diff options
| -rw-r--r-- | r_qtl/r_qtl2.py | 30 |
1 files changed, 29 insertions, 1 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py index 508d3eb..94fa842 100644 --- a/r_qtl/r_qtl2.py +++ b/r_qtl/r_qtl2.py @@ -8,7 +8,6 @@ from functools import reduce from typing import Any, List, Union, Iterator from zipfile import ZipFile, ZipInfo, is_zipfile -from quality_control.debug import __pk__ from r_qtl.errors import InvalidFormat def thread_op(value, *functions): @@ -63,6 +62,35 @@ def genotype_data(zfile: ZipFile, cdata: dict) -> Iterator[dict]: in row.items() } +def genetic_map_data(zfile: ZipFile, cdata: dict) -> dict: + """Read gmap files to get the genome mapping data""" + if not cdata.get("geno_transposed", False): + with zfile.open(cdata["gmap"]) as gmapfile: + reader = csv.DictReader( + filter(lambda line: not line.startswith("#"), + io.TextIOWrapper(gmapfile)), + delimiter=cdata.get("sep", ",")) + return { + line["marker"]: { + key: value for key,value in line.items() if key != "marker" + } for line in reader + } + + with zfile.open(cdata["gmap"]) as gmapfile: + lines = [[field.strip() for field in + line.strip().split(cdata.get("sep", ","))] + for line in + filter(lambda line: not line.startswith("#"), + io.TextIOWrapper(gmapfile))] + + headers = tuple(line[0] for line in lines) + return reduce( + lambda gmap, row: { + **gmap, + row[0]: dict(zip(headers[1:], row[1:]))}, + zip(*(line[1:] for line in lines)), + {}) + def read_r_qtl2_files(filepath: Path): """Read R/qtl2 format zip files.""" with ZipFile(filepath, "r") as zfile: |