diff --git a/python/obitools3/obigrep.py b/python/obitools3/obigrep.py new file mode 100644 index 0000000..20577fe --- /dev/null +++ b/python/obitools3/obigrep.py @@ -0,0 +1,51 @@ +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