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improved organism2directory mapping #103

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Nov 19, 2024
Merged

improved organism2directory mapping #103

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20 changes: 18 additions & 2 deletions BRB/PushButton.py
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,21 @@
from BRB.logger import log
import stat
from pathlib import Path
import re

def organism2Dir(organism):
""" Convert organism name - such as
M. Musculus (mm10 / GRCm39) -> M_Musculus_mm10_GRCm39
The main goal is to have a simple directory name
"""
# Replace all spaces and special characters with underscores
directory = re.sub(r'[^\w]', '_', organism)
# Collapse multiple underscores into one
directory = re.sub(r'_+', '_', directory)
# Remove trailing underscores
directory = re.sub(r'_+$', '', directory)
return directory


def createPath(config, group, project, organism, libraryType, tuples):
"""Ensures that the output path exists, creates it otherwise, and return where it is"""
Expand All @@ -22,8 +37,9 @@ def createPath(config, group, project, organism, libraryType, tuples):
BRB.misc.pacifier(project))
os.makedirs(baseDir, mode=0o700, exist_ok=True)
#org = organism.split(' ')[0].lower() # splitting bad idea for "M. musculus" etc.
org = organism2Org(config, organism)
oDir = os.path.join(baseDir, "{}_{}".format(BRB.misc.pacifier(libraryType), org))
#org = organism2Org(config, organism) # bad when organism is a dir/dir/file.yaml
analysis_dir = organism2Dir(organism)
oDir = os.path.join(baseDir, "{}_{}".format(BRB.misc.pacifier(libraryType), analysis_dir))
os.makedirs(oDir, mode=0o700, exist_ok=True)
return oDir

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