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obi grep: updated to work with the new line selection class and within

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the local sequence environment, and progress bar functioning
This commit is contained in:
Celine Mercier
2016-11-08 11:19:12 +01:00
parent 4bc19c3e49
commit 8291693309
1 changed files with 17 additions and 13 deletions
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30
python/obitools3/commands/grep.pyx
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@ -1,7 +1,7 @@
from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport from obitools3.apps.progress cimport ProgressBar # @UnresolvedImport
from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_NUC_SEQS # TODO cimport doesn't work from obitools3.obidms._obidms import OBIDMS, OBIView, OBIView_line_selection # TODO cimport doesn't work
from functools import reduce
import time import time
__title__="Grep view lines that match the given predicates" __title__="Grep view lines that match the given predicates"
@ -43,7 +43,7 @@ def addOptions(parser):
group=parser.add_argument_group('obi grep specific options') group=parser.add_argument_group('obi grep specific options')
group.add_argument('--predicate','-p', group.add_argument('--predicate','-p',
action="store", dest="grep:predicate", action="append", dest="grep:predicates",
metavar='<PREDICATE>', metavar='<PREDICATE>',
default=None, default=None,
type=str, type=str,
@ -59,29 +59,33 @@ def run(config):
iview = d.open_view(config['obi']['inputview']) iview = d.open_view(config['obi']['inputview'])
# Initialize the progress bar # Initialize the progress bar
#pb = ProgressBar(len(iview), config, seconde=5) pb = ProgressBar(len(iview), config, seconde=5)
# Apply filter # Apply filter
# TODO try both kinds of line selection functions to check efficiency selection = OBIView_line_selection(iview)
selection = []
for i in range(len(iview)) : for i in range(len(iview)) :
#pb(i) pb(i)
line = iview[i] line = iview[i]
if isinstance(iview, OBIView_NUC_SEQS) : # put this somewhere else for efficiency
sequence = line loc_env = {'sequence': line, 'line': line} # TODO add taxonomy
if eval(config['grep']['predicate']) :
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) selection.append(i)
# Create output view with the line selection # Create output view with the line selection
oview = d.new_view(config['obi']['outputview'], view_to_clone=iview, line_selection=selection, comments="obi grep: "+config['grep']['predicate']+"\n") oview = d.new_view(config['obi']['outputview'], line_selection=selection, comments="obi grep: "+str(config['grep']['predicates'])+"\n")
repr(oview) #print("\n")
#print(repr(oview))
iview.close() iview.close()
oview.close() oview.close()
d.close() d.close()
print("Done.")