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Author: Laszlo Kajan <lkajan@rostlab.org>
Description: usage() takes print stream parameter
--- a/score_conservation.py
+++ b/score_conservation.py
@@ -99,7 +99,7 @@
aa_to_index[aa] = i
-def usage():
+def usage( __file = sys.stdout ):
print( """\nUSAGE:\nscore_conservation [options] alignfile\n\t -alignfile must be in fasta, Stockholm or clustal format.\n\nOPTIONS:\n\t
-a\treference sequence. Print scores in reference to a specific sequence (ignoring gaps). Default prints the entire column. [sequence name]\n\t
-b\tlambda for window heuristic linear combination. Default=.5 [real in [0,1]]\n
@@ -113,7 +113,7 @@
-p\tuse gap penalty. Lower the score of columns that contain gaps. Default=True [True|False]\n\t
-s\tconservation estimation method. \n\t\tOptions: shannon_entropy, property_entropy, property_relative_entropy, vn_entropy, relative_entropy, js_divergence, sum_of_pairs. Default=js_divergence\n\t
-w\twindow size. Number of residues on either side included in the window. Default=3 [int]\n\t
- """ )
+ """, file=__file)
@@ -740,17 +740,17 @@
# parse options and args -- see usage()
if len(sys.argv) < 2:
- usage()
+ usage(__file=sys.stderr)
sys.exit(2)
try:
opts, args = getopt.getopt(sys.argv[1:], "hl:d:m:o:s:w:g:p:b:a:n")
except getopt.GetoptError:
- usage()
+ usage(__file=sys.stderr)
sys.exit(1)
if len(args) < 1:
- usage()
+ usage(__file=sys.stderr)
sys.exit(1)
for opt, arg in opts:
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