Commit 0de953a3 by Celine Mercier

pseudo obigrep for tests

parent f3b20b80
import sys
import argparse
from obitools3.obidms._obidms import OBIDMS
if __name__ == '__main__':
parser = argparse.ArgumentParser(description='Pseudo obigrep.')
parser.add_argument('-V', '--view', dest='view', type=str,
help='Name of the view that should be considered')
parser.add_argument('-N', '--new_view', dest='new_view', type=str,
help='Name of the new view that should be created')
# parser.add_argument('-k', '--key', dest='key', type=str,
# help='Name of the key that should be considered')
#
# parser.add_argument('-c', '--comp', dest='comparison', type=int,
# help='Comparison to be made: -1:< ; 0:== ; 1:>')
#
# parser.add_argument('-v', '--value', dest='value', type=object,
# help='Value to be compared')
args = parser.parse_args()
d = OBIDMS('tdms')
#condition = 1
line_selec = []
v = d.open_view(args.view)
i = 0
for l in v :
if l['score'] > 350 :
line_selec.append(i)
i+=1
new_v = d.new_view(args.new_view, view_to_clone=v, line_selection=line_selec, view_type="NUC_SEQS_VIEW", comments="obigrep "+args.view+" to "+args.new_view) #args.key+" "+str(args.comparison)+" "+str(args.value)+" "+)
print("\n")
print(new_v.__repr__())
v.save_and_close()
new_v.save_and_close()
d.close()
print("\nDone.")
\ No newline at end of file
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment