|
|
|
|
|
|
|
|
import os |
|
|
from os.path import join, abspath |
|
|
from subprocess import PIPE, Popen |
|
|
from pkg_resources import resource_filename |
|
|
from .aggrescan_3d import run as run_aggrescan_3d |
|
|
from . import logger |
|
|
import platform |
|
|
|
|
|
_name = "Analysis" |
|
|
if platform.system() == "Windows": |
|
|
_bin_name = "freesasa.exe" |
|
|
elif platform.system() == "Darwin": |
|
|
_bin_name = "freesasa_Darwin" |
|
|
else: |
|
|
_bin_name = "freesasa" |
|
|
|
|
|
|
|
|
def aggregation_analysis(config, target="input.pdb", working_dir=".", agg_work_dir=""): |
|
|
"""Takes Aggrescaan3D Job class config as an argument and should never change it""" |
|
|
os.chdir(working_dir) |
|
|
if config["naccess"]: |
|
|
_run_naccess(target=target, agg=agg_work_dir, naccess_dir=config["naccess"]) |
|
|
else: |
|
|
_run_free_sasa(target=target, agg=agg_work_dir) |
|
|
residues = _run_aggrescan(target=target, working_dir=working_dir, config=config) |
|
|
return residues |
|
|
|
|
|
|
|
|
def _run_aggrescan(target, working_dir, config): |
|
|
""" |
|
|
Takes target pdb file, working directory for analysis |
|
|
and aggrescan config dict as arguments so need the two in sync |
|
|
""" |
|
|
matrix_dir = resource_filename('aggrescan', join("data", "matrices", "aggrescan.mat")) |
|
|
residues = run_aggrescan_3d(target, matrix_dir, config["distance"], working_dir, naccess=config["naccess"], ph=config['ph']) |
|
|
|
|
|
return residues |
|
|
|
|
|
|
|
|
def _run_free_sasa(target="folded.pdb", agg=""): |
|
|
sasa_dir = resource_filename('aggrescan', join("data", "freesasa-2.0.1", "src", _bin_name)) |
|
|
sasa_cmd = [sasa_dir, "--resolution", "100", target, "--radii", "naccess", "--format", "pdb", "--format", "rsa"] |
|
|
logger.debug(module_name="freeSasa", msg="Starting freeSasa with %s" % " ".join(sasa_cmd)) |
|
|
_fname = join(agg, "ASA.error") |
|
|
out, err = Popen(sasa_cmd, stdout=PIPE, stderr=PIPE).communicate() |
|
|
if err: |
|
|
logger.to_file(_fname, content=err) |
|
|
try: |
|
|
err = err.decode() |
|
|
except (UnicodeDecodeError, AttributeError): |
|
|
pass |
|
|
for line in err.split("\n"): |
|
|
if "warning" in line: |
|
|
logger.critical(module_name="freeSasa", msg="Warning detected: %s" % line) |
|
|
logger.critical(module_name="freeSasa", msg="Attempting to continue.") |
|
|
else: |
|
|
raise logger.ASAError(program_name="freeSasa", filename=_fname) |
|
|
logger.to_file(filename="sasa.out", content=out, allow_err=False) |
|
|
|
|
|
|
|
|
def _run_naccess(target="folded.pdb", agg="", naccess_dir=""): |
|
|
naccess_cmd = [naccess_dir, target, "-p", "1.4", "-z", "0.05"] |
|
|
logger.debug(module_name=_name, msg="running naccess program with %s" % " ".join(naccess_cmd)) |
|
|
_fname = join(agg, "ASA.error") |
|
|
try: |
|
|
out, err = Popen(naccess_cmd, stdout=PIPE, stderr=PIPE).communicate() |
|
|
except OSError: |
|
|
raise logger.AggrescanError("Couldn't start the naccess program. Naccess requires csh shell to be present on the system." |
|
|
" If it is present please run the program in debug mode and see if the path printed in " |
|
|
"Naccess command actually contains the file.", module_name="Naccess") |
|
|
if err: |
|
|
logger.to_file(filename=_fname, content=err) |
|
|
raise logger.ASAError(program_name="Naccess", filename=_fname) |
|
|
try: |
|
|
for msg in out.split("\n"): |
|
|
if msg: |
|
|
logger.debug(module_name="Naccess", msg=msg) |
|
|
except AttributeError: |
|
|
pass |
|
|
|
|
|
|
