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+++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "pygenomeviz" -version = "0.4.3" +version = "0.4.4" description = "A genome visualization python package for comparative genomics" authors = ["moshi4"] license = "MIT" diff --git a/src/pygenomeviz/__init__.py b/src/pygenomeviz/__init__.py index 7c1efe6..2497956 100644 --- a/src/pygenomeviz/__init__.py +++ b/src/pygenomeviz/__init__.py @@ -8,7 +8,7 @@ warnings.filterwarnings("ignore") -__version__ = "0.4.3" +__version__ = "0.4.4" __all__ = [ "GenomeViz", diff --git a/src/pygenomeviz/align.py b/src/pygenomeviz/align.py index dff36cc..96629ac 100644 --- a/src/pygenomeviz/align.py +++ b/src/pygenomeviz/align.py @@ -200,7 +200,7 @@ def _run_mummer(self, fa_file1: Path, fa_file2: Path, idx: int) -> list[AlignCoo # Run genome alignment using nucmer or promer prefix = self.outdir / f"out{idx}" delta_file = prefix.with_suffix(".delta") - cmd = f"{self._align_binary} --mum {fa_file1} {fa_file2} --prefix={prefix}" + cmd = f"{self._align_binary} --mum '{fa_file1}' '{fa_file2}' --prefix={prefix}" _ = sp.run(cmd, shell=True, capture_output=True, text=True) # Run delta-filter to map 'one-to-one' or 'many-to-many' relation @@ -341,16 +341,14 @@ def run(self) -> list[AlignCoord]: with tempfile.TemporaryDirectory() as tmpdir: name1 = fa_file1.with_suffix("").name name2 = fa_file2.with_suffix("").name - rbh_result_file = self.outdir / f"{idx+1:02d}_{name1}-{name2}_rbh.tsv" - cmd = f"mmseqs easy-rbh {fa_file1} {fa_file2} {rbh_result_file} " + rbh_file = self.outdir / f"{idx+1:02d}_{name1}-{name2}_rbh.tsv" + cmd = f"mmseqs easy-rbh '{fa_file1}' '{fa_file2}' '{rbh_file}' " cmd += f"{tmpdir} --threads {self.process_num} -e {self.evalue} -v 0" if not self.quiet: print(f"# {idx+1:02d}: {name1}-{name2} RBH search\n$ {cmd}\n") - sp.run(cmd, shell=True) + _ = sp.run(cmd, shell=True, capture_output=True, text=True) - align_coords.extend( - self.parse_rbh_result(rbh_result_file, name1, name2) - ) + align_coords.extend(self.parse_rbh_result(rbh_file, name1, name2)) return align_coords @@ -519,7 +517,7 @@ def parse_pmauve_file(self, bbone_file: str | Path) -> list[AlignCoord]: continue rows.append(row) # Sort by reference seq coordinates - rows = sorted(rows, key=lambda row: row[ref_idx]) + rows = sorted(rows, key=lambda row: row[ref_idx]) # type: ignore align_coords = [] for row in rows: diff --git a/src/pygenomeviz/gui/utils.py b/src/pygenomeviz/gui/utils.py index 81b6631..d166e26 100644 --- a/src/pygenomeviz/gui/utils.py +++ b/src/pygenomeviz/gui/utils.py @@ -31,9 +31,15 @@ def load_gbk_file(gbk_file: str | Path | UploadedFile) -> Genbank: return Genbank(gbk_file) else: filename = Path(gbk_file.name).stem + trans_dict = { + " ": "_", + "|": "_", + "(": "[", + ")": "]", + } return Genbank( StringIO(gbk_file.getvalue().decode("utf-8")), - name=filename.replace(" ", "_").replace("|", "_"), + name=filename.translate(str.maketrans(trans_dict)), ) diff --git a/src/pygenomeviz/track.py b/src/pygenomeviz/track.py index 48d8083..5103d92 100644 --- a/src/pygenomeviz/track.py +++ b/src/pygenomeviz/track.py @@ -499,6 +499,103 @@ def add_exon_feature( ) ) + def add_features( + self, + features: list[SeqFeature], + label_type: str | None = None, + label_handle_func: Callable[[str], str] | None = None, + labelsize: int = 15, + labelcolor: str = "black", + plotstyle: LiteralTypes.PLOTSTYLE = "bigarrow", + facecolor: str = "orange", + edgecolor: str = "black", + linewidth: float = 0, + labelrotation: int = 45, + labelvpos: LiteralTypes.LABELVPOS = "strand", + labelhpos: LiteralTypes.LABELHPOS = "center", + labelha: LiteralTypes.LABELHA = "left", + arrow_shaft_ratio: float = 0.5, + size_ratio: float = 1.0, + patch_kws: dict[str, Any] | None = None, + ) -> None: + """Add features (BioPython's SeqFeature list) + + Parameters + ---------- + features : str, optional + BioPython's SeqFeature list + label_type : str | None, optional + Label type (e.g. `gene`,`protein_id`,`product`,etc...) + label_handle_func : Callable[[str], str] | None, optional + User defined function to handle label. + Useful for filtering out unnecesary labels such as `hypothetical ~~~`, + omitting labels with long characters, etc. + labelsize : int, optional + Feature label size + labelcolor : str, optional + Feature label color + plotstyle : str, optional + Feature plot style (`bigarrow`|`arrow`|`bigbox`|`box`|`bigrbox`|`rbox`) + facecolor : str, optional + Feature facecolor. + If Genbank qualifiers has facecolor key (e.g. `/facecolor="red"`), + facecolor key value is applied preferentially. + edgecolor : str, optional + Feature edgecolor + linewidth : float, optional + Feature edge linewidth + labelrotation : int, optional + Feature label rotation + labelvpos : str, optional + Feature label vertical position (`top`|`center`|`bottom`|`strand`) + If 'strand' is set, 'top' or 'bottom' is auto selected by strand. + labelhpos : str, optional + Feature label horizontal position (`left`|`center`|`right`) + labelha : str, optional + Feature label horizontal alignment (`left`|`center`|`right`) + arrow_shaft_ratio : float, optional + Feature arrow shaft ratio + size_ratio : float, optional + Feature size ratio to track + patch_kws : dict[str, Any] | None, optional + Patch properties (e.g. `dict(fc="red", ec="black", lw=0.5, ...)`) + + """ + for feature in features: + # Check if start & end positions are within appropriate track range + start = int(str(feature.location.start)) + end = int(str(feature.location.end)) + self._within_valid_range(start, end, raise_error_on_false=True) + + # Get label value & apply handle func if exists + label = feature.qualifiers.get(label_type, [""])[0] + if label_handle_func is not None: + label = label_handle_func(label) + feat_fc = feature.qualifiers.get("facecolor", [facecolor])[0] + + self.features.append( + Feature( + start, + end, + feature.strand, + label, + labelsize, + labelcolor, + plotstyle, + feat_fc, + edgecolor, + linewidth, + labelrotation, + labelvpos, + labelhpos, + labelha, + arrow_shaft_ratio, + size_ratio, + patch_kws, + feature, + ) + ) + def add_genbank_features( self, gbk: Genbank, diff --git a/tests/test_genomeviz.py b/tests/test_genomeviz.py index 920c6c4..fa4d303 100644 --- a/tests/test_genomeviz.py +++ b/tests/test_genomeviz.py @@ -200,6 +200,19 @@ def test_add_exon_feature(tmp_path: Path): assert fig_outfile.exists() +def test_add_features(gbk_file: Path, tmp_path: Path): + """Test add features (BioPython's SeqFeature list)""" + gbk = Genbank(gbk_file) + + gv = GenomeViz() + track = gv.add_feature_track(gbk.name, gbk.range_size) + track.add_features(gbk.extract_features()) + + fig_outfile = tmp_path / "result.png" + gv.savefig(fig_outfile) + assert fig_outfile.exists() + + def test_gff_genomeviz(gff_file: Path, tmp_path: Path): """Test add_gff_features""" gff = Gff(gff_file)