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bios4biol
bioinfo-utils
Commits
369fc86a
Commit
369fc86a
authored
Jan 06, 2016
by
Celine Noirot
Browse files
Add enzymatic digestion
parent
b5e6bb3e
Changes
3
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Inline
Side-by-side
bin/insilicoRRBSdigestion.py
View file @
369fc86a
...
...
@@ -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]"
)
...
...
lib/enzyme.txt
0 → 100644
View file @
369fc86a
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
lib/seqio.py
0 → 100644
View file @
369fc86a
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