biopipen 0.28.0__py3-none-any.whl → 0.29.0__py3-none-any.whl

biopipen/scripts/bcftools/BcftoolsSort.py

@@ -1,19 +0,0 @@
-from biopipen.utils.misc import run_command, dict_to_cli_args
-
-infile = {{in.infile | quote}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
-bcftools = {{envs.bcftools | quote}}  # pyright: ignore
-gz = {{envs.gz | repr}}  # pyright: ignore
-args = {{envs.args | repr}}  # pyright: ignore
-tmpdir = {{envs.tmpdir | quote}}  # pyright: ignore
-index = {{envs.index | repr}}  # pyright: ignore
-
-args[""] = bcftools
-args["_"] = infile
-args["o"] = outfile
-args["O"] = "z" if gz or index else "v"
-
-run_command(dict_to_cli_args(args, dashify=True), fg=True)
-
-if index:
-    run_command([bcftools, "index", outfile], fg=True)

biopipen/scripts/gene/GeneNameConversion.py

@@ -1,66 +0,0 @@
-import pandas
-from datar.all import c, right_join, select, relocate
-from biopipen.utils.gene import gene_name_conversion
-
-infile = {{in.infile | quote}}  # pyright: ignore
-outfile = {{out.outfile | quote}}  # pyright: ignore
-inopts = {{envs.inopts | repr}}  # pyright: ignore
-outopts = {{envs.outopts | repr}}  # pyright: ignore
-notfound = {{envs.notfound | repr}}  # pyright: ignore
-genecol = {{envs.genecol | repr}}  # pyright: ignore
-output = {{envs.output | repr}}  # pyright: ignore
-infmt = {{envs.infmt | repr}}  # pyright: ignore
-outfmt = {{envs.outfmt | repr}}  # pyright: ignore
-species = {{envs.species | quote}}  # pyright: ignore
-
-df = pandas.read_csv(infile, **inopts)
-
-if isinstance(genecol, int):
-    genes = df.iloc[:, genecol]
-else:
-    genes = df.loc[:, genecol]
-
-colname = genes.name
-genes = genes.tolist()
-
-#        query  `outfmt`
-#     <object> <object>
-# 0  1255_g_at   GUCA1A
-# 1    1316_at     THRA
-# 2    1320_at   PTPN21
-# 3    1294_at  MIR5193
-converted = gene_name_conversion(
-    genes=genes,
-    species=species,
-    infmt=infmt,
-    outfmt=outfmt,
-    notfound=notfound,
-)
-converted.columns = [colname] + converted.columns[1:].tolist()
-
-if output == "only":
-    out = converted
-
-elif output == "keep":
-    out = df >> right_join(converted, by=colname, suffix=["", "_converted"])
-
-elif output == "drop":
-    out = df >> right_join(
-        converted,
-        by=colname, suffix=["", "_converted"]
-    ) >> select(~c(colname))
-
-elif output == "replace":
-    out = df >> right_join(
-        converted, by=colname, suffix=["", "_converted"]
-    )
-    converted_cols = out.columns[-len(converted.columns)+1:].tolist()
-    pos = df.columns.get_indexer([colname])[0]
-    out = out >> relocate(
-        converted_cols, _after=pos+1
-    ) >> select(~c(colname))
-
-else:
-    raise ValueError(f"Unknown output mode: {output}.")
-
-out.to_csv(outfile, **outopts)