import logging
import os
from .. import util
logger = logging.getLogger(__name__)
[docs]def get_project_label(string):
"""
Return a Genomics Core project label matched in input string.
:type string: str
:param string: any string
:rtype: str
:return: Genomics Core project label (e.g., P00-0) substring or
empty string, if no match found
"""
return util.matchdefault('P+[0-9]+(-[0-9]+){,1}', string)
[docs]def parse_project_label(project_label):
"""
Parse a Genomics Core project label (e.g., P00-0) and return
individual components indicating project ID and subproject ID.
:type project_label: str
:param project_label: String following Genomics Core convention for
project labels, P<project ID>-<subproject ID>
:rtype: dict
:return: a dict with fields for 'project_id' and 'subproject_id'
"""
project_id = int(util.matchdefault('(?<=P)[0-9]+', project_label))
subproject_id = int(util.matchdefault('(?<=-)[0-9]+', project_label))
return {'project_id': project_id, 'subproject_id': subproject_id}
[docs]def get_library_id(string):
"""
Return library ID matched in input string.
:type string: str
:param string: any string that might contain a library ID of the
format 'lib1234'
:rtype: str
:return: the matching substring representing the library ID or an
empty string ('') if no match found
"""
return util.matchdefault('lib[1-9]+[0-9]*', string)
[docs]def get_sample_id(string):
"""
More general than library ID; returns either library ID (if
present), or any word starting with 'Sample_', ends in a number,
and preceeds any non-alphanumeric characters.
:type string: str
:param string: any string that might contain a form of sample ID
:rtype: str
:return: the matching substring representing the sample ID or an
empty string ('') if no match found
"""
sample_id = util.matchdefault('lib[0-9]+', string)
if not len(sample_id):
sample_id = util.matchdefault('Sample_.*[0-9]+', string)
return sample_id
[docs]def parse_flowcell_path(flowcell_path):
"""
Return 'genomics' root and run ID based on directory path.
"""
# TODO: raise some sort of exception, if path doesn't end in valid run id
# return {'genomics_root': util.matchdefault('.*(?=genomics)', flowcell_path),
# 'run_id': os.path.basename(flowcell_path.rstrip('/'))}
# Upon move to Isilon, "genomics" root is now "bioinformatics/pipeline" root
return {'pipeline_root': util.matchdefault('.*(?=pipeline)', flowcell_path),
'run_id': os.path.basename(flowcell_path.rstrip('/'))}
[docs]def parse_batch_file_path(batchfile_path):
"""
Return 'genomics' root and batch file name based on directory path.
"""
# return {'genomics_root': util.matchdefault('.*(?=genomics)',
# batchfile_path),
# 'workflowbatch_filename': os.path.basename(batchfile_path)}
# Upon move to Isilon, "genomics" root is now "bioinformatics/pipeline" root
return {'pipeline_root': util.matchdefault('.*(?=pipeline)',
batchfile_path),
'workflowbatch_filename': os.path.basename(batchfile_path)}