discard support of DeepSig

oschwengers · Nov 11, 2024 · 97245fa · 97245fa
1 parent ac7e00f
commit 97245fa
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diff --git a/Dockerfile b/Dockerfile
@@ -17,7 +17,6 @@ RUN apk update && apk add wget tar bash \
     && cp /root/.bashrc /opt/conda/bashrc
 
 COPY environment.yml /tmp/
-RUN echo -e '\n  - deepsig>=1.2.5' >> /tmp/environment.yml
 
 SHELL ["bash", "-l" ,"-c"]
 

diff --git a/bakta/features/signal_peptides.py b/bakta/features/signal_peptides.py
diff --git a/bakta/json_io.py b/bakta/json_io.py
@@ -181,7 +181,6 @@ def main():
         fh_out.write(f"CDSs: {len(cdss)}\n")
         fh_out.write(f"pseudogenes: {len([cds for cds in cdss if 'pseudogene' in cds])}\n")
         fh_out.write(f"hypotheticals: {len([cds for cds in cdss if 'hypothetical' in cds])}\n")
-        fh_out.write(f"signal peptides: {len([cds for cds in cdss if bc.FEATURE_SIGNAL_PEPTIDE in cds])}\n")
         fh_out.write(f"sORFs: {len([feat for feat in features if feat['type'] == bc.FEATURE_SORF])}\n")
         fh_out.write(f"gaps: {len([feat for feat in features if feat['type'] == bc.FEATURE_GAP])}\n")
         fh_out.write(f"oriCs: {len([feat for feat in features if feat['type'] == bc.FEATURE_ORIC])}\n")

diff --git a/bakta/main.py b/bakta/main.py
@@ -25,7 +25,6 @@
 import bakta.features.crispr as crispr
 import bakta.features.orf as orf
 import bakta.features.cds as feat_cds
-import bakta.features.signal_peptides as sig_peptides
 import bakta.features.s_orf as s_orf
 import bakta.features.gaps as gaps
 import bakta.features.ori as ori
@@ -310,10 +309,6 @@ def main():
                 user_hmm_found = exp_aa_hmms.search(cdss, cfg.user_hmms)
                 print(f'\t\tuser HMM sequences: {len(user_hmm_found)}')
 
-            if(cfg.gram != bc.GRAM_UNKNOWN):
-                sig_peptides_found = sig_peptides.search(cdss, cds_aa_path)
-                print(f'\tsignal peptides: {len(sig_peptides_found)}')
-
             print('\tcombine annotations and mark hypotheticals...')
             log.debug('combine CDS annotations')
             for cds in cdss:
@@ -408,14 +403,6 @@ def main():
             anno.combine_annotation(feat)  # combine IPS and PSC annotations
         data['features'].extend(sorfs_filtered)
         print(f'\tfiltered sORFs: {len(sorfs_filtered)}')
-
-        if(cfg.gram != bc.GRAM_UNKNOWN  and  len(sorfs_filtered) > 0):
-            sorf_aa_path = cfg.tmp_path.joinpath('sorfs.faa')
-            with sorf_aa_path.open(mode='wt') as fh:
-                for sorf in sorfs_filtered:
-                    fh.write(f">{sorf['aa_hexdigest']}-{sorf['sequence']}-{sorf['start']}\n{sorf['aa']}\n")
-            sig_peptides_found = sig_peptides.search(sorfs_filtered, sorf_aa_path)
-            print(f"\tsignal peptides: {len(sig_peptides_found)}")
 
     ############################################################################
     # gap annotation
@@ -526,7 +513,6 @@ def main():
     print(f"\tCDSs: {len(cdss)}")
     print(f"\t\thypotheticals: {len([cds for cds in cdss if 'hypothetical' in cds])}")
     print(f"\t\tpseudogenes: {len([cds for cds in cdss if 'pseudogene' in cds])}")
-    print(f"\t\tsignal peptides: {len([cds for cds in cdss if bc.FEATURE_SIGNAL_PEPTIDE in cds])}")
     print(f"\tsORFs: {len([feat for feat in features if feat['type'] == bc.FEATURE_SORF])}")
     print(f"\tgaps: {len([feat for feat in features if feat['type'] == bc.FEATURE_GAP])}")
     print(f"\toriCs/oriVs: {len([feat for feat in features if (feat['type'] == bc.FEATURE_ORIC or feat['type'] == bc.FEATURE_ORIV)])}")
@@ -619,7 +605,6 @@ def main():
         fh_out.write(f"CDSs: {len(cdss)}\n")
         fh_out.write(f"pseudogenes: {len([cds for cds in cdss if 'pseudogene' in cds])}\n")
         fh_out.write(f"hypotheticals: {len([cds for cds in cdss if 'hypothetical' in cds])}\n")
-        fh_out.write(f"signal peptides: {len([cds for cds in cdss if bc.FEATURE_SIGNAL_PEPTIDE in cds])}\n")
         fh_out.write(f"sORFs: {len([feat for feat in features if feat['type'] == bc.FEATURE_SORF])}\n")
         fh_out.write(f"gaps: {len([feat for feat in features if feat['type'] == bc.FEATURE_GAP])}\n")
         fh_out.write(f"oriCs: {len([feat for feat in features if feat['type'] == bc.FEATURE_ORIC])}\n")

diff --git a/bakta/utils.py b/bakta/utils.py
@@ -45,7 +45,6 @@ def print_version(self):
 DEPENDENCY_PYRODIGAL = (Version(3, 5, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyrodigal', (sys.executable, '-c', 'import pyrodigal; print(pyrodigal.__version__)'), ['--skip-cds'])
 DEPENDENCY_PYHMMER = (Version(0, 10, 15), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Pyhmmer', (sys.executable, '-c', 'import pyhmmer; print(pyhmmer.__version__)'), ['--skip-cds', '--skip-sorf'])
 DEPENDENCY_DIAMOND = (Version(2, 1, 10), 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, 14, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'Blastn', ('blastn', '-version'), ['--skip-ori'])
 DEPENDENCY_AMRFINDERPLUS = (Version(4, 0, 3), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'AMRFinderPlus', ('amrfinder', '--version'), ['--skip-cds'])
 DEPENDENCY_PYCIRCLIZE = (Version(1, 7, 0), Version(VERSION_MAX_DIGIT, VERSION_MAX_DIGIT, VERSION_MAX_DIGIT), VERSION_REGEX, 'pyCirclize', (sys.executable, '-c', 'import pycirclize; print(pycirclize.__version__)'), ['--skip-plot'])
@@ -251,8 +250,6 @@ def test_dependencies():
     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_PYHMMER)
         test_dependency(DEPENDENCY_DIAMOND)
-        if(cfg.gram is not None and cfg.gram != '?'):
-            test_dependency(DEPENDENCY_DEEPSIG)
 
     if(cfg.skip_ori is not None and cfg.skip_ori is False):
         test_dependency(DEPENDENCY_BLASTN)

diff --git a/test/test_bakta.py b/test/test_bakta.py
@@ -11,18 +11,6 @@
 from .conftest import FILES, FILES_IO, SKIP_PARAMETERS
 
 
-def check_deepsig():
-    command = ('deepsig', '--version')
-    is_available = False
-    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
-        sp.check_output(command, stderr=sp.STDOUT)  # stderr must be added in case the tool output is not piped into stdout
-        is_available = True
-    except:
-        print(f"WARNING: {command[0]} not found or not executable! Skip dependen test.")
-    return is_available
-
-
 @pytest.mark.parametrize(
     'db',
     [
@@ -45,7 +33,6 @@ def test_bakta_mock_skipped_features(db, tmpdir):
         assert Path.exists(tmpdir_path.joinpath(file))
 
 
-@pytest.mark.skipif(check_deepsig() == False, reason=f'Skip on unavailable DeepSig')
 def test_bakta_plasmid(tmpdir):
     # full test on plasmid
     proc = run(

diff --git a/test/test_sig_peps.py b/test/test_sig_peps.py