Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
bios4biol
bioinfo-utils
Commits
241d03ba
Commit
241d03ba
authored
Jan 18, 2016
by
Celine Noirot
Browse files
bug 1 base
parent
369fc86a
Changes
1
Hide whitespace changes
Inline
Side-by-side
bin/insilicoRRBSdigestion.py
View file @
241d03ba
...
...
@@ -37,7 +37,6 @@ 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
():
"""
Return the insilicoRRBSdigestion version
...
...
@@ -261,7 +260,7 @@ def compute_fragment_size_per_range(ranges,fragments_length):
ranges
[
key
][
"size"
]
=
0
for
i
in
fragments_length
:
for
key
in
ranges
.
keys
():
if
i
>=
ranges
[
key
][
"coord"
][
0
]
and
i
<
ranges
[
key
][
"coord"
][
1
]
:
if
i
>=
ranges
[
key
][
"coord"
][
0
]
and
i
<
=
ranges
[
key
][
"coord"
][
1
]
:
ranges
[
key
][
"nb_fragment"
]
+=
1
ranges
[
key
][
"size"
]
+=
i
break
...
...
@@ -269,14 +268,12 @@ def compute_fragment_size_per_range(ranges,fragments_length):
if
__name__
==
"__main__"
:
# Get available enzyme
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]"
)
usage
=
"usage: %prog -i file.fa -o output
.stats -c CpGisland
.bed"
usage
=
"usage: %prog -i file.fa -o output
_directory -c file
.bed"
desc
=
"The script simulates a complete enzymatic digestion of the genome to
\
identify all the potential restriction fragments. Then, for each size
\
range (from min to max fragment length of bins size ) it computes different metrics"
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment