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tweak depdendency checks finding Pyrodigal & Pyhmmer versions #219
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@oschwengers
oschwengers committed Aug 11, 2023
1 parent f777614 commit 17bcfc9
Showing 1 changed file with 28 additions and 26 deletions.
54 changes: 28 additions & 26 deletions bakta/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,17 +38,17 @@ def print_version(self):
VERSION_REGEX = re.compile(r'(\d+)\.(\d+)(?:[\.-](\d+))?') # regex to search for version number in tool output. Takes missing patch version into consideration.

# List of dependencies: tuples for: min version, max version, tool name & command line parameter, dependency check exclusion options
DEPENDENCY_TRNASCAN = (Version(2, 0, 11), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('tRNAscan-SE', '-h'), ['--skip-trna'])
DEPENDENCY_ARAGORN = (Version(1, 2, 41), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('aragorn', '-h'), ['skip-tmrna'])
DEPENDENCY_CMSCAN = (Version(1, 1, 4), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('cmscan', '-h'), ['--skip-rrna', '--skip-ncrna', '--skip-ncrna-region'])
DEPENDENCY_PILERCR = (Version(1, 6), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('pilercr', '-options'), ['--skip-crispr'])
DEPENDENCY_PYRODIGAL = (Version(2, 1, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('pyrodigal', '--version'), ['--skip-cds'])
DEPENDENCY_HMMSEARCH = (Version(3, 3, 2), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('hmmsearch', '-h'), ['--skip-cds', '--skip-sorf'])
DEPENDENCY_DIAMOND = (Version(2, 0, 14), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('diamond', 'help'), ['--skip-cds', '--skip-sorf'])
DEPENDENCY_DEEPSIG = (Version(1, 2, 5), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('deepsig', '--version'), ['--gram ?'])
DEPENDENCY_BLASTN = (Version(2, 12, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('blastn', '-version'), ['--skip-ori'])
DEPENDENCY_AMRFINDERPLUS = (Version(3, 11, 2), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('amrfinder', '--version'), ['--skip-cds'])
DEPENDENCY_CIRCOS = (Version(0, 69, 8), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, ('circos', '--version'), ['--skip-plot'])
DEPENDENCY_TRNASCAN = (Version(2, 0, 11), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'tRNAscan-SE', ('tRNAscan-SE', '-h'), ['--skip-trna'])
DEPENDENCY_ARAGORN = (Version(1, 2, 41), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Aragorn', ('aragorn', '-h'), ['skip-tmrna'])
DEPENDENCY_CMSCAN = (Version(1, 1, 4), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'CMscan', ('cmscan', '-h'), ['--skip-rrna', '--skip-ncrna', '--skip-ncrna-region'])
DEPENDENCY_PILERCR = (Version(1, 6), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'PilerCR', ('pilercr', '-options'), ['--skip-crispr'])
DEPENDENCY_PYRODIGAL = (Version(2, 1, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', ('python', '-c', 'import pyrodigal; print(pyrodigal.__version__)'), ['--skip-cds'])
DEPENDENCY_PYHMMER = (Version(0, 8, 1), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyhmmer', ('python', '-c', 'import pyhmmer; print(pyhmmer.__version__)'), ['--skip-cds', '--skip-sorf'])
DEPENDENCY_DIAMOND = (Version(2, 0, 14), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Diamond', ('diamond', 'help'), ['--skip-cds', '--skip-sorf'])
DEPENDENCY_DEEPSIG = (Version(1, 2, 5), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'DeepSig', ('deepsig', '--version'), ['--gram ?'])
DEPENDENCY_BLASTN = (Version(2, 12, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Blastn', ('blastn', '-version'), ['--skip-ori'])
DEPENDENCY_AMRFINDERPLUS = (Version(3, 11, 2), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'AMRFinderPlus', ('amrfinder', '--version'), ['--skip-cds'])
DEPENDENCY_CIRCOS = (Version(0, 69, 8), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Circos', ('circos', '--version'), ['--skip-plot'])


def init_parser(sub_command: str=''):
Expand Down Expand Up @@ -141,27 +141,29 @@ def cleanup(log, tmp_path: Path):
def read_tool_output(dependency):
"""Method for reading tool version with regex. Input: regex expression, tool command. Retursn: version number."""
version_regex = dependency[2]
command = dependency[3]
skip_options = dependency[4]
tool = dependency[3]
command = dependency[4]
skip_options = dependency[5]
try:
tool_output = str(sp.check_output(command, stderr=sp.STDOUT)) # stderr must be added in case the tool output is not piped into stdout
log.debug('tool output: tool=%s, output=%s', tool, tool_output)
except FileNotFoundError:
log.error('dependency not found! tool=%s', command[0])
sys.exit(f"ERROR: {command[0]} not found or not executable! Please make sure {command[0]} is installed and executable or skip requiring workflow steps via via '{' '.join(skip_options)}'.")
log.error('dependency not found! tool=%s', tool)
sys.exit(f"ERROR: {tool} not found or not executable! Please make sure {tool} is installed and executable or skip requiring workflow steps via via '{' '.join(skip_options)}'.")
except sp.CalledProcessError:
log.error('dependency check failed! tool=%s', command[0])
sys.exit(f"ERROR: {command[0]} could not be executed! Please make sure {command[0]} is installed and executable or skip requiring workflow steps via via '{' '.join(skip_options)}'.")
log.error('dependency check failed! tool=%s', tool)
sys.exit(f"ERROR: {tool} could not be executed! Please make sure {tool} is installed and executable or skip requiring workflow steps via via '{' '.join(skip_options)}'.")
version_match = version_regex.search(tool_output)
try:
if version_match is None:
log.error('no dependency version detected! no regex hit in dependency output: regex=%s, command=%s', version_regex, command)
sys.exit('ERROR: Could not detect/read %s version!', command[0])
log.error('no dependency version detected! No regex hit in dependency output: regex=%s, command=%s', version_regex, command)
sys.exit(f'ERROR: Could not detect/read {tool} version! No regex hit in dependency output.')
major = version_match.group(1)
minor = version_match.group(2)
patch = version_match.group(3)
if major is None:
log.error('no dependency version detected! no regex hit in dependency output: regex=%s, command=%s', version_regex, command)
sys.exit('ERROR: Could not detect/read %s version!', command[0])
log.error('no dependency version detected! Major hit is None in dependency output: regex=%s, command=%s', version_regex, command)
sys.exit(f'ERROR: Could not detect/read {tool} version! Major hit is None in dependency output.')
elif minor is None:
version_output = Version(int(major))
elif patch is None:
Expand All @@ -170,8 +172,8 @@ def read_tool_output(dependency):
version_output = Version(int(major), int(minor), int(patch))
return version_output
except:
log.error('no dependency version detected! no regex hit in dependency output: regex=%s, command=%s', version_regex, command)
sys.exit('ERROR: Could not detect/read %s version!', command[0])
log.error('no dependency version detected! Error while reading dependency output: regex=%s, command=%s', version_regex, command)
sys.exit(f'ERROR: Could not detect/read {tool} version! Error while reading dependency output.')


def check_version(tool, min: int, max:int ) -> bool:
Expand Down Expand Up @@ -202,12 +204,12 @@ def test_dependency(dependency):
"""Test the proper installation of the required 3rd party executable."""
version = read_tool_output(dependency)
check_result = check_version(version, dependency[0], dependency[1])
tool_name = dependency[3][0]
tool_name = dependency[3]
if (not check_result):
log.error('wrong dependency version for %s: installed=%s, minimum=%s', tool_name, version, dependency[0])
sys.exit(f'ERROR: Wrong {tool_name} version installed. Please, either install {tool_name} version {dependency[0]} or use {dependency[4]}!')
else:
tool_path = shutil.which(tool_name)
tool_path = shutil.which(dependency[4][0])
log.info('dependency: tool=%s, version=%s, path=%s', tool_name, version, tool_path)


Expand Down Expand Up @@ -243,7 +245,7 @@ def test_dependencies():
sys.exit(f"ERROR: AMRFinderPlus database not installed! Please, install AMRFinderPlus's internal database by executing: 'amrfinder_update --database {amrfinderplus_db_path}'. This must be done only once.")

if((cfg.skip_cds is not None and cfg.skip_cds is False) or (cfg.skip_sorf is not None and cfg.skip_sorf is False)):
test_dependency(DEPENDENCY_HMMSEARCH)
test_dependency(DEPENDENCY_PYHMMER)
test_dependency(DEPENDENCY_DIAMOND)
if(cfg.gram is not None and cfg.gram != '?'):
test_dependency(DEPENDENCY_DEEPSIG)
Expand Down

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