'''

:param dataLocation: Folder containing input data as .fq or .fasta

:param se_or_pe: 'S' or 'P'

:param outputDir:

:param quality_type: 'illumina', 'sanger'or 'solexa'

:param quality_threhold: integer value

param pairedFiles: Pairing of files as specified by user in a dictionary format {'ForwardReads.fq:ReverseReads.fq'}.

'''

# Determine the location of executable

xmlFile = 'configs/executables.xml'

nodeName = 'SICKLE'

tool_path = rx.extractLocationFromExecutables(xmlFile,nodeName)

dataType = ['S','P']

if se_or_pe not in dataType:

logging.error('executeFastqTrim_sickle: Incorrect specification for read data type. Specify S or P, opposed to the provided option - ' + se_or_pe)

return None

# create output dir if doesn't exist

if not os.path.exists(outputDir):

os.makedirs(outputDir)

logging.info('executeFastqTrim_sickle: Directory created at ' + outputDir)

if quality_type not in ['illumina', 'sanger', 'solexa']:

logging.error('Quality type must be one of these : illumina, sanger, solexa')

return None

if se_or_pe == 'S':

# expect a folder with .fq

fq_files = utilities.get_fastq_files(dataLocation)

if fq_files is None:

logging.error('No FASTQ files found.')

# Open file for recording cutadapt output

reportFile = os.path.join(outputDir,'sickleReport.txt')

report = open(reportFile, mode='w')

for fq_file in fq_files:

(dirname, filename) = os.path.split(fq_file)

outPath = os.path.join(outputDir, filename)

sickle_command = [tool_path, 'se', '-f', fq_file, '-t', quality_type, '-q', str(quality_threhold),'-o', outPath]

print('sickle command - ' + ' '.join(sickle_command))

logging.info('executeFastqTrim_sickle: sickle command - ' + ' '.join(sickle_command))

p = subprocess.Popen(sickle_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)

for line in p.stdout:

report.write(str(line))

p.stdout.flush()

report.close()

return 0

else:

# expect a folder and pairing of files. Files should be paired in same way as the adapters are specified.

pairedFiles_dict = pairedFiles[0]

if not isinstance(pairedFiles_dict, dict):

logging.error('executeFastqTrim_sickle: requires dictionary format for using the Paired-end trimming')

return None

# Open file for recording cutadapt output

reportFile = os.path.join(outputDir,'sickleReport.txt')

report = open(reportFile, mode='w')

strand1_files = pairedFiles_dict.keys()

for st1_file in strand1_files:

st2_file = pairedFiles_dict[st1_file]

# Create full path for input files

st1_file_path = os.path.join(dataLocation,st1_file)

st2_file_path = os.path.join(dataLocation,st2_file)

if os.path.exists(st1_file_path) & os.path.exists(st2_file_path):

st1_outPath = os.path.join(outputDir, st1_file)

st2_outPath = os.path.join(outputDir, st2_file)

singles_outPath = os.path.join(outputDir,'trimmedSingles.fastq')

sickle_command = [tool_path, 'pe', '-f', st1_file_path,'-r',st2_file_path, \

'-t', quality_type, '-q', str(quality_threhold), \

'-o', st1_outPath, '-p', st2_outPath, '-s',singles_outPath]

print('sickle command - ' + ' '.join(sickle_command))

logging.info('executeFastqTrim_sickle: sickle command - ' + ' '.join(sickle_command))

p = subprocess.Popen(sickle_command, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)

for line in p.stdout:

report.write(str(line))

p.stdout.flush()

else: # Return with error message if file(s) don't exist

msg = 'Check if files exist: ' + st1_file_path + ',' + st2_file_path

logging.error(msg)

return None

report.close()