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DIADE
dynadiv
GrAnnoT
Commits
225699a8
Commit
225699a8
authored
6 months ago
by
nina.marthe_ird.fr
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removed debug print
parent
b57b0bd3
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GrAnnoT/main.py
+0
-15
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GrAnnoT/main.py
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225699a8
...
...
@@ -8,7 +8,6 @@ from .Functions_output import *
from
.argparser
import
*
#from inference import *
from
pathlib
import
Path
#import psutil
def
main
():
...
...
@@ -16,16 +15,11 @@ def main():
args
=
arg
()
read_args
(
args
)
#print(psutil.Process().memory_info().rss)
# intersect is in the output directory
intersect
=
Path
(
args
.
outdir
.
joinpath
(
"
intersect
"
)).
resolve
()
gfa
=
args
.
graph
load_intersect
(
intersect
.
as_posix
(),
args
.
verbose
)
#print(psutil.Process().memory_info().rss / 1024**2) # B -> MiB
#print(psutil.Process().memory_info().rss)
segments
=
args
.
segment_coordinates_path
.
joinpath
(
"
segments.txt
"
)
# outputs the gff and gaf of the graph
...
...
@@ -56,8 +50,6 @@ def main():
args
.
target
.
append
(
genome_name
)
if
args
.
verbose
:
print
(
f
"
Genomes found :
{
args
.
target
}
"
)
#print(psutil.Process().memory_info().rss)
# get haplotypes for each target genome
if
args
.
haplotype
:
...
...
@@ -81,7 +73,6 @@ def main():
# build a dictionnary with the segment sizes to compute the coverage and id
if
not
args
.
graph_gaf
:
seg_size
=
get_segments_length
(
segments
,
args
.
verbose
)
#print(psutil.Process().memory_info().rss)
genome_index
=
0
for
target_genome
in
args
.
target
:
print
(
f
'
\n
{
target_genome
}
transfer :
'
)
...
...
@@ -96,7 +87,6 @@ def main():
print
(
f
'
Loading the walks for the genome
{
target_genome
}
'
)
walks_path
=
args
.
segment_coordinates_path
.
joinpath
(
"
walks.txt
"
).
as_posix
()
target_genome_paths
=
get_paths
(
walks_path
,
target_genome
,
args
.
haplotype
)
#print(psutil.Process().memory_info().rss)
if
not
args
.
verbose
:
print
(
"
Loading the segments coordinates
"
)
for
file
in
segment_coord_files
:
...
...
@@ -113,9 +103,7 @@ def main():
list_feat_absent
=
[]
# do the annotation transfer (or var/aln)
#print(psutil.Process().memory_info().rss)
transfer_on_target
(
segments
,
out_target_gff
,
out_target_var
,
out_target_aln
,
target_genome
,
target_genome_paths
,
list_feat_absent
,
seg_size
,
args
)
#print(psutil.Process().memory_info().rss)
# if pav matrix is asked, add the information of this transfer on the matrix
if
args
.
pav_matrix
:
for
feat
in
list_feat_absent
:
...
...
@@ -136,6 +124,3 @@ def main():
out_pav
=
args
.
outdir
.
joinpath
(
"
PAV_matrix.txt
"
)
with
open
(
out_pav
,
'
w
'
)
as
file_out_pav
:
file_out_pav
.
write
(
pav_output
)
#print(tracemalloc.get_traced_memory())
#tracemalloc.stop()
\ No newline at end of file
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