Commit 369fc86a authored by Celine Noirot's avatar Celine Noirot
Browse files

Add enzymatic digestion

parent b5e6bb3e
......@@ -31,11 +31,12 @@ from subprocess import Popen, PIPE
import tempfile
import json
import re
sys.path.insert(0, os.path.join(os.path.dirname(os.path.realpath(__file__)), '..', '..', '..', 'src'))
import jflow.seqio as seqio
sys.path.insert(0, os.path.join(os.path.dirname(os.path.realpath(__file__)),'..', 'lib'))
import seqio as seqio
GRAPH_CLASS_PARTITION = 100
MAX_FRAGMENT_LEN_IN_HISTOGRAM = 5000
ENZYME_PATH=os.path.join(os.path.dirname(os.path.realpath(__file__)),"..","lib","enzyme.txt")
def version_string ():
"""
......@@ -268,7 +269,10 @@ def compute_fragment_size_per_range(ranges,fragments_length):
if __name__ == "__main__":
# Get available enzyme
all_enzymes = get_available_enzymes(os.path.join(os.path.dirname(os.path.realpath(__file__)),"enzyme.txt"))
all_enzymes = {'None':0}
if os.path.exists(ENZYME_PATH) :
all_enzymes = get_available_enzymes(ENZYME_PATH)
parser = OptionParser(usage="Usage: insilicoRRBS.py -i FILE [options]")
......
SbfI CCTGCAGG CCTGCA*GG
PstI CTGCAG CTGCA*G
NsiI ATGCAT ATGCA*T
NotI GCGGCCGC GC*GGCCGC
EagI CGGCCG C*GGCCG
EcoRI GAATTC G*AATTC
MfeI CAATTG C*AATTG
BamHI GGATCC G*GATCC
BclI TGATCA T*GATCA
BglII AGATCT A*GATCT
BbvCI CCTCAGC CC*TCAGC
HaeIII GGCC GG*CC
RsaI GTAC GT*AC
MspI CCGG C*CGG
TaqI TCGA T*CGA
Alu AGCT AG*CT
\ No newline at end of file
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