Update argument defaults

atram.py

@@ -71,12 +71,12 @@ def parse_command_line():
     group.add_argument(
         '-a', '--assembler', default='none',
         choices=['abyss', 'trinity', 'velvet', 'spades', 'none'],
-        help="""Which assembler to use. Choosing "none" (the default) will do
-            a single blast run and stop before any assembly.""")
+        help="""Which assembler to use. Choosing "none" will do a single blast run
+        and stop before any assembly. (default %(default)s)""")
 
     group.add_argument(
         '-i', '--iterations', type=int, default=5, metavar='N',
-        help="""The number of pipeline iterations. The default is "5".""")
+        help="""The number of pipeline iterations. (default %(default)s)""")
 
     group = parser.add_argument_group('optional arguments')
 
@@ -87,8 +87,8 @@ def parse_command_line():
 
     group.add_argument(
         '--fraction', type=float, default=1.0,
-        help="""Use only the specified fraction of the aTRAM database. The
-            default is 1.0.""")
+        help="""Use only the specified fraction of the aTRAM database.
+            (default %(default)s)""")
 
     cpus = min(10, os.cpu_count() - 4 if os.cpu_count() > 4 else 1)
     group.add_argument(
@@ -102,8 +102,8 @@ def parse_command_line():
         '--log-level', choices=['debug', 'info', 'error', 'fatal'],
         default='info',
         help="""Log messages of the given level (or above). 'debug' shows the
-            most messages and 'fatal' shows the least. The default is
-            'info'""")
+            most messages and 'fatal' shows the least.
+            (default %(default)s)""")
 
     group.add_argument(
         '--path',
@@ -123,8 +123,8 @@ def parse_command_line():
     group.add_argument(
         '-T', '--timeout', metavar='SECONDS', default=600, type=int,
         help="""How many seconds to wait for an assembler or BLAST before
-            stopping the run. To wait forever set this to 0. The default
-            is "600" (10 minutes).""")
+            stopping the run. To wait forever set this to 0.
+            (default %(default)s)""")
 
     group = parser.add_argument_group(
         'optional values for filtering contigs')
@@ -136,14 +136,15 @@ def parse_command_line():
 
     group.add_argument(
         '--bit-score', type=float, default=70.0, metavar='SCORE',
-        help="""Remove contigs that have a value less than this. The default
-            is "70.0". This is turned off by the --no-filter argument.""")
+        help="""Remove contigs that have a value less than this.
+            (default %(default)s) This is turned off by the
+            --no-filter argument.""")
 
     group.add_argument(
         '--contig-length', '--length', type=int, default=100,
-        help="""Remove blast hits that are shorter than this length. The
-            default is "100". This is turned off by the --no-filter argument.
-            """)
+        help="""Remove blast hits that are shorter than this length.
+            (default %(default)s) This is turned off by the
+            --no-filter argument.""")
 
     blast.command_line_args(parser)
     assembly.command_line_args(parser)

atram_framer.py

@@ -43,8 +43,8 @@ def parse_command_line():
 
     parser.add_argument(
         '-m', '--min-length', metavar='LENGTH', default=100, type=int,
-        help="""Remove contigs that are less than this length. The default is
-            100.""")
+        help="""Remove contigs that are less than this length.
+            (default %(default)s)""")
 
     parser.add_argument(
         '-t', '--temp-dir', metavar='DIR',
@@ -61,8 +61,8 @@ def parse_command_line():
         '--log-level', choices=['debug', 'info', 'error', 'fatal'],
         default='info',
         help="""Log messages of the given level (or above). 'debug' shows the
-            most messages and 'fatal' shows the least. The default is
-            'info'""")
+            most messages and 'fatal' shows the least.
+            (default %(default)s)""")
 
     parser.add_argument(
         '-o', '--output-prefix',
@@ -76,8 +76,8 @@ def parse_command_line():
         help="""Use this to filter files in the assemblies directory. For
             example '*filtered*.fasta' will select all fasta files in the
             assemblies directory with the word filtered in them. The default
-            is to select all fasta files in the assemblies directory
-            '*.fasta'.""")
+            is to select all fasta files in the assemblies directory.
+           (default %(default)s)""")
 
     parser.add_argument(
         '--reference-name', action='store_true',
@@ -89,7 +89,7 @@ def parse_command_line():
     parser.add_argument(
         '--long-contig', type=float, default=0.7,
         help="""A long contig is considered to be this fraction [0-1] of the
-            longest contig assembled by exonerate. The default is 0.7.""")
+            longest contig assembled by exonerate. (default %(default)s)""")
 
     args = parser.parse_args()
 

atram_preprocessor.py

@@ -87,14 +87,14 @@ def parse_command_line():
         '-b', '--blast-db', '--db', default=blast_db, metavar='DB',
         help="""This is the prefix of all of the blast database files. So you
             can identify different blast database sets. You may include a
-            directory as part of the prefix. The default is "{}".
+            directory as part of the prefix. (default %(default)s)
             """.format(blast_db))
 
     cpus = min(10, os.cpu_count() - 4 if os.cpu_count() > 4 else 1)
     group.add_argument(
         '--cpus', '--processes', '--max-processes', type=int, default=cpus,
-        help="""Number of CPU threads to use. On this machine the default is
-        ("{}")""".format(cpus))
+        help="""Number of CPU threads to use. (default %(default)s)
+            """.format(cpus))
 
     group.add_argument(
         '-t', '--temp-dir', metavar='DIR',
@@ -111,8 +111,8 @@ def parse_command_line():
         '--log-level', choices=['debug', 'info', 'error', 'fatal'],
         default='info',
         help="""Log messages of the given level (or above). 'debug' shows the
-            most messages and 'fatal' shows the least. The default is
-            'info'""")
+            most messages and 'fatal' shows the least.
+            (default %(default)s)""")
 
     group.add_argument(
         '-s', '--shards', '--number', type=int, metavar='SHARDS',

atram_stitcher.py

@@ -45,7 +45,7 @@ def parse_command_line():
     parser.add_argument(
         '-O', '--overlap', type=int, default=10,
         help="""Contigs must overlap by this many codons before it is
-            considered a real overlap.""")
+            considered a real overlap. (default %(default)s)""")
 
     parser.add_argument(
         '-t', '--temp-dir', metavar='DIR',
@@ -62,13 +62,13 @@ def parse_command_line():
         '--log-level', choices=['debug', 'info', 'error', 'fatal'],
         default='info',
         help="""Log messages of the given level (or above). 'debug' shows the
-            most messages and 'fatal' shows the least. The default is
-            'info'""")
+            most messages and 'fatal' shows the least.
+            (default %(default)s)""")
 
     parser.add_argument(
         '-i', '--iterations', type=int, default=2, metavar='N',
         help="""The number of times to run the main stitcher loop. This
-            must be either 1 or 2, the default is 2.""")
+            must be either 1 or 2. (default %(default)s)""")
 
     parser.add_argument(
         '-o', '--output-prefix',
@@ -82,8 +82,8 @@ def parse_command_line():
         help="""Use this to filter files in the assemblies directory. For
             example '*filtered*.fasta' will select all fasta files in the
             assemblies directory with the word filtered in them. The default
-            is to select all fasta files in the assemblies directory
-            '*.fasta'.""")
+            is to select all fasta files in the assemblies directory.
+            (default %(default)s)""")
 
     parser.add_argument(
         '--reference-name', action='store_true',

lib/assemblers/abyss.py

@@ -75,7 +75,7 @@ def command_line_args(parser):
 
         group.add_argument(
             '--abyss-kmer', type=int, default=64,
-            help="""k-mer size. I passes k=<int> (default 64).""")
+            help="""k-mer size. It passes k=<int>. (default %(default)s)""")
 
         group.add_argument(
             '--abyss-np', type=int,

lib/assemblers/spades.py

@@ -64,7 +64,7 @@ def command_line_args(parser):
         group.add_argument(
             '--spades-threads', type=int, default=cpus,
             help="""Number of threads to use.
-                Default will use {} threads.""".format(cpus))
+                (default %(default)s)""".format(cpus))
 
         total_mem = psutil.virtual_memory().available >> 30
         max_mem = max(1.0, total_mem >> 1)
@@ -84,7 +84,7 @@ def command_line_args(parser):
             '--spades-cov-cutoff', default='off',
             help="""Read coverage cutoff value. Must be a positive float value,
                 or "auto", or "off". It passes  --cov-cutoff
-                <keyword or int>.""")
+                <keyword or int>. (default %(default)s)""")
 
     @staticmethod
     def validate_cov_cutoff(log, cov_cutoff):

lib/assemblers/velvet.py

@@ -73,19 +73,19 @@ def command_line_args(parser):
 
         group.add_argument(
             '--velvet-kmer', type=int, default=31,
-            help="""k-mer size (default 31).""")
+            help="""k-mer size. ((default %(default)s)""")
 
         group.add_argument(
             '--velvet-exp-cov', type=int, default=30,
-            help="""The expected coverage of the region. -exp_cov <int>
-                (default 30).""")
+            help="""The expected coverage of the region. -exp_cov <int>.
+                ((default %(default)s)""")
 
         group.add_argument(
             '--velvet-ins-length', type=int, default=300,
             help="""The size of the fragments used in the short-read library.
-                -ins_length <int> (default 300).""")
+                -ins_length <int>. ((default %(default)s)""")
 
         group.add_argument(
             '--velvet-min-contig-lgth', type=int, default=100,
             help="""The minimum contig length used by the assembler itself.
-                -min_contig_lgth <int> (default is 100).""")
+                -min_contig_lgth <int>. ((default %(default)s)""")

lib/blast.py

@@ -134,10 +134,10 @@ def command_line_args(parser):
     group.add_argument('--blast-db-gencode', '--db-gencode', type=int,
                        default=1, metavar='CODE',
                        help="""The genetic code to use during blast runs.
-                            The default is "1".""")
+                             (default %(default)s)""")
 
     group.add_argument('--blast-evalue', '--evalue', type=float, default=1e-10,
-                       help="""The default evalue is "1e-10".""")
+                       help="""(default %(default)s)""")
 
     group.add_argument('--blast-word-size', '--word-size', type=int,
                        help="""Word size for wordfinder algorithm.