1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
|
from pysam.csamtools import *
from pysam.ctabix import *
import pysam.csamtools as csamtools
import pysam.ctabix as ctabix
from pysam.cvcf import *
import pysam.cvcf as cvcf
import pysam.Pileup as Pileup
import sys
import os
class SamtoolsError( Exception ):
'''exception raised in case of an error incurred in the samtools library.'''
def __init__(self, value):
self.value = value
def __str__(self):
return repr(self.value)
class SamtoolsDispatcher(object):
'''samtools dispatcher.
Emulates the samtools command line as module calls.
Captures stdout and stderr.
Raises a :class:`pysam.SamtoolsError` exception in case
samtools exits with an error code other than 0.
Some command line options are associated with parsers.
For example, the samtools command "pileup -c" creates
a tab-separated table on standard output. In order to
associate parsers with options, an optional list of
parsers can be supplied. The list will be processed
in order checking for the presence of each option.
If no parser is given or no appropriate parser is found,
the stdout output of samtools commands will be returned.
'''
dispatch=None
parsers=None
def __init__(self,dispatch, parsers):
self.dispatch = dispatch
self.parsers = parsers
self.stderr = []
def __call__(self, *args, **kwargs):
'''execute a samtools command
'''
retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch, args )
if retval: raise SamtoolsError( 'csamtools returned with error %i: %s' % (retval, "\n".join( stderr ) ))
self.stderr = stderr
# samtools commands do not propagate the return code correctly.
# I have thus added this patch to throw if there is output on stderr.
# Note that there is sometimes output on stderr that is not an error,
# for example: [sam_header_read2] 2 sequences loaded.
# Ignore messages like these
stderr = [ x for x in stderr \
if not (x.startswith( "[sam_header_read2]" ) or \
x.startswith("[bam_index_load]") or \
x.startswith("[bam_sort_core]") or \
x.startswith("[samopen] SAM header is present") )
]
if stderr: raise SamtoolsError( "\n".join( stderr ) )
# call parser for stdout:
if not kwargs.get("raw") and stdout and self.parsers:
for options, parser in self.parsers:
for option in options:
if option not in args: break
else:
return parser(stdout)
return stdout
def getMessages( self ):
return self.stderr
def usage(self):
'''return the samtools usage information for this command'''
retval, stderr, stdout = csamtools._samtools_dispatch( self.dispatch )
return "".join(stderr)
#
# samtools command line options to export in python
#
# import is a python reserved word.
SAMTOOLS_DISPATCH = {
# samtools 'documented' commands
"view" : ( "view", None ),
"sort" : ( "sort", None),
"mpileup" : ( "mpileup", None),
"depth" : ("depth", None),
"faidx" : ("faidx", None),
"tview" : ("tview", None),
"index" : ("index", None),
"idxstats" : ("idxstats", None),
"fixmate" : ("fixmate", None),
"flagstat" : ("flagstat", None),
"calmd" : ("calmd", None),
"merge" : ("merge", None),
"rmdup" : ("rmdup", None),
"reheader" : ("reheader", None),
"cat" : ("cat", None),
"targetcut" : ("targetcut", None),
"phase" : ("phase", None),
# others
"samimport": ( "import", None),
"bam2fq" : ("bam2fq", None),
"pad2unpad" : ("pad2unpad", None),
"depad" : ("pad2unpad", None),
"bedcov" : ("bedcov", None),
"bamshuf" : ("bamshuf", None),
# obsolete
# "pileup" : ( "pileup", ( (("-c",), Pileup.iterate ), ), ),
}
# instantiate samtools commands as python functions
for key, options in SAMTOOLS_DISPATCH.items():
cmd, parser = options
globals()[key] = SamtoolsDispatcher(cmd, parser)
# hack to export all the symbols from csamtools
__all__ = \
csamtools.__all__ + \
ctabix.__all__ + \
cvcf.__all__ +\
[ "SamtoolsError", "SamtoolsDispatcher" ] + list(SAMTOOLS_DISPATCH) +\
["Pileup" ]
from pysam.version import __version__, __samtools_version__
###########################################################
# Utility functions for compilation
def get_include():
'''return a list of include directories.'''
dirname = os.path.abspath(os.path.join(os.path.dirname(__file__)))
return [ dirname,
os.path.join(dirname, 'include', 'samtools'),
os.path.join(dirname, 'include', 'tabix') ]
def get_defines():
'''return a list of defined compilation parameters.'''
return [('_FILE_OFFSET_BITS','64'), ('_USE_KNETFILE','')]
|
