def get_pmc_list(path):
"""Retrieves the PMC id list and unzips it to the specified path"""
with pushd(path):
cmd = shlex.split(
'wget ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz')
check_call(cmd)
cmd = shlex.split('gzip -d PMC-ids.csv.gz')
check_call(cmd)
def get_pmc_list(path):
"""Retrieves the PMC id list and unzips it to the specified path"""
with pushd(path):
cmd = shlex.split('wget ftp://ftp.ncbi.nlm.nih.gov/pub/pmc/PMC-ids.csv.gz')
check_call(cmd)
cmd = shlex.split('gzip -d PMC-ids.csv.gz')
check_call(cmd)
def get_uniprot_mapping(path):
"""Retrieves the PMC id list and unzips it to the specified path"""
with pushd(path):
cmd = shlex.split('wget -N ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/idmapping.dat.gz')
check_call(cmd)
cmd = shlex.split('gzip -d idmapping.dat.gz')
check_call(cmd)
cmd = shlex.split('wget -N ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz')
check_call(cmd)
cmd = shlex.split('gzip -d gene_info.gz')
check_call(cmd)
touch('idmapping.dat')
touch('gene_info')
def run_phylip(direc, progtype, input_args = ['y'], capture_output = False,
clean_direc = True):
"""Runs the phylip suite of programs"""
with pushd(direc):
with open('input', 'w') as handle:
handle.write('\n'.join(input_args+['']))
inbuf = open('input')
if progtype == 'proml':
check_files = ('infile', input_args[0])
rmfiles = ('outfile', 'outtree')
cmd = 'phylip proml'
elif progtype == 'consense':
check_files = ('intree', input_args[0])
rmfiles = ('outfile', 'outtree')
cmd = 'phylip consense'
else:
raise TypeError, 'Unrecognized phylip program: %s' % progtype
if clean_direc:
for f in rmfiles:
try:
os.remove(f)
except OSError:
pass
if not any([os.path.exists(x) for x in check_files]):
raise OSError, 'Could not find any input files!'
if capture_output:
out = open('screenout', 'w')
else:
out = open(os.devnull, 'w')
args = shlex.split(cmd)
call(args, stdin = inbuf, stdout = out)
