def get_params():
from helpers import log_stderr
"""
Gets the params dictionary that hold all the configuration
information of the program. This is loaded from 'inmembrane.config'
which should be found in the same place as the main binary.
If 'inmembrane.config' is not a found, a default 'inmembrane.config'
is generated from 'default_params_str'. The config file should
be edited if the binaries are not available on the path, or have
different names.
"""
config = os.path.join(os.getcwd(), 'inmembrane.config')
if not os.path.isfile(config):
log_stderr("# Couldn't find inmembrane.config file")
log_stderr("# So, will generate a default config " + config)
abs_hmm_profiles = os.path.join(module_dir, 'hmm_profiles')
fh = open(config, 'w')
fh.write(default_params_str)
fh.close()
else:
log_stderr("# Loading existing inmembrane.config")
params = eval(open(config).read())
return params
def get_params():
from helpers import log_stderr
"""
Gets the params dictionary that hold all the configuration
information of the program. This is loaded from 'inmembrane.config'
which should be found in the same place as the main binary.
If 'inmembrane.config' is not a found, a default 'inmembrane.config'
is generated from 'default_params_str'. The config file should
be edited if the binaries are not available on the path, or have
different names.
"""
config = os.path.join(os.getcwd(), 'inmembrane.config')
if not os.path.isfile(config):
log_stderr("# Couldn't find inmembrane.config file")
log_stderr("# So, will generate a default config " + config)
abs_hmm_profiles = os.path.join(module_dir, 'hmm_profiles')
fh = open(config, 'w')
fh.write(default_params_str)
fh.close()
else:
log_stderr("# Loading existing inmembrane.config")
params = eval(open(config).read())
return params
def process(params):
"""
Main program loop. Triggers the 'protocol' found in the params
to annotate all proteins give the list of annotations needed by
'protocol'. Then outputs to screen and a .csv file.
"""
from helpers import dict_get, create_proteins_dict, log_stdout, log_stderr
# will load all plugins in the plugins/ directory
from inmembrane.plugins import *
# initializations
exec(import_protocol_python(params))
init_output_dir(params)
seqids, proteins = create_proteins_dict(params['fasta'])
# TODO: ideally this loop needs to be run within the protocol,
# since for some protocols not all plugins
# will be run for every sequence, conditional
# on the outcome of a previous analysis
# eg. protocol.run(params, proteins)
# annotates with external binaries as found in plugins
for plugin_str in protocol.get_annotations(params):
plugin = eval(plugin_str)
plugin.annotate(params, proteins)
# do protocol analysis on the results of the annotations
for seqid in seqids:
protein = proteins[seqid]
protocol.post_process_protein(params, protein)
log_stdout(protocol.protein_output_line(seqid, proteins))
# print a summary table of classifications to stderr
log_stderr(protocol.summary_table(params, proteins))
# always write to biologist-friendly csv file
f = open(params['csv'], 'w')
for seqid in seqids:
f.write(protocol.protein_csv_line(seqid, proteins))
f.close()
log_stderr("\n")
log_stderr("Output written to %s" % (params['csv']))
# TODO: citations for specific HMMs (PFAM etc ?)
# write citations to a file and gracefully deal with plugins
# without a citation defined
import codecs
import textwrap
f = codecs.open(params['citations'], mode='w', encoding='utf-8')
programs_used = []
for program in protocol.get_annotations(params):
plugin = eval(program)
try:
f.write(plugin.citation['name']+":\n")
f.write(textwrap.fill(plugin.citation['ref']))
except AttributeError:
f.write("%s - no citation provided." % program)
f.write("\n\n")
try:
programs_used.append(plugin.citation['name'])
except (AttributeError, KeyError):
programs_used.append(program)
f.close()
log_stderr("\n")
log_stderr("This run used %s." % (", ".join(programs_used)) )
log_stderr("References have been written to %s \n"
"# - please cite as appropriate." %
(params['citations']) )
return proteins
def process(params):
"""
Main program loop. Triggers the 'protocol' found in the params
to annotate all proteins give the list of annotations needed by
'protocol'. Then outputs to screen and a .csv file.
"""
from helpers import dict_get, create_proteins_dict, log_stdout, log_stderr
# will load all plugins in the plugins/ directory
from inmembrane.plugins import *
# initializations
exec(import_protocol_python(params))
init_output_dir(params)
seqids, proteins = create_proteins_dict(params['fasta'])
# TODO: ideally this loop needs to be run within the protocol,
# since for some protocols not all plugins
# will be run for every sequence, conditional
# on the outcome of a previous analysis
# eg. protocol.run(params, proteins)
# annotates with external binaries as found in plugins
for plugin_str in protocol.get_annotations(params):
plugin = eval(plugin_str)
plugin.annotate(params, proteins)
# do protocol analysis on the results of the annotations
for seqid in seqids:
protein = proteins[seqid]
protocol.post_process_protein(params, protein)
log_stdout(protocol.protein_output_line(seqid, proteins))
# print a summary table of classifications to stderr
log_stderr(protocol.summary_table(params, proteins))
# always write to biologist-friendly csv file
f = open(params['csv'], 'w')
for seqid in seqids:
f.write(protocol.protein_csv_line(seqid, proteins))
f.close()
log_stderr("\n")
log_stderr("Output written to %s" % (params['csv']))
# TODO: citations for specific HMMs (PFAM etc ?)
# write citations to a file and gracefully deal with plugins
# without a citation defined
import codecs
import textwrap
f = codecs.open(params['citations'], mode='w', encoding='utf-8')
programs_used = []
for program in protocol.get_annotations(params):
plugin = eval(program)
try:
f.write(plugin.citation['name'] + ":\n")
f.write(textwrap.fill(plugin.citation['ref']))
except AttributeError:
f.write("%s - no citation provided." % program)
f.write("\n\n")
try:
programs_used.append(plugin.citation['name'])
except (AttributeError, KeyError):
programs_used.append(program)
f.close()
log_stderr("\n")
log_stderr("This run used %s." % (", ".join(programs_used)))
log_stderr("References have been written to %s \n"
"# - please cite as appropriate." % (params['citations']))
return proteins
