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authorFrederick Muriuki Muriithi2023-12-20 12:25:44 +0300
committerFrederick Muriuki Muriithi2023-12-20 12:25:44 +0300
commit16fc2613bb7f3e5f3596f1470e0de2741bd55f5a (patch)
treed6cbe4754667dac6cc2d0cc1bc8fc487eb2b06b0 /r_qtl/r_qtl2.py
parent7cb6a3449547c7d160457c69475a194bfc936d1d (diff)
downloadgn-uploader-16fc2613bb7f3e5f3596f1470e0de2741bd55f5a.tar.gz
Read R/qtl2 format files
* Set up error objects. * Read the control data.
Diffstat (limited to 'r_qtl/r_qtl2.py')
-rw-r--r--r_qtl/r_qtl2.py32
1 files changed, 32 insertions, 0 deletions
diff --git a/r_qtl/r_qtl2.py b/r_qtl/r_qtl2.py
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+++ b/r_qtl/r_qtl2.py
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+"""The R/qtl2 parsing and processing code."""
+import json
+import yaml
+from pathlib import Path
+from typing import List, Union
+from zipfile import ZipFile, ZipInfo, is_zipfile
+
+from quality_control.debug import __pk__
+from r_qtl.errors import InvalidFormat
+
+def control_data(zfile: ZipFile) -> dict:
+ """Retrieve the control file from the zip file info."""
+ files = tuple(filename
+ for filename in zfile.namelist()
+ if (filename.endswith(".yaml") or filename.endswith(".json")))
+ num_files = len(files)
+ if num_files == 0:
+ raise InvalidFormat("Expected a json or yaml control file.")
+
+ if num_files > 1:
+ raise InvalidFormat("Found more than one possible control file.")
+
+ return (json.loads(zfile.read(files[0]))
+ if files[0].endswith(".json")
+ else yaml.safe_load(zfile.read(files[0])))
+
+
+def read_r_qtl2_files(filepath: Path):
+ """Read R/qtl2 format zip files."""
+ with ZipFile(filepath, "r") as zfile:
+ cf = control_data(zfile)
+ raise NotImplementedError("Implementation is incomplete.")