FunVIP 0.3.20__py3-none-any.whl

src/command.py

@@ -0,0 +1,360 @@
+# FunVIP_dev/FunVIP/src/command.py
+
+import argparse
+from importlib.metadata import version
+
+
+class CommandParser:
+    def __init__(self) -> None:
+        self.parser = argparse.ArgumentParser(
+            description="Fungal Validation & Identification Pipeline", prog="FunVIP"
+        )
+
+    def get_args(self) -> argparse.Namespace:
+        # Mandatory options
+        group_required = self.parser.add_argument_group(
+            title="required", description="Main options"
+        )
+        group_required.add_argument(
+            "--query",
+            "-q",
+            nargs="*",
+            help="Query fasta or table files, delimitated by space",
+            type=str,
+        )
+        group_required.add_argument(
+            "--db",
+            "-d",
+            nargs="+",
+            help="Database table files, delimitated by space",
+            type=str,
+        )
+        group_required.add_argument(
+            "--gene", "-g", nargs="*", help="Gene names to be analyzed", type=str
+        )
+
+        # Mandatory when NCBI download - raise Exception when manage input
+        group_ncbi = self.parser.add_mutually_exclusive_group(required=False)
+        group_ncbi.add_argument(
+            "--email",
+            "-e",
+            help="E-mail notation to download data from GenBank",
+            type=str,
+        )
+        group_ncbi.add_argument(
+            "--api",
+            "-a",
+            help="NCBI API strings to download data from GenBank",
+            type=str,
+        )
+
+        # Test settings
+        group_test = self.parser.add_argument_group(
+            title="test", description="Test run setups"
+        )
+        group_test.add_argument(
+            "--test",
+            help="Use test dataset, [Penicillium]",
+            type=str,
+        )
+
+        # Running options
+        group_run = self.parser.add_argument_group(
+            title="run", description="Running options"
+        )
+        group_run.add_argument(
+            "--thread",
+            "-t",
+            help="Threads to be used for pipeline, default : system maximum",
+            type=int,
+        )
+        group_run.add_argument(
+            "--memory",
+            "-m",
+            help="Max memory limit in 'nG' form, ex: '16G', should be more than 4G, default : system maximum",
+            type=str,
+        )
+        group_run.add_argument(
+            "--outdir", help="Out file location, default : current directory", type=str
+        )
+        group_run.add_argument(
+            "--runname",
+            help="Name prefix to current run : default : current timestamp",
+            type=str,
+        )
+        group_run.add_argument(
+            "--mode",
+            help="Mode setup in species identification, see documents for detailed explanations, [validation, identification] default : validation",
+            type=str,
+        )
+        group_run.add_argument(
+            "--continue",
+            dest="continue_from_previous",
+            action="store_true",
+            help="Continue from previous run",
+        )
+        group_run.add_argument(
+            "--step",
+            help="[WIP] Steps to continue from previous run, will be ignored if invalid --continue option [setup, search, cluster, align, trim, concatenate, modeltest, tree, visualize, report]",
+            type=str,
+        )
+        group_run.add_argument(
+            "--level",
+            help="Taxonomic level for each phylogenetic tree. Should be one of [subseries, series, subsection, section, subtribe, tribe, subfamily, family, suborder, order, subclass, class, subphylum, phylum, subdivision, division, subkingdom, kingdom]",
+            type=str,
+        )
+        group_run.add_argument(
+            "--all",
+            action="store_true",
+            help="Run FunVIP for all database sequences, regardless of corrresponding sequences exists in query, default : False",
+        )
+        group_run.add_argument(
+            "--confident",
+            help="Skip blast analysis among database sequences, use it when your database sequences contains large number of misidentified sequences, default : False",
+        )
+
+        # Method options
+        group_method = self.parser.add_argument_group(
+            title="method", description="Methods for each step of pipeline"
+        )
+        group_method.add_argument(
+            "--search",
+            help="Search methods to be used in selecting genes, groups and outgroups, [blast, mmseqs], default : mmseqs",
+            type=str,
+        )
+        group_method.add_argument(
+            "--alignment",
+            help="Multiple sequence alignment methods, [mafft], default : mafft",
+            type=str,
+        )
+        group_method.add_argument(
+            "--trim",
+            help="Trimming methods, [trimal, gblocks, none], default : trimal",
+            type=str,
+        )
+        group_method.add_argument(
+            "--modeltest",
+            help="Model test methods, [iqtree, modeltestng, none], default : none",
+            type=str,
+        )
+        group_method.add_argument(
+            "--tree",
+            help="Tree methods to build phylogenetic tree, [fasttree, iqtree, raxml], default : fasttree",
+            type=str,
+        )
+
+        # Visualize
+        group_visualize = self.parser.add_argument_group(
+            title="visualize",
+            description="Visualization options for drawing phylogenetic tree",
+        )
+        group_visualize.add_argument(
+            "--bscutoff",
+            help="Bootstrap cutoff for visualize, default : 70",
+            type=int,
+        )
+        group_visualize.add_argument(
+            "--highlight",
+            help="Color to highlight query sequences in tree visualization. Either in html svg recognizable string or hex code, default: #AA0000",
+            type=str,
+        )
+        group_visualize.add_argument(
+            "--heightmultiplier",
+            help="Height multiplier in drawing collapsing nodes. Change it if you want to show collapse node more or less expanded. Default: 6",
+            type=float,
+        )
+        group_visualize.add_argument(
+            "--maxwordlength",
+            help="Maximum letters to be shown in single line of tree annotation. Default: 48",
+            type=int,
+        )
+
+        group_visualize.add_argument(
+            "--backgroundcolor",
+            help='List of background colors to be shown in tree, default: #f4f4f4, #c6c6c6. Input should be used with quotes, delimit with spaces and recommended to be used as hex codes. To remove background, use --backgroundcolor "#FFFFFF" "#FFFFFF" ',
+            nargs="*",
+            type=str,
+        )
+        group_visualize.add_argument(
+            "--outgroupcolor",
+            help="Background colors to indicate outgroup, default: #999999",
+            type=str,
+        )
+
+        group_visualize.add_argument(
+            "--ftype",
+            help="Font to use for phylogenetic tree, default: Arial",
+            type=str,
+        )
+        group_visualize.add_argument(
+            "--fsize",
+            help="Font size to use for phylogenetic tree, default: 10",
+            type=float,
+        )
+        group_visualize.add_argument(
+            "--fsize_bootstrap",
+            help="Font size to use for bootstrap support in phylogenetic tree, default: 9",
+            type=float,
+        )
+
+        # Advanced
+        group_advanced = self.parser.add_argument_group(
+            title="advanced", description="Advanced options for minor controls"
+        )
+        group_advanced.add_argument(
+            "--verbose",
+            "-v",
+            help="Verbosity level, 0: quiet, 1: info, 2: warning, 3: debug, default : 2",
+            type=int,
+        )
+        group_run.add_argument(
+            "--maxoutgroup",
+            help="Maximum outgroup numbers to include in phylogenetic analysis, default : 1",
+        )
+        group_advanced.add_argument(
+            "--collapsedistcutoff",
+            help="Maximum tree distance to be considered as same species, default : 0.01",
+            type=float,
+        )
+        group_advanced.add_argument(
+            "--collapsebscutoff",
+            help="Minimum bootstrap to be considered as same species, default : 100",
+            type=float,
+        )
+        group_advanced.add_argument(
+            "--bootstrap",
+            help="Boostrap number for tree analysis, will be ignored if fasttree is selected for tree method, default : 1000",
+            type=int,
+        )
+        group_advanced.add_argument(
+            "--solveflat",
+            action="store_true",
+            help="Whether to automatically detect 0 length branch and automatically solve them, default : True",
+        )
+        group_advanced.add_argument(
+            "--regex",
+            nargs="*",
+            help="Regex groups to parse strain numbers from your input. Maybe useful if your sequence descriptions are dirty. See documentation",
+            type=str,
+        )
+
+        group_advanced.add_argument(
+            "--cluster-cutoff",
+            dest="cluster_cutoff",
+            help="Minimum percent identity to be considered as same group in clustering analysis. Should be between 0 and 1, default : 0.97",
+            type=float,
+        )
+        group_advanced.add_argument(
+            "--cluster-evalue",
+            dest="cluster_evalue",
+            help="E-value cutoffs for blast/mmseqs search, default : 0.0000001",
+            type=float,
+        )
+        group_advanced.add_argument(
+            "--cluster-wordsize",
+            dest="cluster_wordsize",
+            help="Word size for blast/mmseqs search, default : 7",
+            type=int,
+        )
+        group_advanced.add_argument(
+            "--mafft-algorithm",
+            dest="mafft_algorithm",
+            help="MAFFT algorithm for alignment, see mafft documents, will be ignored if mafft not selected for alignment option, default : auto",
+        )
+        group_advanced.add_argument(
+            "--mafft-op",
+            dest="mafft_op",
+            help="MAFFT op (gap opening penalty) value, default : 1.3",
+            type=float,
+        )
+        group_advanced.add_argument(
+            "--mafft-ep",
+            dest="mafft_ep",
+            help="MAFFT ep value, default : 0.1",
+            type=float,
+        )
+        group_advanced.add_argument(
+            "--trimal-algorithm",
+            dest="trimal_algorithm",
+            help="Trimal algorithm for trimming, see trimal documents, will be ignored if trimal not selected for trimming option, default : gt",
+        )
+        group_advanced.add_argument(
+            "--trimal-gt", dest="trimal_gt", help="gt value for trimal", type=float
+        )
+        group_advanced.add_argument(
+            "--allow-innertrimming",
+            dest="allow_innertrimming",
+            help="Turn off FunVIP adjustment to not to trim inner alignment columns",
+            action="store_true",
+        )
+        group_advanced.add_argument(
+            "--criterion",
+            help="Modeltest criterion to use, either AIC, AICc or BIC",
+            type=str,
+        )
+
+        group_advanced.add_argument(
+            "--noavx",
+            action="store_true",
+            help="do not use AVX for RAxML, default: False",
+        )
+        group_advanced.add_argument(
+            "--outgroupoffset",
+            help="outgroupoffset value. Highering this value may select more distant outgroup, default : 20",
+            type=int,
+        )
+
+        # Cache
+        group_cache = self.parser.add_argument_group(
+            title="cache",
+            description="Save search database for faster run in next time",
+        )
+        group_cache.add_argument(
+            "--cachedb",
+            action="store_true",
+            help="Cache current search database, turn off if your database is too big for system directory, default : True",
+        )
+        group_cache.add_argument(
+            "--usecache",
+            action="store_true",
+            help="Use cached search database, turn off if your cached database makes error, default : True",
+        )
+
+        # Save
+        group_save = self.parser.add_argument_group(
+            title="save", description="Run saving options"
+        )
+        # Compatibility test required for this one
+        """
+        group_save.add_argument(
+            "--tableformat",
+            help="Default format for table files, [csv, xlsx, parquet, feather], default : csv",
+        )
+        """
+        group_save.add_argument(
+            "--tableformat",
+            help="Default format for table files, [csv, xlsx], default : csv",
+        )
+
+        group_save.add_argument(
+            "--nosearchresult",
+            action="store_true",
+            help="Do not save blast/mmseqs search matrix, use when dataset gets too big and generates IO bottleneck",
+        )
+
+        # Preset
+        group_setting = self.parser.add_argument_group(
+            title="setting", description="Presets for one-step settings"
+        )
+        group_setting.add_argument(
+            "--preset",
+            help="[fast, accurate], or json formatted option config file. Check documentation for each preset, default : fast",
+            type=str,
+        )
+
+        # version
+        self.parser.add_argument(
+            "--version", action="version", version=f"FunVIP {version('FunVIP')}"
+        )
+
+        return self.parser.parse_args()