114 catch_stdout=True)
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115 # some tools write usage to stderr, such as mpileup
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116 if stderr:
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117 return stderr
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118 else:
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119 return stdout
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120
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121
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122 class unquoted_str(str):
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123 '''Tag a value as an unquoted string. Meta-information in the VCF
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124 header takes the form of key=value pairs. By default, pysam will
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125 enclose the value in quotation marks. Tagging that value with
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126 unquoted_str will prevent this quoting.'''
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