obitools/obitools3
2
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases 66 Wiki Activity

Cython API: compiling but not working

Browse Source
This commit is contained in:
Celine Mercier
2017-03-06 16:07:02 +01:00
parent 778acc48cd
commit 381194194c
19 changed files with 1404 additions and 1531 deletions
Download Patch File Download Diff File Expand all files Collapse all files

59
python/obitools3/commands/grep.pyx
View File

@ -1,5 +1,6 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection # TODO cimport doesn't work
from obitools3.dms.dms import OBIDMS # TODO cimport doesn't work
#, OBIView, OBIView_line_selection # TODO cimport doesn't work
from functools import reduce
import time
@ -56,34 +57,34 @@ def run(config):
d = OBIDMS(config['obi']['defaultdms'])
# Open input view 1
iview = d.open_view(config['obi']['inputview'])
# Initialize the progress bar
pb = ProgressBar(len(iview), config, seconde=5)
# Apply filter
selection = OBIView_line_selection(iview)
for i in range(len(iview)) :
pb(i)
line = iview[i]
loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
good = (reduce(lambda bint x, bint y: x and y,
(bool(eval(p, loc_env, line))
for p in config['grep']['predicates']), True))
if good :
selection.append(i)
# Create output view with the line selection
oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
#print("\n")
#print(repr(oview))
iview.close()
oview.close()
# iview = d.open_view(config['obi']['inputview'])
#
# # Initialize the progress bar
# pb = ProgressBar(len(iview), config, seconde=5)
#
# # Apply filter
# selection = OBIView_line_selection(iview)
# for i in range(len(iview)) :
# pb(i)
# line = iview[i]
#
# loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
#
# good = (reduce(lambda bint x, bint y: x and y,
# (bool(eval(p, loc_env, line))
# for p in config['grep']['predicates']), True))
#
# if good :
# selection.append(i)
#
# # Create output view with the line selection
# oview = d.clone_view_with_line_selection(config['obi']['outputview'], selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
#
# #print("\n")
# #print(repr(oview))
#
# iview.close()
# oview.close()
d.close()