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populate symbols for samtools and bcftools. #1143

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merged 2 commits into from
Mar 8, 2023
Merged

populate symbols for samtools and bcftools. #1143

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6bd222a
populate symbols for samtools and bcftools.
Kentalot Oct 31, 2022
3d2028a
add return type for call function of PysamDispatcher
Kentalot Oct 31, 2022
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54 changes: 28 additions & 26 deletions pysam/bcftools.py
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Original file line number Diff line number Diff line change
@@ -1,29 +1,31 @@
from typing import Final

from pysam.utils import PysamDispatcher

BCFTOOLS_DISPATCH = [
"index",
"annotate",
"concat",
"convert",
"isec",
"merge",
"norm",
"plugin",
"query",
"reheader",
"sort",
"view",
"head",
"call",
"consensus",
"cnv",
"csq",
"filter",
"gtcheck",
"mpileup",
"roh",
"stats"]

# instantiate bcftools commands as python functions
for cmd in BCFTOOLS_DISPATCH:
globals()[cmd] = PysamDispatcher("bcftools", cmd, None)
def _wrap_command(dispatch: str) -> PysamDispatcher:
return PysamDispatcher("bcftools", dispatch, ())


index: Final[PysamDispatcher] = _wrap_command("index")
annotate: Final[PysamDispatcher] = _wrap_command("annotate")
concat: Final[PysamDispatcher] = _wrap_command("concat")
convert: Final[PysamDispatcher] = _wrap_command("convert")
isec: Final[PysamDispatcher] = _wrap_command("isec")
merge: Final[PysamDispatcher] = _wrap_command("merge")
norm: Final[PysamDispatcher] = _wrap_command("norm")
plugin: Final[PysamDispatcher] = _wrap_command("plugin")
query: Final[PysamDispatcher] = _wrap_command("query")
reheader: Final[PysamDispatcher] = _wrap_command("reheader")
sort: Final[PysamDispatcher] = _wrap_command("sort")
view: Final[PysamDispatcher] = _wrap_command("view")
head: Final[PysamDispatcher] = _wrap_command("head")
call: Final[PysamDispatcher] = _wrap_command("call")
consensus: Final[PysamDispatcher] = _wrap_command("consensus")
cnv: Final[PysamDispatcher] = _wrap_command("cnv")
csq: Final[PysamDispatcher] = _wrap_command("csq")
filter: Final[PysamDispatcher] = _wrap_command("filter")
gtcheck: Final[PysamDispatcher] = _wrap_command("gtcheck")
mpileup: Final[PysamDispatcher] = _wrap_command("mpileup")
roh: Final[PysamDispatcher] = _wrap_command("roh")
stats: Final[PysamDispatcher] = _wrap_command("stats")
217 changes: 169 additions & 48 deletions pysam/samtools.py
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Original file line number Diff line number Diff line change
@@ -1,55 +1,176 @@
from typing import (
Final,
Callable,
List,
Tuple,
Iterable,
Union,
)

from pysam.utils import PysamDispatcher

# samtools command line options to export in python
SAMTOOLS_DISPATCH = {
_SAMTOOLS_DISPATCH = {
# samtools 'documented' commands
"view": ("view", None),
"head": ("head", None),
"sort": ("sort", None),
"mpileup": ("mpileup", None),
"consensus": ("consensus", None),
"depth": ("depth", None),
"faidx": ("faidx", None),
"fqidx": ("fqidx", None),
"tview": ("tview", None),
"index": ("index", None),
"idxstats": ("idxstats", None),
"fixmate": ("fixmate", None),
"flagstat": ("flagstat", None),
"calmd": ("calmd", None),
"merge": ("merge", None),
"markdup": ("markdup", None),
"rmdup": ("rmdup", None),
"reference": ("reference", None),
"reheader": ("reheader", None),
"cat": ("cat", None),
"targetcut": ("targetcut", None),
"phase": ("phase", None),
"bam2fq": ("bam2fq", None),
"dict": ("dict", None),
"addreplacerg": ("addreplacerg", None),
"pad2unpad": ("pad2unpad", None),
"depad": ("pad2unpad", None),
"bedcov": ("bedcov", None),
"coverage": ("coverage", None),
"bamshuf": ("bamshuf", None),
"collate": ("collate", None),
"stats": ("stats", None),
"fasta": ("fasta", None),
"fastq": ("fastq", None),
"quickcheck": ("quickcheck", None),
"split": ("split", None),
"flags": ("flags", None),
"ampliconclip": ("ampliconclip", None),
"ampliconstats": ("ampliconstats", None),
"version": ("version", None),
"fqimport": ("import", None),
"samples": ("samples", None),
"view": ("view", ()),
"head": ("head", ()),
"sort": ("sort", ()),
"mpileup": ("mpileup", ()),
"consensus": ("consensus", ()),
"depth": ("depth", ()),
"faidx": ("faidx", ()),
"fqidx": ("fqidx", ()),
"tview": ("tview", ()),
"index": ("index", ()),
"idxstats": ("idxstats", ()),
"fixmate": ("fixmate", ()),
"flagstat": ("flagstat", ()),
"calmd": ("calmd", ()),
"merge": ("merge", ()),
"markdup": ("markdup", ()),
"rmdup": ("rmdup", ()),
"reference": ("reference", ()),
"reheader": ("reheader", ()),
"cat": ("cat", ()),
"targetcut": ("targetcut", ()),
"phase": ("phase", ()),
"bam2fq": ("bam2fq", ()),
"dict": ("dict", ()),
"addreplacerg": ("addreplacerg", ()),
"pad2unpad": ("pad2unpad", ()),
"depad": ("pad2unpad", ()),
"bedcov": ("bedcov", ()),
"coverage": ("coverage", ()),
"bamshuf": ("bamshuf", ()),
"collate": ("collate", ()),
"stats": ("stats", ()),
"fasta": ("fasta", ()),
"fastq": ("fastq", ()),
"quickcheck": ("quickcheck", ()),
"split": ("split", ()),
"flags": ("flags", ()),
"ampliconclip": ("ampliconclip", ()),
"ampliconstats": ("ampliconstats", ()),
"version": ("version", ()),
"fqimport": ("import", ()),
"import_": ("import", ()),
"samples": ("samples", ()),
}

# instantiate samtools commands as python functions
for key, options in SAMTOOLS_DISPATCH.items():
cmd, parser = options
globals()[key] = PysamDispatcher("samtools", cmd, parser)

__all__ = list(SAMTOOLS_DISPATCH)
def _wrap_command(
dispatch: str,
parsers: Iterable[Tuple[str, Callable[[Union[str, List[str]]], Union[str, List[str]]]]],
) -> PysamDispatcher:
return PysamDispatcher("samtools", dispatch, parsers)


view: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["view"][0], _SAMTOOLS_DISPATCH["view"][1])

head: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["head"][0], _SAMTOOLS_DISPATCH["head"][1])

sort: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["sort"][0], _SAMTOOLS_DISPATCH["sort"][1])

mpileup: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["mpileup"][0], _SAMTOOLS_DISPATCH["mpileup"][1])

consensus: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["consensus"][0],
_SAMTOOLS_DISPATCH["consensus"][1],
)

depth: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["depth"][0], _SAMTOOLS_DISPATCH["depth"][1])

faidx: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["faidx"][0], _SAMTOOLS_DISPATCH["faidx"][1])

fqidx: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["fqidx"][0], _SAMTOOLS_DISPATCH["fqidx"][1])

tview: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["tview"][0], _SAMTOOLS_DISPATCH["tview"][1])

index: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["index"][0], _SAMTOOLS_DISPATCH["index"][1])

idxstats: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["idxstats"][0], _SAMTOOLS_DISPATCH["idxstats"][1])

fixmate: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["fixmate"][0], _SAMTOOLS_DISPATCH["fixmate"][1])

flagstat: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["flagstat"][0], _SAMTOOLS_DISPATCH["flagstat"][1])

calmd: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["calmd"][0], _SAMTOOLS_DISPATCH["calmd"][1])

merge: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["merge"][0], _SAMTOOLS_DISPATCH["merge"][1])

markdup: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["markdup"][0], _SAMTOOLS_DISPATCH["markdup"][1])

rmdup: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["rmdup"][0], _SAMTOOLS_DISPATCH["rmdup"][1])

reference: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["reference"][0],
_SAMTOOLS_DISPATCH["reference"][1],
)

reheader: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["reheader"][0], _SAMTOOLS_DISPATCH["reheader"][1])

cat: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["cat"][0], _SAMTOOLS_DISPATCH["cat"][1])

targetcut: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["targetcut"][0],
_SAMTOOLS_DISPATCH["targetcut"][1],
)

phase: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["phase"][0], _SAMTOOLS_DISPATCH["phase"][1])

bam2fq: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["bam2fq"][0], _SAMTOOLS_DISPATCH["bam2fq"][1])

dict: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["dict"][0], _SAMTOOLS_DISPATCH["dict"][1])

addreplacerg: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["addreplacerg"][0],
_SAMTOOLS_DISPATCH["addreplacerg"][1],
)

pad2unpad: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["pad2unpad"][0],
_SAMTOOLS_DISPATCH["pad2unpad"][1],
)

depad: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["depad"][0], _SAMTOOLS_DISPATCH["depad"][1])

bedcov: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["bedcov"][0], _SAMTOOLS_DISPATCH["bedcov"][1])

coverage: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["coverage"][0], _SAMTOOLS_DISPATCH["coverage"][1])

bamshuf: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["bamshuf"][0], _SAMTOOLS_DISPATCH["bamshuf"][1])

collate: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["collate"][0], _SAMTOOLS_DISPATCH["collate"][1])

stats: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["stats"][0], _SAMTOOLS_DISPATCH["stats"][1])

fasta: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["fasta"][0], _SAMTOOLS_DISPATCH["fasta"][1])

fastq: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["fastq"][0], _SAMTOOLS_DISPATCH["fastq"][1])

quickcheck: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["quickcheck"][0],
_SAMTOOLS_DISPATCH["quickcheck"][1],
)

split: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["split"][0], _SAMTOOLS_DISPATCH["split"][1])

flags: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["flags"][0], _SAMTOOLS_DISPATCH["flags"][1])

ampliconclip: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["ampliconclip"][0],
_SAMTOOLS_DISPATCH["ampliconclip"][1],
)

ampliconstats: Final[PysamDispatcher] = _wrap_command(
_SAMTOOLS_DISPATCH["ampliconstats"][0],
_SAMTOOLS_DISPATCH["ampliconstats"][1],
)

version: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["version"][0], _SAMTOOLS_DISPATCH["version"][1])

fqimport: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["fqimport"][0], _SAMTOOLS_DISPATCH["fqimport"][1])

import_: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["import_"][0], _SAMTOOLS_DISPATCH["import_"][1])

samples: Final[PysamDispatcher] = _wrap_command(_SAMTOOLS_DISPATCH["samples"][0], _SAMTOOLS_DISPATCH["samples"][1])
20 changes: 17 additions & 3 deletions pysam/utils.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,11 @@
from typing import (
Callable,
List,
Tuple,
Iterable,
Union,
)

from pysam.libcutils import _pysam_dispatch


Expand Down Expand Up @@ -36,14 +44,20 @@ class PysamDispatcher(object):
parsers = None
collection = None

def __init__(self, collection, dispatch, parsers):
def __init__(
self,
collection: str,
dispatch: str,
parsers: Iterable[Tuple[str, Callable[[Union[str, List[str]]], Union[str, List[str]]]]],
):
self.collection = collection
self.dispatch = dispatch
self.parsers = parsers
self.stderr = []

def __call__(self, *args, **kwargs):
'''execute a samtools command.
def __call__(self, *args: str, **kwargs) -> Union[str, List[str]]:
'''
execute a samtools command.

Keyword arguments:
catch_stdout -- redirect stdout from the samtools command and
Expand Down