config.py

import os

# sample prefixes:
#SAMPLES_CONTROL = ['6685_04-06-2015', '6690_04-06-2015', '6695_04-06-2015', '6704_04-06-2015']
#SAMPLES_TREATED = ['6683_16-06-2015', '6685_16-06-2015', '6690_16-06-2015', '6695_16-06-2015', '6704_16-06-2015']
SAMPLES_CONTROL = ['C2', 'C3', ]
SAMPLES_TREATED = ['T1', 'T2', 'T3']

# sample suffix for paired reads
#SUFFIX1 = "_depl_1.fq.gz"
#SUFFIX2 = "_depl_2.fq.gz"
SUFFIX1 = "_1.fq"
SUFFIX2 = "_2.fq"

INDIR=os.path.dirname(os.path.abspath(__file__))) + "/test_data"
OUTDIR="~/heurystyki_test"

SGADIR=""

# SGA settings:
QUALFILTER=5
CORRECTK=21
OVERLAP=31

# other settings:
threads=4
READLEN=100

# simplification and filtering
MIN_LENGTH = 200
DEADENDS_REMOVE_ROUNDS = 10
DEADENDS_MIN_LENGTH = 200

# heuristics to run:
HEURISTICS = {"longest", "longestfc", "bestfc"}
MIN_FC = 2
MIN_CONTIG_LENGTH=200