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Merge branch 'master' of github.com:biopython/biopython

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Michiel de Hoon Michiel de Hoon
Michiel de Hoon authored and Michiel de Hoon committed Dec 25, 2012
2 parents 3d92676 + 9548a51 commit fc836be385f8251a127049d5fb1bb03125f00920
Showing with 77 additions and 77 deletions.
  1. +1 −1 Bio/Align/AlignInfo.py
  2. +1 −1 Bio/Align/Applications/_Mafft.py
  3. +1 −1 Bio/Align/__init__.py
  4. +1 −1 Bio/Application/__init__.py
  5. +2 −2 Bio/Blast/Applications.py
  6. +2 −2 Bio/Blast/NCBIStandalone.py
  7. +1 −1 Bio/Blast/NCBIXML.py
  8. +3 −3 Bio/Emboss/Applications.py
  9. +1 −1 Bio/GenBank/Scanner.py
  10. +1 −1 Bio/Graphics/Comparative.py
  11. +2 −2 Bio/HMM/Trainer.py
  12. +2 −2 Bio/Motif/Applications/_AlignAce.py
  13. +2 −2 Bio/Motif/_Motif.py
  14. +6 −6 Bio/NeuralNetwork/BackPropagation/Layer.py
  15. +2 −2 Bio/NeuralNetwork/BackPropagation/Network.py
  16. +1 −1 Bio/NeuralNetwork/Gene/Motif.py
  17. +1 −1 Bio/NeuralNetwork/Gene/Schema.py
  18. +3 −3 Bio/Nexus/Trees.py
  19. +1 −1 Bio/PDB/Atom.py
  20. +1 −1 Bio/PDB/Entity.py
  21. +1 −1 Bio/PDB/PDBParser.py
  22. +1 −1 Bio/PDB/Polypeptide.py
  23. +1 −1 Bio/Pathway/__init__.py
  24. +1 −1 Bio/Phylo/Applications/_Raxml.py
  25. +2 −2 Bio/Restriction/PrintFormat.py
  26. +2 −2 Bio/Restriction/Restriction.py
  27. +4 −4 Bio/Restriction/_Update/RestrictionCompiler.py
  28. +1 −1 Bio/SCOP/Raf.py
  29. +1 −1 Bio/SeqIO/PirIO.py
  30. +1 −1 Bio/SeqIO/SffIO.py
  31. +1 −1 Bio/SeqIO/__init__.py
  32. +1 −1 Bio/SeqIO/_index.py
  33. +1 −1 Bio/Sequencing/Phd.py
  34. +1 −1 Bio/SubsMat/FreqTable.py
  35. +1 −1 Bio/SubsMat/__init__.py
  36. +1 −1 Bio/cpairwise2module.c
  37. +8 −8 Doc/Tutorial.tex
  38. +3 −3 Doc/biopdb_faq.lyx
  39. +3 −3 Doc/biopdb_faq.tex
  40. +1 −1 NEWS
  41. +1 −1 Tests/common_BioSQL.py
  42. +1 −1 Tests/test_NNGeneral.py
  43. +1 −1 Tests/test_SeqIO_FastaIO.py
  44. +1 −1 Tests/test_SeqIO_QualityIO.py
  45. +2 −2 Tests/test_SeqIO_convert.py
View
@@ -322,7 +322,7 @@ def _get_all_letters(self):
return all_letters
def _get_base_replacements(self, skip_items = []):
- """Get a zeroed dictonary of all possible letter combinations.
+ """Get a zeroed dictionary of all possible letter combinations.
This looks at the type of alphabet and gets the letters for it.
It then creates a dictionary with all possible combinations of these
@@ -327,7 +327,7 @@ def __init__(self, cmd="mafft", **kwargs):
equate=False),
#The old solution of also defining extra parameters with
#["--seed", "seed1"] etc worked, but clashes with the recent
- #code in the base class to look for duplicate paramters and raise
+ #code in the base class to look for duplicate parameters and raise
#an error. Perhaps that check should be ignored here, or maybe
#we can handle this more elegantly...
#TODO - Create an _OptionList parameter which allows a list to be
View
@@ -15,7 +15,7 @@
from Bio.SeqRecord import SeqRecord
from Bio import Alphabet
-#We only import this and subclass it for some limited backward compatibilty.
+#We only import this and subclass it for some limited backward compatibility.
from Bio.Align.Generic import Alignment as _Alignment
@@ -385,7 +385,7 @@ def __call__(self, stdin=None, stdout=True, stderr=True,
by sending it to /dev/null to avoid wasting memory (False). In the
later case empty string(s) are returned.
- The optional cwd argument is a string giving the working directory to
+ The optional cwd argument is a string giving the working directory
to run the command from. See Python's subprocess module documentation
for more details.
@@ -1383,10 +1383,10 @@ def __init__(self, cmd="blast_formatter", **kwargs):
self.parameters = [
# Input options
_Option(["-rid", "rid"],
- "BLAST Request ID (RID), not compatiable with archive arg",
+ "BLAST Request ID (RID), not compatible with archive arg",
equate=False),
_Option(["-archive", "archive"],
- "Archive file of results, not compatiable with rid arg.",
+ "Archive file of results, not compatible with rid arg.",
filename=True,
equate=False),
# Restrict search or results
@@ -17,7 +17,7 @@
NCBI BLAST, tools blastall, rpsblast and blastpgp via three helper functions of
the same name. These functions are very limited for dealing with the output as
files rather than handles, for which the wrappers in Bio.Blast.Applications are
-prefered. Furthermore, the NCBI themselves regard these command line tools as
+preferred. Furthermore, the NCBI themselves regard these command line tools as
"legacy", and encourage using the new BLAST+ tools instead. Biopython has
wrappers for these under Bio.Blast.Applications (see the tutorial).
@@ -2217,6 +2217,6 @@ def _diagnose_error(self, handle, data_record):
# to indicate a failure to perform the BLAST due to
# low quality sequence
if line.startswith('Searchingdone'):
- raise LowQualityBlastError("Blast failure occured on query: ",
+ raise LowQualityBlastError("Blast failure occurred on query: ",
data_record.query)
line = handle.readline()
View
@@ -437,7 +437,7 @@ def _end_Hsp_bit_score(self):
self._descr.bits = float(self._value)
def _end_Hsp_evalue(self):
- """expect value value of the HSP
+ """expect value of the HSP
"""
self._hsp.expect = float(self._value)
if self._descr.e is None:
@@ -640,7 +640,7 @@ def __init__(self, cmd = "fdnapars", **kwargs):
_Option(["-njumble", "njumble"],
"number of times to randomise input order (default is 0)"),
_Option(["-seed", "seed"],
- "provde random seed"),
+ "provide random seed"),
_Option(["-outgrno", "outgrno"],
"Specify outgroup"),
_Option(["-thresh", "thresh"],
@@ -684,7 +684,7 @@ def __init__(self, cmd = "fprotpars", **kwargs):
_Option(["-njumble", "njumble"],
"number of times to randomise input order (default is 0)"),
_Option(["-seed", "seed"],
- "provde random seed"),
+ "provide random seed"),
_Option(["-outgrno", "outgrno"],
"Specify outgroup"),
_Option(["-thresh", "thresh"],
@@ -735,7 +735,7 @@ def __init__(self, cmd = "fprotdist", **kwargs):
_Option(["-ttratio", "ttratio"],
"Transition/transversion ratio (0-1)"),
_Option(["-basefreq", "basefreq"],
- "DNA base frequencies (space seperated list)")]
+ "DNA base frequencies (space separated list)")]
_EmbossCommandLine.__init__(self, cmd, **kwargs)
View
@@ -1257,7 +1257,7 @@ def _feed_header_lines(self, consumer, lines):
#species names (as more and more strains and sub strains get
#sequenced) the oragnism name can now get wrapped onto multiple
#lines. The NCBI say we have to recognise the lineage line by
- #the presense of semi-colon delimited entries. In the long term,
+ #the presence of semi-colon delimited entries. In the long term,
#they are considering adding a new keyword (e.g. LINEAGE).
#See Bug 2591 for details.
organism_data = data
@@ -46,7 +46,7 @@ def __init__(self, output_format = 'pdf'):
# the information we'll be writing
self.display_info = []
- # inital colors and shapes used for drawing points
+ # initial colors and shapes used for drawing points
self.color_choices = [colors.red, colors.green, colors.blue,
colors.yellow, colors.orange, colors.black]
self.shape_choices = [makeFilledCircle, makeEmptySquare,
View
@@ -2,7 +2,7 @@
These should be used to 'train' a Markov Model prior to actually using
it to decode state paths. When supplied training sequences and a model
-to work from, these classes will estimate paramters of the model.
+to work from, these classes will estimate parameters of the model.
This aims to estimate two parameters:
@@ -53,7 +53,7 @@ def log_likelihood(self, probabilities):
Arguments:
o probabilities -- A list of the probabilities of each training
- sequence under the current paramters, calculated using the forward
+ sequence under the current parameters, calculated using the forward
algorithm.
"""
total_likelihood = 0
@@ -29,7 +29,7 @@
class AlignAceCommandline(AbstractCommandline):
"""Create a commandline for the AlignAce program.
- XXX This could use more checking for valid paramters to the program.
+ XXX This could use more checking for valid parameters to the program.
"""
def __init__(self, cmd="AlignACE", **kwargs):
self.parameters = \
@@ -64,7 +64,7 @@ def __init__(self, cmd="AlignACE", **kwargs):
class CompareAceCommandline(AbstractCommandline):
"""Create a commandline for the CompareAce program.
- XXX This could use more checking for valid paramters to the program.
+ XXX This could use more checking for valid parameters to the program.
"""
def __init__(self, cmd="CompareACE", **kwargs):
import os.path
View
@@ -842,7 +842,7 @@ def dist_pearson_at(self,motif,offset):
def dist_product(self,other):
"""
- A similarity measure taking into account a product probability of generating overlaping instances of two motifs
+ A similarity measure taking into account a product probability of generating overlapping instances of two motifs
"""
warnings.warn("""\
This function is now obsolete, and will be deprecated and removed
@@ -972,7 +972,7 @@ def __str__(self,masked=False):
def __len__(self):
"""return the length of a motif
- Please use this method (i.e. invoke len(m)) instead of refering to the m.length directly.
+ Please use this method (i.e. invoke len(m)) instead of referring to m.length directly.
"""
if self.length is None:
return 0
@@ -111,7 +111,7 @@ def update(self, inputs):
for input_num in range(len(inputs)):
self.values[input_num + 1] = inputs[input_num]
- # propogate the update to the next layer
+ # propagate the update to the next layer
self._next_layer.update(self)
def backpropagate(self, outputs, learning_rate, momentum):
@@ -126,7 +126,7 @@ def backpropagate(self, outputs, learning_rate, momentum):
o outputs - The output info we are using to calculate error.
"""
- # first backpropogate to the next layers
+ # first backpropagate to the next layers
next_errors = self._next_layer.backpropagate(outputs, learning_rate,
momentum)
@@ -203,7 +203,7 @@ def update(self, previous_layer):
self.values[update_node] = self._activation(sum)
- # propogate the update to the next layer
+ # propagate the update to the next layer
self._next_layer.update(self)
def backpropagate(self, outputs, learning_rate, momentum):
@@ -219,7 +219,7 @@ def backpropagate(self, outputs, learning_rate, momentum):
o outputs - The output values we are using to see how good our
network is at predicting things.
"""
- # first backpropogate to the next layers
+ # first backpropagate to the next layers
next_errors = self._next_layer.backpropagate(outputs, learning_rate,
momentum)
@@ -241,7 +241,7 @@ def backpropagate(self, outputs, learning_rate, momentum):
# --- calculate error terms
errors = {}
for error_node in self.nodes:
- # get the error info propogated from the next layer
+ # get the error info propagated from the next layer
previous_error = 0.0
for next_node in self._next_layer.nodes:
previous_error += (next_errors[next_node] *
@@ -282,7 +282,7 @@ def update(self, previous_layer):
Arguments:
- o previous_layer -- The hidden layer preceeding this.
+ o previous_layer -- The hidden layer preceding this.
"""
# update all of the nodes in this layer
for update_node in self.nodes:
@@ -65,10 +65,10 @@ def train(self, training_examples, validation_examples,
for example in training_examples:
# update the predicted values for all of the nodes
# based on the current weights and the inputs
- # This propogates over the entire network from the input.
+ # This propagates over the entire network from the input.
self._input.update(example.inputs)
- # calculate the error via back propogation
+ # calculate the error via back propagation
self._input.backpropagate(example.outputs,
learning_rate, momentum)
@@ -178,7 +178,7 @@ def representation(self, sequence):
This converts a sequence into a representation based on the motifs.
The representation is returned as a list of the relative amount of
- each motif (number of times a motif occured divided by the total
+ each motif (number of times a motif occurred divided by the total
number of motifs in the sequence). The values in the list correspond
to the input order of the motifs specified in the initializer.
"""
@@ -47,7 +47,7 @@ def __init__(self, ambiguity_info):
o ambiguity_info - A dictionary which maps letters in the motifs to
the ambiguous characters which they might represent. For example,
- {'R' : 'AG'} specifies that Rs in the motif can match a A or a G.
+ {'R' : 'AG'} specifies that Rs in the motif can match an A or a G.
All letters in the motif must be represented in the ambiguity_info
dictionary.
"""
View
@@ -527,7 +527,7 @@ def randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=No
def display(self):
"""Quick and dirty lists of all nodes."""
table=[('#','taxon','prev','succ','brlen','blen (sum)','support','comment')]
- #Sort this to be consistent accross CPython, Jython, etc
+ #Sort this to be consistent across CPython, Jython, etc
for i in sorted(self.all_ids()):
n=self.node(i)
if not n.data:
@@ -754,9 +754,9 @@ def merge_with_support(self,bstrees=None,constree=None,threshold=0.5,outgroup=No
"""
if bstrees and constree:
- raise TreeError('Specify either list of boostrap trees or consensus tree, not both')
+ raise TreeError('Specify either list of bootstrap trees or consensus tree, not both')
if not (bstrees or constree):
- raise TreeError('Specify either list of boostrap trees or consensus tree.')
+ raise TreeError('Specify either list of bootstrap trees or consensus tree.')
# no outgroup specified: use the smallest clade of the root
if outgroup is None:
try:
View
@@ -65,7 +65,7 @@ def __init__(self, name, coord, bfactor, occupancy, altloc, fullname, serial_num
self.siguij_array=None
self.sigatm_array=None
self.serial_number=serial_number
- # Dictionary that keeps addictional properties
+ # Dictionary that keeps additional properties
self.xtra={}
assert not element or element == element.upper(), element
self.element = self._assign_element(element)
View
@@ -24,7 +24,7 @@ def __init__(self, id):
self.parent=None
self.child_list=[]
self.child_dict={}
- # Dictionary that keeps addictional properties
+ # Dictionary that keeps additional properties
self.xtra={}
# Special methods
View
@@ -47,7 +47,7 @@ def __init__(self, PERMISSIVE=True, get_header=False,
o structure_builder - an optional user implemented StructureBuilder class.
o QUIET - Evaluated as a Boolean. If true, warnings issued in constructing
- the SMCRA data will be supressed. If false (DEFAULT), they will be shown.
+ the SMCRA data will be suppressed. If false (DEFAULT), they will be shown.
These warnings might be indicative of problems in the PDB file!
"""
if structure_builder is not None:
View
@@ -337,7 +337,7 @@ def build_peptides(self, entity, aa_only=1):
is_connected=self._is_connected
accept=self._accept
level=entity.get_level()
- # Decide wich entity we are dealing with
+ # Decide which entity we are dealing with
if level=="S":
model=entity[0]
chain_list=model.get_list()
View
@@ -16,7 +16,7 @@
Network objects are used to represent the connectivity between species in pathways
and reaction networks.
-For applications where it is not neccessary to explicitly represent network connectivity,
+For applications where it is not necessary to explicitly represent network connectivity,
the specialized classes Reaction and System should be used in place of Interacton and
Network.
@@ -354,7 +354,7 @@ def __init__(self, cmd='raxmlHPC', **kwargs):
_Option(['-N', '-#', 'num_replicates'],
"Number of alternative runs on distinct starting trees. "
"In combination with the '-b' option, this will invoke a "
- "multiple boostrap analysis. "
+ "multiple bootstrap analysis. "
"DEFAULT: 1 single analysis."
"Note that '-N' has been added as an alternative since "
"'-#' sometimes caused problems with certain MPI job "
@@ -55,7 +55,7 @@
>>> new.print_that(dct)
...
- Some of the methods of PrintFormat are meant to be overriden by derived
+ Some of the methods of PrintFormat are meant to be overridden by derived
class.
"""
@@ -100,7 +100,7 @@ def print_that(self, dct, title='', s1=''):
dct is a dictionary as returned by a RestrictionBatch.search()
title is the title of the map.
- It must be a formated string, i.e. you must include the line break.
+ It must be a formatted string, i.e. you must include the line break.
s1 is the title separating the list of enzymes that have sites from
those without sites.
@@ -802,7 +802,7 @@ def is_methylable(self):
class Meth_Undep(AbstractCut):
- """Implement informations about methylation sensitibility.
+ """Implement information about methylation sensitibility.
Enzymes of this class are not sensible to methylation."""
@@ -2265,7 +2265,7 @@ def with_name(self, names, dct=None):
Limit the search to the enzymes named in list_of_names."""
for i, enzyme in enumerate(names):
if not enzyme in AllEnzymes:
- print "no datas for the enzyme:", str(name)
+ print "no data for the enzyme:", str(name)
del names[i]
if not dct:
return RestrictionBatch(names).search(self.sequence)
@@ -30,9 +30,9 @@
The Rebase files are in the emboss format:
- emboss_e.### -> contains informations about the restriction sites.
- emboss_r.### -> contains general informations about the enzymes.
- emboss_s.### -> contains informations about the suppliers.
+ emboss_e.### -> contains information about the restriction sites.
+ emboss_r.### -> contains general information about the enzymes.
+ emboss_s.### -> contains information about the suppliers.
### is a 3 digit number. The first digit is the year and the two last the month.
"""
@@ -485,7 +485,7 @@ def build_dict(self):
results.write("rest_dict[%s] = _temp()\n" % repr(name))
results.write("\n")
print 'OK.\n'
- print 'Writing the dictionary containing the suppliers datas.\t\t',
+ print 'Writing the dictionary containing the suppliers data.\t\t',
results.write('suppliers = {}\n')
for name in sorted(suppliersdict) :
results.write("def _temp():\n")
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