Initial commit

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.gitignore

@@ -0,0 +1,129 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

PyIsland/Drivers/__init__.py

@@ -0,0 +1,2 @@
+from . import mmseqs
+from . import hhsuite

PyIsland/Drivers/hhsuite.py

@@ -0,0 +1,118 @@
+from pathlib import Path
+import subprocess
+
+
+def update_hhsuite_db(old_db, new_db, datfile):
+    "removes entries from HHsuite DB"
+
+    # for file in Path('../data/interim/profiles/aln1/').glob('aln1HHdb*.ff*'):
+    #    print(file)
+
+    old_db_ffindex = Path(old_db).with_suffix(".ffindex")
+    old_db_ffdata = Path(old_db).with_suffix(".ffdata")
+
+    assert (
+        old_db_ffindex.is_file() and old_db_ffdata.is_file()
+    ), f"""
+    Cant find {old_db_ffindex} and/or {old_db_ffdata}
+    """
+
+    new_db_ffindex = Path(new_db).with_suffix(".ffindex")
+    new_db_ffdata = Path(new_db).with_suffix(".ffdata")
+
+    # make a copy of the oldDB
+    shutil.copyfile(old_db_ffindex, new_db_ffindex)
+    shutil.copyfile(old_db_ffdata, new_db_ffdata)
+
+    # remove entries
+    subprocess.run(
+        f"ffindex_modify -s -u -f {datfile} {new_db_ffindex}", shell=True, check=True
+    )
+
+    # check
+    total_ids = 0
+    with open(old_db_ffindex) as infile:
+        for line in infile:
+            total_ids += 1
+
+    num_ids_to_remove = 0
+    with open(datfile) as infile:
+        for line in infile:
+            num_ids_to_remove += 1
+
+    remaining_ids = 0
+    with open(new_db_ffindex) as infile:
+        for line in infile:
+            remaining_ids += 1
+
+    assert (
+        total_ids - num_ids_to_remove == remaining_ids
+    ), f"""
+    There are {total_ids} in the HHsuite DB, and you asked to remove {num_ids_to_remove},
+    leaving {total_ids - num_ids_to_remove} IDs in the new HHSuite DB.
+    However, there are {remaining_ids} in the new DB, so something is off.
+    Did you check the ID extension in the datfile? 
+    It should probably end in .a3m or .hhm
+    """
+
+
+def get_hhsuite_neff(msa):
+    p1 = subprocess.run(
+        f"hhalign -i {msa} -o /dev/null -diff inf -id 100 -cpu 12",
+        shell=True,
+        capture_output=True,
+        text=True,
+    )
+
+    neff = float(p1.stdout.strip().split()[10])
+    return round(neff, 2)
+
+def align_clusters_with_hhalign(input_dir, output_dir, df_clustering):
+    """
+    accepts a table of profile, length and cluster assignment
+    runs hhalign of the longest query versus all templates in the cluster
+    singletons are converted to a3m
+    """
+    input_dir = Path(input_dir)
+    assert input_dir.is_dir(), f"{input_dir} isnt a directory!"
+
+    output_dir = Path(output_dir)
+    if not output_dir.is_dir():
+        output_dir.mkdir(parents=True)
+
+    # df = pd.read_csv(clustering_table)
+    grouped = df_clustering.groupby("cluster")
+
+    # make a
+
+    for name, group in grouped:
+        output_a3m = output_dir / Path(f"cls_{name}").with_suffix(".a3m")
+
+        # sort by profile length≈
+        profiles = group.sort_values(by="qlen", ascending=False).qseq.tolist()
+
+        # get the first, longest profile
+        query_profile = input_dir / Path(f"{profiles[0]}.afa")
+
+        # for singletons, just convert to a3m
+        if len(group) < 2:
+            subprocess.run(
+                f"reformat.pl fas a3m {query_profile} {output_a3m}",
+                shell=True,
+                check=True,
+            )
+        else:
+            # make a string of all the remaining profiles to pass to hhalign
+            templates = ""
+            for profile in profiles[1:]:
+                subject = input_dir / Path(f"{profile}.afa")
+
+                assert subject.is_file(), f"cant find {subject}"
+                templates = templates + f"-t {subject} "
+
+            # run hhalign
+            subprocess.run(
+                f"hhalign -i {query_profile} {templates} -M 50 -glob -id 100 -diff inf -oa3m {output_a3m}",
+                shell=True,
+                check=True,
+            )