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Remove trailing spaces in docstrings

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commit 588cca76fbfa3adac11033851ffe553b1924af50 1 parent c4e6bf4
Peter Cock authored July 15, 2013

Showing 1 changed file with 28 additions and 28 deletions. Show diff stats Hide diff stats

  1. 56  Bio/Phylo/Applications/_Fasttree.py
56  Bio/Phylo/Applications/_Fasttree.py
@@ -70,7 +70,7 @@ def __init__(self, cmd='fasttree', **kwargs):
70 70
                 """-quote -- add quotes to sequence names in output.
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                     Quote sequence names in the output and allow spaces, commas,
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-                    parentheses, and colons in them but not ' characters (fasta files only) """,
  73
+                    parentheses, and colons in them but not ' characters (fasta files only).""",
74 74
                 ),
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             _Option(['-pseudo', 'pseudo'],
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                 """-pseudo [weight] -- Pseudocounts are used with sequence distance estimation.
@@ -91,7 +91,7 @@ def __init__(self, cmd='fasttree', **kwargs):
91 91
                     it will compute minimum-evolution bootstrap supports instead
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                     In either case, the support values are proportions ranging from 0 to 1
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-                    Use -nosupport to turn off support values or -boot 100 to use just 100 resamples """,
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+                    Use -nosupport to turn off support values or -boot 100 to use just 100 resamples.""",
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                 checker_function=_is_int,
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                 equate=False,
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                 ),
@@ -104,28 +104,28 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     it will compute minimum-evolution bootstrap supports instead
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                     In either case, the support values are proportions ranging from 0 to 1
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-                    Use -nosupport to turn off support values or -boot 100 to use just 100 resamples """,
  107
+                    Use -nosupport to turn off support values or -boot 100 to use just 100 resamples.""",
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                 ),
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             _Option(['-intree', 'intree'],
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                 """-intree newickfile -- read the starting tree in from newickfile.
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                     Any branch lengths in the starting trees are ignored.
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-                    -intree with -n will read a separate starting tree for each alignment. """,
  113
+                    -intree with -n will read a separate starting tree for each alignment.""",
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                 filename=True,
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                 equate=False,
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                 ),
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             _Option(['-intree1', 'intree1'],
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-                """-intree1 newickfile -- read the same starting tree for each alignment """,
  118
+                """-intree1 newickfile -- read the same starting tree for each alignment.""",
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                 filename=True,
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                 equate=False,
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                 ),
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             _Switch(['-quiet', 'quiet'],
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                 """-quiet -- do not write to standard error during normal operation
124 124
 
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-                    (no progress indicator, no options summary, no likelihood values, etc.) """,
  125
+                    (no progress indicator, no options summary, no likelihood values, etc.)""",
126 126
                 ),
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             _Switch(['-nopr', 'nopr'],
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-                """-nopr -- do not write the progress indicator to stderr """,
  128
+                """-nopr -- do not write the progress indicator to stderr.""",
129 129
                 ),
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             _Option(['-nni', 'nni'],
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                 """Set the rounds of minimum-evolution nearest-neighbor interchanges
@@ -136,7 +136,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     where N is the number of unique sequences, 2 rounds of
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                     subtree-prune-regraft (SPR) moves (also min. evo.), and
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                     up to 2*log(N) rounds of maximum-likelihood NNIs.
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-                    Use -nni to set the number of rounds of min. evo. NNIs """,
  139
+                    Use -nni to set the number of rounds of min. evo. NNIs.""",
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                 checker_function=_is_int,
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                 equate=False,
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                 ),
@@ -150,12 +150,12 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     subtree-prune-regraft (SPR) moves (also min. evo.), and
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                     up to 2*log(N) rounds of maximum-likelihood NNIs.
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                     Use -nni to set the number of rounds of min. evo. NNIs,
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-                    and -spr to set the rounds of SPRs. """,
  153
+                    and -spr to set the rounds of SPRs.""",
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                 checker_function=_is_int,
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                 equate=False,
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                 ),
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             _Switch(['-noml', 'noml'],
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-                """Deactivate min-evo NNIs and SPRs
  158
+                """Deactivate min-evo NNIs and SPRs.
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                     Topology refinement:
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                     By default, FastTree tries to improve the tree with up to 4*log2(N)
@@ -169,7 +169,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     an approximately maximum-likelihood tree with further NNIs) """,
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                 ),
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             _Switch(['-mllen', 'mllen'],
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-                """Optimize branch lengths on a fixed topology
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+                """Optimize branch lengths on a fixed topology.
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                     Topology refinement:
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                     By default, FastTree tries to improve the tree with up to 4*log2(N)
@@ -180,10 +180,10 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     Use -nni to set the number of rounds of min. evo. NNIs,
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                     and -spr to set the rounds of SPRs.
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                     Use -mllen to optimize branch lengths without ML NNIs
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-                    Use -mllen -nome with -intree to optimize branch lengths on a fixed topology """,
  183
+                    Use -mllen -nome with -intree to optimize branch lengths on a fixed topology.""",
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                 ),
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             _Switch(['-nome', 'nome'],
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-                """Changes support values calculation to a minimum-evolution bootstrap method
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+                """Changes support values calculation to a minimum-evolution bootstrap method.
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                     Topology refinement:
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                     By default, FastTree tries to improve the tree with up to 4*log2(N)
@@ -200,10 +200,10 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     By default, FastTree computes local support values by resampling the site
201 201
                     likelihoods 1,000 times and the Shimodaira Hasegawa test. If you specify -nome,
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                     it will compute minimum-evolution bootstrap supports instead
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-                    In either case, the support values are proportions ranging from 0 to 1""",
  203
+                    In either case, the support values are proportions ranging from 0 to 1.""",
204 204
                 ),
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             _Option(['-mlnni', 'mlnni'],
206  
-                """Set the number of rounds of maximum-likelihood NNIs
  206
+                """Set the number of rounds of maximum-likelihood NNIs.
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                     Topology refinement:
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                     By default, FastTree tries to improve the tree with up to 4*log2(N)
@@ -213,12 +213,12 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     up to 2*log(N) rounds of maximum-likelihood NNIs.
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                     Use -nni to set the number of rounds of min. evo. NNIs,
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                     and -spr to set the rounds of SPRs.
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-                    Use -mlnni to set the number of rounds of maximum-likelihood NNIs """,
  216
+                    Use -mlnni to set the number of rounds of maximum-likelihood NNIs.""",
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                 checker_function=_is_int,
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                 equate=False,
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                 ),
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             _Option(['-mlacc', 'mlacc'],
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-                """Option for optimization of branches at each NNI
  221
+                """Option for optimization of branches at each NNI.
222 222
 
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                     Topology refinement:
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                     By default, FastTree tries to improve the tree with up to 4*log2(N)
@@ -229,12 +229,12 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     Use -nni to set the number of rounds of min. evo. NNIs,
230 230
                     and -spr to set the rounds of SPRs.
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                     Use -mlacc 2 or -mlacc 3 to always optimize all 5 branches at each NNI,
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-                    and to optimize all 5 branches in 2 or 3 rounds """,
  232
+                    and to optimize all 5 branches in 2 or 3 rounds.""",
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                 checker_function=_is_int,
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                 equate=False,
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                 ),
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             _Switch(['-slownni', 'slownni'],
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-                """Turn off heuristics to avoid constant subtrees with NNIs
  237
+                """Turn off heuristics to avoid constant subtrees with NNIs.
238 238
 
239 239
                     Topology refinement:
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                     By default, FastTree tries to improve the tree with up to 4*log2(N)
@@ -245,7 +245,7 @@ def __init__(self, cmd='fasttree', **kwargs):
245 245
                     Use -nni to set the number of rounds of min. evo. NNIs,
246 246
                     and -spr to set the rounds of SPRs.
247 247
                     Use -slownni to turn off heuristics to avoid constant subtrees (affects both
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-                    ML and ME NNIs) """,
  248
+                    ML and ME NNIs).""",
249 249
                 ),
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             _Switch(['-wag', 'wag'],
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                 """Maximum likelihood model options: Whelan-And-Goldman 2001 model instead of (default) Jones-Taylor-Thorton 1992 model (a.a. only)""",
@@ -254,7 +254,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                 """Maximum likelihood model options: Use generalized time-reversible instead of (default) Jukes-Cantor (nt only)""",
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                 ),
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             _Option(['-cat', 'cat'],
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-                """Maximum likelihood model options: Specify the number of rate categories of sites (default 20) """,
  257
+                """Maximum likelihood model options: Specify the number of rate categories of sites (default 20).""",
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                 checker_function=_is_int,
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                 equate=False,
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                 ),
@@ -262,7 +262,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                 """Maximum likelihood model options: No CAT model (just 1 category)""",
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                 ),
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             _Switch(['-gamma', 'gamma'],
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-                """Report the likelihood under the discrete gamma model
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+                """Report the likelihood under the discrete gamma model.
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267 267
                     Maximum likelihood model options:
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                     -gamma -- after the final round of optimizing branch lengths with the CAT model,
@@ -274,7 +274,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     GammaLogToPaup.pl and documentation on the FastTree web site.""",
275 275
                 ),
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             _Switch(['-slow', 'slow'],
277  
-                """Use an exhaustive search
  277
+                """Use an exhaustive search.
278 278
 
279 279
                     Searching for the best join:
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                     By default, FastTree combines the 'visible set' of fast neighbor-joining with
@@ -283,7 +283,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     -slow takes half an hour instead of 8 seconds for 1,250 proteins""",
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                 ),
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             _Switch(['-fastest', 'fastest'],
286  
-                """Search the visible set (the top hit for each node) only
  286
+                """Search the visible set (the top hit for each node) only.
287 287
 
288 288
                     Searching for the best join:
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                     By default, FastTree combines the 'visible set' of fast neighbor-joining with
@@ -295,7 +295,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     -fastest sets -2nd on as well, use -fastest -no2nd to avoid this""",
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                 ),
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             _Switch(['-2nd', 'second'],
298  
-                """Turn 2nd-level top hits heuristic on
  298
+                """Turn 2nd-level top hits heuristic on.
299 299
 
300 300
                     Top-hit heuristics:
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                     By default, FastTree uses a top-hit list to speed up search
@@ -309,7 +309,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     (By default, -fastest turns on -2nd.)""",
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                 ),
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             _Switch(['-no2nd', 'no2nd'],
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-                """Turn 2nd-level top hits heuristic off
  312
+                """Turn 2nd-level top hits heuristic off.
313 313
 
314 314
                     Top-hit heuristics:
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                     By default, FastTree uses a top-hit list to speed up search
@@ -323,7 +323,7 @@ def __init__(self, cmd='fasttree', **kwargs):
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                     (By default, -fastest turns on -2nd.)""",
324 324
                 ),
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             _Option(['-seed', 'seed'],
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-                """Use -seed to initialize the random number generator
  326
+                """Use -seed to initialize the random number generator.
327 327
 
328 328
                     Support value options:
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                     By default, FastTree computes local support values by resampling the site
@@ -444,7 +444,7 @@ def __init__(self, cmd='fasttree', **kwargs):
444 444
 
445 445
                     -log logfile -- save intermediate trees so you can extract
446 446
                     the trees and restart long-running jobs if they crash
447  
-                    -log also reports the per-site rates (1 means slowest category) """,
  447
+                    -log also reports the per-site rates (1 means slowest category).""",
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                 filename=True,
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                 equate=False,
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                 ),

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