'''

:param adapterDict: Adaptar dictionary in form compatible with "cutadapt". Like [ADAPTER:-a] for a 3' adapter type,

[ADAPTER:-g] for a 5' adapter,[ADAPTER$:-a] for anchored 3' adapter,[^ADAPTER:-g] for anchored 5' adapter, and

[ADAPTER:b] for both 5' and 3' adapter type. Similarly, it can take -A, -B and -G for paired versions.

Details - "http://cutadapt.readthedocs.org/en/stable/guide.html#removing-adapters"

:param se_or_pe: Single or paired end data. Options - 'S' or 'P'

:param fixBaseNumber: Remove fixed number of bases. -u option like -u 5 (remove first 5 bases)

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

'''

dataType = ['S','P']

# Determine the location of executable

xmlFile = 'configs/executables.xml'

nodeName = 'CUTADAPT'

tool_path = rx.extractLocationFromExecutables(xmlFile,nodeName)

if se_or_pe not in dataType:

logging.error('removeAdaptors_cutadapt: 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('removeAdaptors_cutadapt: Directory created at ' + outputDir)

# check if correct adapter types specified

allowedAdapterTypes = ['-a', '-g', '-b', '-A', '-G', '-B'] # As specified by cutadapt

userProvidedAdapterTypes = adapterDict.values()

for type in userProvidedAdapterTypes:

if type not in allowedAdapterTypes:

logging.error('removeAdaptors_cutadapt: Wrong keys provided for specifying adapters. Wrong entry found is : ' + type)

return None

# Arrange adapter list to a string

adapters = adapterDict.keys()

adapter_parameter_format = ''

for adapter in adapters:

adapter_parameter_format = adapter_parameter_format + adapterDict[adapter] + ' ' + adapter + ' '

print('Adapters and parameters :' + adapter_parameter_format)

logging.info('removeAdaptors_cutadapt: Adapters and parameters :' + adapter_parameter_format)

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,'cutadaptReport.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)

cutadapt_command = [tool_path, adapter_parameter_format, '-u',fixBaseNumber,'-o', outPath,fq_file]

print('cutadapt command - ' + ' '.join(cutadapt_command))

logging.info('removeAdaptors_cutadapt: cutadapt command - ' + ' '.join(cutadapt_command))

p = subprocess.Popen(cutadapt_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('removeAdaptors_cutadapt: requires dictionary format for using the Paired-end trimming')

return None

# Open file for recording cutadapt output

reportFile = os.path.join(outputDir,'cutadaptReport.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)

cutadapt_command = [tool_path, adapter_parameter_format, '-u',fixBaseNumber,'-o', st1_outPath, '-p',st2_outPath, st1_file_path, st2_file_path]

print('cutadapt command - ' + ' '.join(cutadapt_command))

logging.info('removeAdaptors_cutadapt: cutadapt command - ' + ' '.join(cutadapt_command))

p = subprocess.Popen(cutadapt_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()