Punctuation problem in help string

Author: Will Trimble

scripts/mg-abundant-functions.py

@@ -48,7 +48,7 @@ def main(args):
     parser.add_argument("--filter_level", dest="filter_level", default=None, help="function level to filter by")
     parser.add_argument("--top", dest="top", type=int, default=10, help="display only the top N taxa, default is 10")
     parser.add_argument("--evalue", dest="evalue", type=int, default=5, help="negative exponent value for maximum e-value cutoff, default is 5")
-    parser.add_argument("--identity", dest="identity", type=int, default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", dest="identity", type=int, default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", dest="length", type=int, default=15, help="value for minimum alignment length cutoff, default is 15")
     parser.add_argument("--version", type=int, dest="version", default=1, help="M5NR annotation version to use, default is 1")
 

scripts/mg-abundant-taxa.py

@@ -48,7 +48,7 @@ def main(args):
     parser.add_argument("--filter_level", dest="filter_level", default=None, help="taxon level to filter by")
     parser.add_argument("--top", dest="top", type=int, default=10, help="display only the top N taxa, default is 10")
     parser.add_argument("--evalue", dest="evalue", type=int, default=5, help="negative exponent value for maximum e-value cutoff, default is 5")
-    parser.add_argument("--identity", dest="identity", type=int, default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", dest="identity", type=int, default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", dest="length", type=int, default=15, help="value for minimum alignment length cutoff, default is 15")
     parser.add_argument("--version", type=int, dest="version", default=1, help="M5NR annotation version to use, default is 1")
 

scripts/mg-compare-functions.py

@@ -55,7 +55,7 @@ def main(args):
     parser.add_argument("--output", dest="output", default='-', help="output: filename or stdout (-), default is stdout")
     parser.add_argument("--format", dest="format", default='biom', help="output format: 'text' for tabbed table, 'biom' for BIOM format, default is biom")
     parser.add_argument("--evalue", type=int, dest="evalue", default=15, help="negative exponent value for maximum e-value cutoff, default is 15")
-    parser.add_argument("--identity", type=int, dest="identity", default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", type=int, dest="identity", default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", type=int, dest="length", default=15, help="value for minimum alignment length cutoff, default is 15")
     parser.add_argument("--version", type=int, dest="version", default=1, help="M5NR annotation version to use, default is 1")
     parser.add_argument("--temp", dest="temp", default=None, help="filename to temporarly save biom output at each iteration")

scripts/mg-compare-taxa.py

@@ -56,7 +56,7 @@ def main(args):
     parser.add_argument("--output", dest="output", default='-', help="output: filename or stdout (-), default is stdout")
     parser.add_argument("--format", dest="format", default='biom', help="output format: 'text' for tabbed table, 'biom' for BIOM format, default is biom")
     parser.add_argument("--evalue", type=int, dest="evalue", default=15, help="negative exponent value for maximum e-value cutoff, default is 15")
-    parser.add_argument("--identity", type=int, dest="identity", default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", type=int, dest="identity", default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", type=int, dest="length", default=15, help="value for minimum alignment length cutoff, default is 15")
     parser.add_argument("--version", type=int, dest="version", default=1, help="M5NR annotation version to use, default is 1")
     parser.add_argument("--temp", dest="temp", default=None, help="filename to temporarly save biom output at each iteration")

scripts/mg-extract-sequences.py

@@ -45,7 +45,7 @@ def main(args):
     parser.add_argument("--level", dest="level", default='function', help="function level to filter by")
     parser.add_argument("--source", dest="source", default='Subsystems', help="datasource to filter results by, default is Subsystems")
     parser.add_argument("--evalue", dest="evalue", default=5, help="negative exponent value for maximum e-value cutoff, default is 5")
-    parser.add_argument("--identity", dest="identity", default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", dest="identity", default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", dest="length", default=15, help="value for minimum alignment length cutoff, default is 15")
     parser.add_argument("--status", dest="status", default="public", help="types of metagenomes to return. 'both' for all data (public and private), 'public' for public data, 'private' for users private data, default is public")
     for sfield in SEARCH_FIELDS:

scripts/mg-get-sequences-for-taxon.py

@@ -45,7 +45,7 @@ def main(args):
     parser.add_argument("--level", dest="level", default=None, type=str, help="taxon level to filter by")
     parser.add_argument("--source", dest="source", default='SEED', type=str,  help="datasource to filter results by, default is SEED")
     parser.add_argument("--evalue", dest="evalue", default=5, type=float, help="negative exponent value for maximum e-value cutoff, default is 5")
-    parser.add_argument("--identity", dest="identity", default=60, type=float, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", dest="identity", default=60, type=float, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", dest="length", default=15, type=float, help="value for minimum alignment length cutoff, default is 15")
 
     # get inputs

scripts/mg-get-similarity-for-function.py

@@ -45,7 +45,7 @@ def main(args):
     parser.add_argument("--level", dest="level", default=None, help="function level to filter by")
     parser.add_argument("--source", dest="source", default='Subsystems', help="datasource to filter results by, default is Subsystems")
     parser.add_argument("--evalue", dest="evalue", default=5, help="negative exponent value for maximum e-value cutoff, default is 5")
-    parser.add_argument("--identity", dest="identity", default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", dest="identity", default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", dest="length", default=15, help="value for minimum alignment length cutoff, default is 15")
 
     # get inputs

scripts/mg-get-similarity-for-taxon.py

@@ -45,7 +45,7 @@ def main(args):
     parser.add_argument("--level", dest="level", default=None, help="taxon level to filter by")
     parser.add_argument("--source", dest="source", default='SEED', help="datasource to filter results by, default is SEED")
     parser.add_argument("--evalue", dest="evalue", default=5, help="negative exponent value for maximum e-value cutoff, default is 5")
-    parser.add_argument("--identity", dest="identity", default=60, help="percent value for minimum % identity cutoff, default is 60")
+    parser.add_argument("--identity", dest="identity", default=60, help="percent value for minimum %% identity cutoff, default is 60")
     parser.add_argument("--length", dest="length", default=15, help="value for minimum alignment length cutoff, default is 15")
 
     # get inputs