diff options
| author | Frederick Muriuki Muriithi | 2021-09-27 04:48:53 +0300 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2021-09-27 04:48:53 +0300 |
| commit | 19783a18c2bc7941fc5980e593f19fb1d18c3623 (patch) | |
| tree | f3a6e241be3c6224b9647c8258c516a7b741a28c /gn3/computations | |
| parent | 8d9bc0f29ce9208306915b079818e6f0c31785e2 (diff) | |
| download | genenetwork3-19783a18c2bc7941fc5980e593f19fb1d18c3623.tar.gz | |
Update terminology: `strain` to `sample`
Issue:
https://github.com/genenetwork/gn-gemtext-threads/blob/main/topics/gn1-migration-to-gn2/clustering.gmi
* Update the terminology used: use `sample` in place of `strain` according to
Zachary's direction at
https://github.com/genenetwork/genenetwork3/pull/37#issuecomment-926043306
Diffstat (limited to 'gn3/computations')
| -rw-r--r-- | gn3/computations/parsers.py | 10 | ||||
| -rw-r--r-- | gn3/computations/qtlreaper.py | 8 |
2 files changed, 9 insertions, 9 deletions
diff --git a/gn3/computations/parsers.py b/gn3/computations/parsers.py index 94387ff..1af35d6 100644 --- a/gn3/computations/parsers.py +++ b/gn3/computations/parsers.py @@ -14,7 +14,7 @@ def parse_genofile(file_path: str) -> Tuple[List[str], 'h': 0, 'u': None, } - genotypes, strains = [], [] + genotypes, samples = [], [] with open(file_path, "r") as _genofile: for line in _genofile: line = line.strip() @@ -22,8 +22,8 @@ def parse_genofile(file_path: str) -> Tuple[List[str], continue cells = line.split() if line.startswith("Chr"): - strains = cells[4:] - strains = [strain.lower() for strain in strains] + samples = cells[4:] + samples = [sample.lower() for sample in samples] continue values = [__map.get(value.lower(), None) for value in cells[4:]] genotype = { @@ -32,7 +32,7 @@ def parse_genofile(file_path: str) -> Tuple[List[str], "cm": cells[2], "mb": cells[3], "values": values, - "dicvalues": dict(zip(strains, values)), + "dicvalues": dict(zip(samples, values)), } genotypes.append(genotype) - return strains, genotypes + return samples, genotypes diff --git a/gn3/computations/qtlreaper.py b/gn3/computations/qtlreaper.py index 8b2893e..166d2dd 100644 --- a/gn3/computations/qtlreaper.py +++ b/gn3/computations/qtlreaper.py @@ -9,17 +9,17 @@ from typing import Union from gn3.random import random_string from gn3.settings import TMPDIR, REAPER_COMMAND -def generate_traits_file(strains, trait_values, traits_filename): +def generate_traits_file(samples, trait_values, traits_filename): """ Generate a traits file for use with `qtlreaper`. PARAMETERS: - strains: A list of strains to use as the headers for the various columns. - trait_values: A list of lists of values for each trait and strain. + samples: A list of samples to use as the headers for the various columns. + trait_values: A list of lists of values for each trait and sample. traits_filename: The tab-separated value to put the values in for computation of QTLs. """ - header = "Trait\t{}\n".format("\t".join(strains)) + header = "Trait\t{}\n".format("\t".join(samples)) data = ( [header] + ["{}\t{}\n".format(i+1, "\t".join([str(i) for i in t])) |