def iterate( infile ):
'''iterate over ``samtools pileup -c`` formatted file.
*infile* can be any iterator over a lines.
The function yields named tuples of the type :class:`pysam.Pileup.PileupSubstitution`
or :class:`pysam.Pileup.PileupIndel`.
.. note::
The parser converts to 0-based coordinates
'''
conv_subst = (str,lambda x: int(x)-1,str,str,int,int,int,int,str,str)
conv_indel = (str,lambda x: int(x)-1,str,str,int,int,int,int,str,str,int,int,int)
for line in infile:
d = line[:-1].split()
if d[2] == "*":
try:
yield PileupIndel( *[x(y) for x,y in zip(conv_indel,d) ] )
except TypeError:
raise pysam.SamtoolsError( "parsing error in line: `%s`" % line)
else:
try:
yield PileupSubstitution( *[x(y) for x,y in zip(conv_subst,d) ] )
except TypeError:
raise pysam.SamtoolsError( "parsing error in line: `%s`" % line)
def setUp(self):
'''setup tests.
For setup, all commands will be run before the first test is
executed. Individual tests will then just compare the output
files.
'''
if BinaryTest.first_time:
# remove previous files
if os.path.exists(WORKDIR):
shutil.rmtree(WORKDIR)
pass
# copy the source files to WORKDIR
os.makedirs(WORKDIR)
for f in ("ex1.fa", "ex1.sam.gz", "ex1.sam", "ex2.bam", "ex1.bed"):
shutil.copy(os.path.join(DATADIR, f), os.path.join(WORKDIR, f))
# cd to workdir
savedir = os.getcwd()
os.chdir(WORKDIR)
for label in self.order:
sys.stdout.write("preparing test {}".format(label))
command = self.commands[label]
# build samtools command and target and run
samtools_target, samtools_command = command[0]
runSamtools(" ".join((SAMTOOLS, samtools_command)))
sys.stdout.write(" samtools ok")
# get pysam command and run
try:
pysam_target, pysam_command = command[1]
except ValueError as msg:
raise ValueError("error while setting up %s=%s: %s" %
(label, command, msg))
pysam_method, pysam_options = pysam_command
try:
output = pysam_method(*pysam_options.split(" "),
raw=True,
catch_stdout=True)
except pysam.SamtoolsError as msg:
raise pysam.SamtoolsError(
"error while executing %s: options=%s: msg=%s" %
(label, pysam_options, msg))
sys.stdout.write(" pysam ok\n")
if ">" in samtools_command:
with open(pysam_target, "wb") as outfile:
if type(output) == list:
if IS_PYTHON3:
for line in output:
outfile.write(line.encode('ascii'))
else:
for line in output:
outfile.write(line)
else:
outfile.write(output)
os.chdir(savedir)
BinaryTest.first_time = False
samtools_version = getSamtoolsVersion()
def _r(s):
# patch - remove any of the alpha/beta suffixes, i.e., 0.1.12a ->
# 0.1.12
if s.count('-') > 0:
s = s[0:s.find('-')]
return re.sub("[^0-9.]", "", s)
if _r(samtools_version) != _r(pysam.__samtools_version__):
raise ValueError(
"versions of pysam/samtools and samtools differ: %s != %s" %
(pysam.__samtools_version__, samtools_version))