def find_fastq_parent_dir(sequencer_output_path):
"""
Searches for the subdirectory containing .fastq.gz files. If .fastq.gz files are not found two levels deep in the passed ``sequencer_output_path``, then a subdirectory containing .fastq.gz files will be returned, if found. Otherwise, raises an exception if no .fastq.gz files could be found.
Parameters
----------
sequencer_output_path: str
path to directory to search
Returns
-------
str
path to the directory with .fastq files to use for the ``sns`` analysis
Notes
-----
Ignores 'Undetermined' .fastq files
"""
inclusion_patterns = ('*.fastq.gz',)
exclusion_patterns = ('*Undetermined*',)
# search just the top 2 levels
matches = []
matches = find.find(search_dir = sequencer_output_path,
inclusion_patterns = inclusion_patterns,
exclusion_patterns = exclusion_patterns,
search_type = 'file',
num_limit = 1,
level_limit = 2,
match_mode = "any")
if len(matches) > 0:
logger.debug('Found .fastq files near the top level of the sequencer_output_path, returning sequencer_output_path: {0}'.format(sequencer_output_path))
return(sequencer_output_path)
# search deeper; this might take a while
logger.debug('.fastq files were not found near the top level of the sequencer_output_path, searching deeper...')
matches = []
matches = find.find(search_dir = sequencer_output_path,
inclusion_patterns = inclusion_patterns,
exclusion_patterns = exclusion_patterns,
search_type = 'file',
num_limit = 1,
match_mode = "any")
if len(matches) > 0:
fastq_dir = os.path.dirname(matches[0])
logger.debug('Found .fastq files in directory: {0}\nThis directory will be used for the sns analysis'.format(fastq_dir))
return(fastq_dir)
else:
raise _e.AnalysisFileMissing(message = 'sequencer_output_path does not contain .fastq.gz files: {0}'.format(sequencer_output_path), errors = '')
def find_available_NextSeq_runs(sequencer_dir):
'''
Find directories in the sequencer_dir that match
sequencer_dir = "/ifs/data/molecpathlab/quicksilver"
import find
find.find(search_dir = sequencer_dir, search_type = 'dir', level_limit = 0)
return a list of NextSeqRun objects
'''
# directory name patterns that correspond to test and debug dirs that should be excluded from the monitoring program
excludes = [
"to_be_demultiplexed", "automatic_demultiplexing_logs", "ArcherRun",
"run_index", "*_test*", "*_run_before_sequencing_done*"
]
sequencer_dirs = {}
for item in find.find(search_dir=sequencer_dir,
exclusion_patterns=excludes,
search_type='dir',
level_limit=0):
item_id = os.path.basename(item)
sequencer_dirs[item_id] = item
runs = [
NextSeqRun(
id=name,
config=configs,
extra_handlers=[x for x in log.get_all_handlers(logger=logger)])
for name, path in sequencer_dirs.items()
]
NGS580_runs = []
for run in runs:
if run.validate():
NGS580_runs.append(run)
# logger.debug(NGS580_runs)
return (NGS580_runs)
def get_output_files(self, analysis_step, pattern):
"""
Gets a file from the sample's analysis output, based on the ``analysis_output_index`` config listing the expected file types at each output, in addition to the criteria specified by the function args
Parameters
----------
analysis_step: str
the name of a directory in the analysis output from which to search for a sample's output file
pattern: str
a filename pattern to use when searching for the file
Returns
-------
list
a list of files for the sample from an analysis step
"""
# get the dirpath for the analysis step from the analysis dir; return None if there isn't one set for the provided step
search_dir = self.list_none(
self.analysis_config['dirs'][analysis_step])
patterns = [pattern, self.search_pattern]
f = []
if search_dir:
# self.logger.debug("Searching for {0} files in {1}, dir: {2}".format(patterns, analysis_step, search_dir))
f = find.find(search_dir=search_dir,
inclusion_patterns=patterns,
search_type='file',
match_mode='all')
# self.logger.debug('Found: {0}'.format(f))
else:
raise AnalysisItemMissing(
message="search_dir not found for {0}, dir: {1}".format(
analysis_step, search_dir),
errors='')
return (f)
def get_qsub_logfiles(self, logdir=None):
"""
Gets the list of log files from the analysis' qsub logs directory
Parameters
----------
logdir: str
the path to the qsub log directory. If ``None``, a directory called ``logs-qsub`` will be searched for in the analysis output directory and used instead
Returns
-------
list
a list of file paths to qsub logs
"""
log_files = []
# try to get the logdir from self
if not logdir:
logdir = self.list_none(self.get_dirs('logs-qsub'))
if not logdir:
raise AnalysisItemMissing(
message='Qsub log dir not found for the analysis', errors='')
else:
# find all the log files
for item in find.find(logdir, search_type='file'):
log_files.append(item)
return (log_files)
def demo():
'''
Demo some functions of the program
'''
find.find(search_dir='.', inclusion_patterns='*.py', num_limit=3)
logger.debug("Here is the file handler: {0}".format(
log.get_logger_handler(logger=logger, handler_name="main")))
find.find(search_dir='.', pattern='*.py')
find.find(search_dir='.', pattern='t*', level_limit=1)
find.find(search_dir='.', pattern='t*', search_type='file', level_limit=2)
def _init_files(self):
"""
Initializes the paths to files that might not have consistent naming
including: the targets .bed file with the chromosome target regions
"""
self.set_file(name='targets_bed',
path=find.find(search_dir=self.dir,
inclusion_patterns="*.bed",
exclusion_patterns='*.pad10.bed',
search_type='file',
num_limit=1,
level_limit=0))
def find_completed_NGS580_runs(analysis_output_dir):
'''
Find the NGS580 runs that have been done already
return a dict of NGS580_dirs[item_id] = item
'''
excludes = ["targets"]
NGS580_dirs = {}
for item in find.find(search_dir=analysis_output_dir,
exclusion_patterns=excludes,
search_type='dir',
level_limit=0):
item_id = os.path.basename(item)
NGS580_dirs[item_id] = item
# logger.debug(NGS580_dirs.items())
return (NGS580_dirs)
def find_samplesheets():
'''
Search for valid samplesheets, representing potential runs to check for demultiplexing
ex:
/ifs/data/molecpathlab/quicksilver/to_be_demultiplexed/NGS580/170519_NB501073_0010_AHCLLMBGX2-SampleSheet.csv
'''
# global samplesheet_source_dir
file_pattern = "*-SampleSheet.csv"
samplesheet_files = [
item for item in find.find(search_dir=samplesheet_source_dir,
inclusion_patterns=file_pattern,
search_type='file',
level_limit=1)
]
logger.debug("Samplesheets found: {0}".format(samplesheet_files))
return (samplesheet_files)
def _init_dirs(self):
"""
Initializes the path attributes for items associated with the sequencing run
from list of dirnames and filename patterns for the output steps in the sns WES analysis output
Todo
----
This is obtaining configs from the local config file; don't use these configs anymore, dont use these attributes, need to remove them. When using this module with ``snsxt``, the tasks should instead get the files explicitly from the tasks' ``input_dir``
"""
for name, attributes in self.analysis_output_index.items():
if name not in ['_parent']:
self.set_dir(name=name,
path=find.find(search_dir=self.dir,
inclusion_patterns=name,
search_type="dir",
num_limit=1,
level_limit=0))
def fastq_present(search_dir):
"""
Checks that '.fastq.gz' files are present in a directory
Parameters
----------
search_dir: str
path to directory to search
Returns
-------
bool
``True`` or ``False`` if any .fastq.gz file was found
"""
matches = None
# check that .fastq files are present in the output
matches = find.find(search_dir = search_dir, inclusion_patterns = ('*.fastq.gz',), search_type = 'file', num_limit = 1)
return(bool(matches))
def search_for_samples_pairs_sheet(self, id, search_dir, sheet_pattern):
'''
Search for a tumor-normal samples pairs samplesheet to match the current sequencing run
from util import find
search_dir = '/ifs/data/molecpathlab/quicksilver/to_be_demultiplexed/NGS580'
id = '170824_NB501073_0020_AHHK37BGX3'
sheet_pattern = '*-samples.pairs.csv'
'''
sheet = []
patterns = [str(id) + '*', sheet_pattern]
sheet = find.find(search_dir=search_dir,
search_type='file',
inclusion_patterns=patterns,
level_limit=0,
match_mode='all')
self.logger.debug(
'Found tumor-normal samplesheet for run {0}: {1}'.format(
id, sheet))
return (sheet)
def copy_sequencer_files(analysis_dir, sequencer_output_path, other_files = None):
"""
Copies files specified in ``settings.py`` from the ``sequencer_output_path`` directory to the ``analysis_dir``
Parameters
----------
sequencer_output_path: str
path to the directory containing the sequencer output to search in
analysis_dir: str
path to the directory to copy analysis files to
other_files: list
a list of other files to copy over to the analysis_dir, or ``None``
"""
# get the file basenames to search for from the settings
sequencer_files = settings.sequencer_files.split(',')
# get the files form the sequencer_dir to copy over
copy_files = []
for sequencer_file in sequencer_files:
logger.debug(sequencer_file)
inclusion_patterns = (sequencer_file,)
matches = find.find(search_dir = sequencer_output_path,
inclusion_patterns = inclusion_patterns,
search_type = 'file',
num_limit = 1,
match_mode = "any")
logger.debug(matches)
if len(matches) > 0:
copy_files.append(matches[0])
# include any other files passed
if other_files:
for other_file in other_files:
copy_files.append(other_file)
# copy all the files over
for copy_file in copy_files:
file_basename = os.path.basename(copy_file)
output_path = os.path.join(analysis_dir, file_basename)
logger.debug('Copying file from:\n{0}\nto:\n{1}'.format(copy_file, output_path))
shutil.copy2(copy_file, output_path)
"""
import os
import sys
import csv
from util import samplesheet
from util import find
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "tuco.settings")
import django
django.setup()
from lims.models import SequencingSampleSheet
sheets_dir = os.path.realpath(sys.argv[1])
# find all the samplesheets in the dir
for sheet_file in find.find(search_dir = sheets_dir, inclusion_patterns = ['SampleSheet.csv']):
sheet = samplesheet.IEMFile(path = os.path.realpath(sheet_file))
seqtype_file = os.path.join(os.path.dirname(sheet_file), 'seqtype.txt')
Run_ID = os.path.basename(os.path.dirname(sheet_file))
# load seqtype
if os.path.exists(seqtype_file):
with open(seqtype_file) as f:
lines = f.readlines()
Seq_Type = lines[0].strip()
# get the samplesheet entry from database
sheet_instance = SequencingSampleSheet.objects.get(md5 = sheet.meta['Sheet_md5'])
# check if it already has seq_type..
if not sheet_instance.seq_type or sheet_instance.seq_type == '' and Seq_Type != '':
...
"""
import os
import sys
import datetime
from util import find
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "tuco.settings")
import django
django.setup()
from lims.models import SequencingRun
seq_dir = os.path.realpath(sys.argv[1])
for run_dir in find.find(search_dir=seq_dir,
search_type='dir',
exclusion_patterns=['.*'],
level_limit=0):
Run_ID = os.path.basename(run_dir)
Run_path = os.path.realpath(run_dir)
seqtype_file = os.path.join(Run_path, 'seqtype.txt')
parts = Run_ID.split('_')
Date = ''
Sequencer_Serial = ''
Run_Num = ''
Flowcell_ID = ''
# check if Run_ID can be parsed
if len(parts) == 4: # ['180711', 'NB501073', '0057', 'AHFLL2BGX7']
Date = datetime.datetime.strptime(parts[0], '%y%m%d')
Sequencer_Serial = parts[1]
Run_Num = parts[2]
# get the date for the run from the first 6 digits of the runID
runDate = datetime.datetime.strptime(config['runID'][:6],
'%y%m%d').strftime('%Y-%m-%d')
# read list of sampleIDs from the deliverables sheet
sampleIDs = []
with open(deliverables_sheet) as f:
for line in f:
sampleIDs.append(line.strip())
# find all matching .fastq.gz files in the output locations
deliverableFiles = []
for sampleID in sampleIDs:
for item in find.find(
search_dir=outputDir,
inclusion_patterns=['{0}*.fastq.gz'.format(sampleID)]):
deliverableFiles.append(item)
deliverableFiles = list(set(deliverableFiles))
# set up deliverables directories
deliverableSubdir = os.path.join(deliverableDir, deliverableID, runDate,
'fastq')
try:
os.makedirs(deliverableSubdir)
except OSError:
if not os.path.isdir(deliverableSubdir):
raise
# symlink the files to the deliverables dir
for item in deliverableFiles:
