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global_params.py
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import os
if os.path.exists('/groups/pupko/orenavr2/'):
src_dir = '/groups/pupko/orenavr2/igomeProfilingPipeline/src'
else:
src_dir = '/Users/Oren/Dropbox/Projects/gershoni/src'
# modules to load
python = "python/python-anaconda3.6.5"
gcc = "gcc/gcc-8.2.0"
mafft = "mafft/7.123"
# external scripts
pssm_score_peptide_script = "/groups/pupko/orenavr2/igomeProfilingPipeline/src/PSSM_score_Peptide/PSSM_score_Peptide"
qsub_script = "/bioseq/bioSequence_scripts_and_constants/q_submitter_power.py"
biggest_cluster = 100
biggest_cluster_sec = 400
max_peptide = 1000
maximal_gap_frequency_allowed_per_column = 0.1 # alignment columns with more than gap_threshold proportion of gaps are discarded
split_num = 10
MistakeAllowed = 1 # default
if __name__ == '__main__':
# user input
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('input_path', type=lambda x: x.rstrip('/'), help='A path to the data folder')
parser.add_argument('output_path', type=lambda x: x.rstrip('/'), help='A path to which the results will be written')
parser.add_argument('fastq', help='A path to the fastq file')
parser.add_argument('barcode2samplename', help='A path to a table with barcode to sample name mapping')
parser.add_argument('samplename2biologicalcondition',
help='A path to a table with sample name to biological condition mapping')
parser.add_argument('-q', '--queue_name', help='The cluster to which the job(s) will be submitted to',
choices=['pupkoweb', 'pupkolab', 'pupkotmp',
'pupkowebr', 'pupkolabr', 'pupkotmpr',
'itaym', 'lilach', 'bioseq', 'bental',
'oren.q', 'bioseq20.q'], default='pupkolab')
args = parser.parse_args()
folder_input = args.input_path
folder_output = args.output_path
fastq_file = args.fastq
barcode2samplename_path = args.barcode2samplename
samplename2biologicalcondition_path = args.samplename2biologicalcondition
queue_name = args.q