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Louis BECQUEY
/
RNANetLegacy
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Authored by
Louis BECQUEY
2021-07-13 17:50:37 +0200
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Commit
8422deccfe75b517eda1bbc9c635a880c919d6f5
8422decc
2 parents
68dc5df1
2f2ecc16
Merge branch 'stage_aglae'
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2 changed files
with
6 additions
and
7 deletions
RNAnet.py
statistics.py
RNAnet.py
View file @
8422dec
...
...
@@ -321,8 +321,7 @@ class Chain:
self
.
file
=
path_to_3D_data
+
"rna_mapped_to_Rfam/"
+
self
.
chain_label
+
".cif"
else
:
status
=
f
"Extract {self.pdb_id}-{self.pdb_chain_id}"
self
.
file
=
path_to_3D_data
+
"renumbered_rna_only/"
+
self
.
chain_label
+
".cif"
#self.file = path_to_3D_data+"rna_only/"+self.chain_label+".cif"
self
.
file
=
path_to_3D_data
+
"rna_only/"
+
self
.
chain_label
+
".cif"
# Check if file exists, if yes, abort (do not recompute)
if
os
.
path
.
exists
(
self
.
file
):
...
...
@@ -1517,9 +1516,9 @@ class Pipeline:
# extract chains of pure RNA
os.makedirs(path_to_3D_data + "rna_only")
'''
if
(
not
self
.
HOMOLOGY
)
and
not
os
.
path
.
isdir
(
path_to_3D_data
+
"r
enumbered_r
na_only"
):
if
(
not
self
.
HOMOLOGY
)
and
not
os
.
path
.
isdir
(
path_to_3D_data
+
"rna_only"
):
# extract chains of pure RNA
os
.
makedirs
(
path_to_3D_data
+
"r
enumbered_r
na_only"
)
os
.
makedirs
(
path_to_3D_data
+
"rna_only"
)
# define and run jobs
joblist
=
[]
...
...
statistics.py
View file @
8422dec
...
...
@@ -1503,7 +1503,7 @@ def measure_from_structure(f):
warnings
.
simplefilter
(
'ignore'
,
Bio
.
PDB
.
PDBExceptions
.
PDBConstructionWarning
)
warnings
.
simplefilter
(
'ignore'
,
Bio
.
PDB
.
PDBExceptions
.
BiopythonWarning
)
parser
=
MMCIFParser
()
s
=
parser
.
get_structure
(
f
,
os
.
path
.
abspath
(
path_to_3D_data
+
"r
enumbered_r
na_only/"
+
f
))
s
=
parser
.
get_structure
(
f
,
os
.
path
.
abspath
(
path_to_3D_data
+
"rna_only/"
+
f
))
measures_aa
(
name
,
s
,
thr_idx
)
if
DO_HIRE_RNA_MEASURES
:
...
...
@@ -1837,7 +1837,7 @@ def measures_hrna(name, s, thr_idx):
@trace_unhandled_exceptions
def
measures_hrna_basepairs
(
name
,
s
,
thr_idx
):
"""
Open a r
enumbered_r
na_only/ file, and run measures_hrna_basepairs_chain() on every chain
Open a rna_only/ file, and run measures_hrna_basepairs_chain() on every chain
"""
setproctitle
(
f
"RNANet statistics.py Worker {thr_idx+1} measures_hrna_basepairs({name})"
)
...
...
@@ -2884,7 +2884,7 @@ if __name__ == "__main__":
# if n_unmapped_chains:
# os.makedirs(runDir+"/results/geometry/all-atoms/distances/", exist_ok=True)
# liste_struct = os.listdir(path_to_3D_data + "r
enumbered_r
na_only")
# liste_struct = os.listdir(path_to_3D_data + "rna_only")
# if '4zdo_1_E.cif' in liste_struct:
# liste_struct.remove('4zdo_1_E.cif') # weird cases to remove for now
# if '4zdp_1_E.cif' in liste_struct:
...
...
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