def get_shrimp_2_version():
try:
text = subprocess.Popen(['gmapper-ls'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()[1]
except OSError:
raise Error("Couldn't run 'gmapper-ls'. SHRiMP 2 not installed?")
for line in text.split('\n'):
parts = line.strip().split()
if len(parts) >= 2 and parts[0] == 'SHRiMP':
return parts[1]
raise Error("gmapper-ls didn't output a version number as expected")
def require_shrimp_2():
version = get_shrimp_2_version()
version_parts = version.split('.')
major = int(version_parts[0])
minor = int(version_parts[1])
if major < 2 or (major == 2 and minor < 1):
raise Error("SHRiMP version 2.1 or higher required")
def require_sff2fastq():
try:
text = subprocess.Popen(['sff2fastq'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()[1]
except OSError:
raise Error("Couldn't run 'sff2fastq'. Not installed?")
def require_shrimp_1():
try:
text = subprocess.Popen(['rmapper-ls'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()[1]
except OSError:
raise Error("Couldn't run 'rmapper-ls'. SHRiMP 1 not installed?")
def get_numpy():
try:
import numpy
except ImportError:
try:
import numpypy as numpy
except ImportError:
raise Error('Neither numpy nor numpypy are available.')
return numpy
def get_option_value(args,
option,
conversion_function,
default,
log=None,
displayer='%s',
description=''):
""" Get a command line option """
args = args[:]
value = default
while True:
try:
location = args.index(option)
except ValueError: #Not found
break
if location == len(args) - 1:
raise Error('Option %s requires a paramter' % option)
try:
value = conversion_function(args[location + 1])
except Exception:
raise Error('Option for %s not in expected format' % option)
del args[location:location + 2]
if log:
if isinstance(displayer, str):
display = displayer % value
else:
display = displayer(value)
log.log('%18s %-8s - %s\n' %
(option, display, word_wrap(description, 49).replace(
'\n', '\n' + ' ' * 30)))
return value, args
def require_sff2fastq():
if not can_execute('sff2fastq'):
raise Error("Couldn't run 'sff2fastq'. Not installed?")
def require_samtools():
if not can_execute('samtools'):
raise Error("Couldn't run 'samtools'. Not installed?")
def require_shrimp_1():
if not can_execute('rmapper-ls'):
raise Error("Couldn't run 'rmapper-ls'. SHRiMP 1 not installed?")
def default_command(args):
if args:
raise Error('Don\'t know what to do with %s' % (' '.join(args)))
def expect_no_further_options(args):
for arg in args:
if arg.startswith('-'):
raise Error('Unexpected flag "%s"' % arg)