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Assorted fixes for typos, duplicate words etc.

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commit 723313c427f4a6d8289124db8399479b95dce49a 1 parent 316c42a
@cbrueffer cbrueffer authored peterjc committed
View
2  Bio/AlignIO/FastaIO.py
@@ -117,7 +117,7 @@ def build_hsp():
if tool in ["TFASTX"] and len(match_seq) == len(q):
m = match_seq
#Quick hack until I can work out how -, * and / characters
- #and the apparent mix of aa and bp coordindates works.
+ #and the apparent mix of aa and bp coordinates works.
else:
m = _extract_alignment_region(match_seq, match_tags)
assert len(q) == len(m)
View
4 Bio/AlignIO/__init__.py
@@ -299,7 +299,7 @@ def parse(handle, format, seq_count=None, alphabet=None):
Arguments:
- handle - handle to the file, or the filename as a string
- (note older verions of Biopython only took a handle).
+ (note older versions of Biopython only took a handle).
- format - string describing the file format.
- alphabet - optional Alphabet object, useful when the sequence type
cannot be automatically inferred from the file itself
@@ -376,7 +376,7 @@ def read(handle, format, seq_count=None, alphabet=None):
Arguments:
- handle - handle to the file, or the filename as a string
- (note older verions of Biopython only took a handle).
+ (note older versions of Biopython only took a handle).
- format - string describing the file format.
- alphabet - optional Alphabet object, useful when the sequence type
cannot be automatically inferred from the file itself
View
2  Bio/Blast/Applications.py
@@ -217,7 +217,7 @@ def __init__(self, cmd="blastall",**kwargs):
self.parameters = [
#Sorted in the same order as the output from blastall --help
#which should make it easier to keep them up to date in future.
- #Note that some arguments are defined the the base clases (above).
+ #Note that some arguments are defined in the base classes (above).
_Option(["-p", "program"],
"The blast program to use (e.g. blastp, blastn).",
is_required=True,
View
6 Bio/GA/Organism.py
@@ -20,7 +20,7 @@ def function_population(new_genome, num_organisms, fitness_calculator):
o num_organisms - The number of individuals we want in the population.
- o fitness_calculator -- A funtion that will calculate the fitness
+ o fitness_calculator -- A function that will calculate the fitness
of the organism when given the organisms genome.
"""
all_orgs = []
@@ -46,7 +46,7 @@ def random_population(genome_alphabet, genome_size, num_organisms,
o num_organism -- The number of organisms we want in the population.
- o fitness_calculator -- A funtion that will calculate the fitness
+ o fitness_calculator -- A function that will calculate the fitness
of the organism when given the organisms genome.
"""
all_orgs = []
@@ -105,7 +105,7 @@ def __init__(self, genome, fitness_calculator, start_fitness = None):
o genome -- A MutableSeq object representing the sequence of the
genome.
- o fitness_calculator -- A funtion that will calculate the fitness
+ o fitness_calculator -- A function that will calculate the fitness
of the organism when given the organisms genome.
o start_fitness - the starting fitness corresponding with the
View
4 Bio/Graphics/BasicChromosome.py
@@ -591,7 +591,7 @@ def __init__(self, bp_length, features,
Note we require 0 <= start <= end <= bp_length, and within the vertical
space allocated to this segmenet lines will be places according to the
- start/end coordindates (starting from the top).
+ start/end coordinates (starting from the top).
Positive stand features are drawn on the right, negative on the left,
otherwise all the way across.
@@ -731,7 +731,7 @@ def _draw_segment(self, cur_drawing):
cap_wedge.fillColor = self.fill_color
cur_drawing.add(cap_wedge)
- #Now draw an arc for the the curved edge of the wedge,
+ #Now draw an arc for the curved edge of the wedge,
#omitting the flat end.
cap_arc = ArcPath()
cap_arc.addArc(center_x, center_y, width / 2,
View
2  Bio/HotRand.py
@@ -3,7 +3,7 @@
# license. Please see the LICENSE file that should have been included
# as part of this package.
-"""handles true random numbers supplied from the the web server of
+"""handles true random numbers supplied from the web server of
fourmilab. Based on atmospheric noise. The motivation is to
support biosimulations that rely on random numbers.
"""
View
2  Bio/PDB/PDBParser.py
@@ -181,7 +181,7 @@ def _parse_coordinates(self, coords_trailer):
z = float(line[46:54])
except:
# Should we allow parsing to continue in permissive mode?
- # If so, what coordindates should we default to? Easier to abort!
+ # If so, what coordinates should we default to? Easier to abort!
raise PDBConstructionException("Invalid or missing coordinate(s) at line %i."
% global_line_counter)
coord = numpy.array((x, y, z), "f")
View
2  Bio/SCOP/Cla.py
@@ -117,7 +117,7 @@ def __init__(self, filename):
f.close()
def __getitem__(self, key):
- """ Return an item from the indexed file. """
+ """Return an item from the indexed file."""
position = dict.__getitem__(self,key)
f = open(self.filename, "rU")
View
4 Bio/SCOP/Hie.py
@@ -4,7 +4,7 @@
# as part of this package.
-""" Handle the SCOP HIErarchy files, which describe the SCOP hierarchy in
+"""Handle the SCOP HIErarchy files, which describe the SCOP hierarchy in
terms of SCOP unique identifiers (sunid).
The file format is described in the scop
@@ -21,7 +21,7 @@ class Record(object):
sunid -- SCOP unique identifiers of this node
- parent -- Parents sunid
+ parent -- Parents sunid
children -- Sequence of childrens sunids
"""
View
2  Bio/SCOP/Residues.py
@@ -18,7 +18,7 @@ class Residues(object):
"""A collection of residues from a PDB structure.
This class provides code to work with SCOP domain definitions. These
- are concisely expressed as a one or more chain fragments. For example,
+ are concisely expressed as one or more chain fragments. For example,
"(1bba A:10-20,B:)" indicates residue 10 through 20 (inclusive) of
chain A, and every residue of chain B in the pdb structure 1bba. The pdb
id and brackets are optional. In addition "-" indicates every residue of
View
2  Bio/SearchIO/ExonerateIO/__init__.py
@@ -36,7 +36,7 @@
- Cigar line - 'exonerate-cigar' - parsing, indexing
On Exonerate, these output formats are not exclusive to one another. For
-example, you may have both plain text and vulgar ouput in the same file.
+example, you may have both plain text and vulgar output in the same file.
ExonerateIO can only handle one of these at a time, however. If you have a file
containing both plain text and vulgar lines, for example, you have to pick
either 'exonerate-text' or 'exonerate-vulgar' to parse it.
View
2  Bio/SearchIO/HmmerIO/__init__.py
@@ -44,7 +44,7 @@
accordingly to fit SearchIO's object model. If HmmerIO sees that the output file
to parse was written by hmmsearch or phmmer, all 'hmm' coordinates will be the
hit coordinates and 'ali' coordinates will be the query coordinates. Conversely,
-if the the HMMER flavor is hmmscan, 'hmm' will be query and 'ali' will be hit.
+if the HMMER flavor is hmmscan, 'hmm' will be query and 'ali' will be hit.
This is why the 'hmmer3-domtab' format has to be specified with the source HMMER
flavor. The parsers need to know which is the hit and which is the query.
View
2  Bio/SearchIO/HmmerIO/hmmer3_text.py
@@ -192,7 +192,7 @@ def _parse_hit(self, qid):
'bitscore': float(row[1]),
'bias': float(row[2]),
# row[3:6] is not parsed, since the info is available
- # at the the HSP level
+ # at the HSP level
'domain_exp_num': float(row[6]),
'domain_obs_num': int(row[7]),
'description': row[9],
View
2  Bio/SearchIO/_model/hsp.py
@@ -34,7 +34,7 @@ class HSP(_BaseHSP):
with one HSPFragments are BLAST, HMMER, and FASTA. Other programs such as
BLAT or Exonerate may produce HSPs containing more than one HSPFragment.
However, their native terminologies may differ: in BLAT these fragments
- are called 'blocks' while in in Exonerate they are called exons or NER.
+ are called 'blocks' while in Exonerate they are called exons or NER.
Here are examples from each type of HSP. The first one comes from a BLAST
search:
View
2  Bio/SearchIO/_model/query.py
@@ -165,7 +165,7 @@ class QueryResult(_BaseSearchObject):
Hit(id='gi|301171322|ref|NR_035857.1|', query_id='33211', 2 hsps)
If you need access to all the hits in a QueryResult object, you can get
- them in a list using the `hits` property. Similary, access to all hit IDs is
+ them in a list using the `hits` property. Similarly, access to all hit IDs is
available through the `hit_keys` property.
>>> qresult.hits
View
8 Bio/SeqFeature.py
@@ -73,7 +73,7 @@ class SeqFeature(object):
o ref_db - A different database for the reference accession number.
Note this is a shortcut for the reference property of the location
o qualifiers - A dictionary of qualifiers on the feature. These are
- analagous to the qualifiers from a GenBank feature table. The keys of
+ analogous to the qualifiers from a GenBank feature table. The keys of
the dictionary are qualifier names, the values are the qualifier
values.
o sub_features - Additional SeqFeatures which fall under this 'parent'
@@ -529,8 +529,8 @@ class FeatureLocation(object):
Note that for a parent sequence of length n, the FeatureLocation
start and end must satisfy the inequality 0 <= start <= end <= n.
This means even for features on the reverse strand of a nucleotide
- sequence, we expect the 'start' coordindate to be less than the
- 'end' coordindate.
+ sequence, we expect the 'start' coordinate to be less than the
+ 'end' coordinate.
>>> from Bio.SeqFeature import FeatureLocation
>>> r = FeatureLocation(122, 150, strand=-1)
@@ -947,7 +947,7 @@ class WithinPosition(int, AbstractPosition):
This allows dealing with a position like ((1.4)..100). This
indicates that the start of the sequence is somewhere between 1
- and 4. Since this is a start coordindate, it should acts like
+ and 4. Since this is a start coordinate, it should acts like
it is at position 1 (or in Python counting, 0).
>>> p = WithinPosition(10,10,13)
View
2  Bio/SeqIO/InsdcIO.py
@@ -403,7 +403,7 @@ def _write_single_line(self, tag, text):
text.replace("\n", " ")))
def _write_multi_line(self, tag, text):
- """Used in the the 'header' of each GenBank record."""
+ """Used in the 'header' of each GenBank record."""
#TODO - Do the line spliting while preserving white space?
max_len = self.MAX_WIDTH - self.HEADER_WIDTH
lines = self._split_multi_line(text, max_len)
View
4 Bio/SeqIO/__init__.py
@@ -451,7 +451,7 @@ def parse(handle, format, alphabet=None):
r"""Turns a sequence file into an iterator returning SeqRecords.
- handle - handle to the file, or the filename as a string
- (note older verions of Biopython only took a handle).
+ (note older versions of Biopython only took a handle).
- format - lower case string describing the file format.
- alphabet - optional Alphabet object, useful when the sequence type
cannot be automatically inferred from the file itself
@@ -561,7 +561,7 @@ def read(handle, format, alphabet=None):
"""Turns a sequence file into a single SeqRecord.
- handle - handle to the file, or the filename as a string
- (note older verions of Biopython only took a handle).
+ (note older versions of Biopython only took a handle).
- format - string describing the file format.
- alphabet - optional Alphabet object, useful when the sequence type
cannot be automatically inferred from the file itself
View
2  Bio/SeqUtils/__init__.py
@@ -86,7 +86,7 @@ def GC123(seq):
def GC_skew(seq, window = 100):
- """Calculates GC skew (G-C)/(G+C) for multuple windows along the sequence.
+ """Calculates GC skew (G-C)/(G+C) for multiple windows along the sequence.
Returns a list of ratios (floats), controlled by the length of the sequence
and the size of the window.
View
4 Bio/SwissProt/__init__.py
@@ -93,9 +93,9 @@ class Reference(object):
Members:
number Number of reference in an entry.
- positions Describes extent of work. list of strings.
+ positions Describes extent of work. List of strings.
comments Comments. List of (token, text).
- references References. List of (dbname, identifier)
+ references References. List of (dbname, identifier).
authors The authors of the work.
title Title of the work.
location A citation for the work.
View
2  BioSQL/Loader.py
@@ -447,7 +447,7 @@ def _get_taxon_id_from_ncbi_lineage(self, taxonomic_lineage):
- ScientificName (string)
(and that is all at the time of writing)
- This method will record all the lineage given, returning the the taxon id
+ This method will record all the lineage given, returning the taxon id
(database key, not NCBI taxon id) of the final entry (the species).
"""
ncbi_taxon_id = taxonomic_lineage[-1]["TaxId"]
View
6 DEPRECATED
@@ -59,7 +59,7 @@ and removed in Release 1.59.
Bio.Parsers and Bio.Parsers.spark
=================================
This module was a copy of John Aycock's SPARK parser included with Biopython
-soley for use in Bio.GenBank.LocationParser. Declared obsolete in Release
+solely for use in Bio.GenBank.LocationParser. Declared obsolete in Release
1.55, deprecated in Release 1.56, and removed in Release 1.59.
Bio.Restriction.DNAUtils and check_bases
@@ -398,7 +398,7 @@ Function 'reverse' in Bio.SeqUtils was deprecated in Release 1.54, and
removed in Release 1.58. Instead just use the string's slice method with
a step of minus one.
-Funtions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
+Functions GC_Frame, fasta_uniqids, apply_on_multi_fasta, and
quicker_apply_on_multi_fasta were deprecated in Release 1.55, and removed
in Release 1.58.
@@ -424,7 +424,7 @@ Use Bio.SeqUtils instead.
Bio.SVM
=======
Deprecated as of Release 1.30, removed in Release 1.42.
-The Support Vector Machine code in Biopython has been superceeded by a
+The Support Vector Machine code in Biopython has been superseded by a
more robust (and maintained) SVM library, which includes a python
interface. We recommend using LIBSVM:
View
28 Doc/Tutorial.tex
@@ -237,7 +237,7 @@ \section{Frequently Asked Questions (FAQ)}
You need Biopython 1.53 or later. Alternatively, use \verb|str(my_seq).upper()| to get an upper case string.
If you need a Seq object, try \verb|Seq(str(my_seq).upper())| but be careful about blindly re-using the same alphabet.
- \item \emph{Why does't the} \verb|Seq| \emph{object translation method support the} \verb|cds| \emph{option described in this Tutorial?} \\
+ \item \emph{Why doesn't the} \verb|Seq| \emph{object translation method support the} \verb|cds| \emph{option described in this Tutorial?} \\
You need Biopython 1.51 or later.
\item \emph{Why doesn't} \verb|Bio.SeqIO| \emph{work? It imports fine but there is no parse function etc.} \\
@@ -1385,7 +1385,7 @@ \section{Working with directly strings}
\chapter{Sequence Record objects}
\label{chapter:SeqRecord}
-Chapter~\ref{chapter:Bio.Seq} introduced the sequence classes. Immediately ``above'' the \verb|Seq| class is the Sequence Record or \verb|SeqRecord| class, defined in the \verb|Bio.SeqRecord| module. This class allows higher level features such as identifiers and features to be associated with the sequence, and is used thoughout the sequence input/output interface \verb|Bio.SeqIO| described fully in Chapter~\ref{chapter:Bio.SeqIO}.
+Chapter~\ref{chapter:Bio.Seq} introduced the sequence classes. Immediately ``above'' the \verb|Seq| class is the Sequence Record or \verb|SeqRecord| class, defined in the \verb|Bio.SeqRecord| module. This class allows higher level features such as identifiers and features to be associated with the sequence, and is used throughout the sequence input/output interface \verb|Bio.SeqIO| described fully in Chapter~\ref{chapter:Bio.SeqIO}.
If you are only going to be working with simple data like FASTA files, you can probably skip this chapter
for now. If on the other hand you are going to be using richly annotated sequence data, say from GenBank
@@ -1411,13 +1411,13 @@ \section{The SeqRecord object}
\item[id] -- The primary ID used to identify the sequence -- a string. In most cases this is something like an accession number.
- \item[name] -- A ``common'' name/id for the sequence -- a string. In some cases this will be the same as the accession number, but it could also be a clone name. I think of this as being analagous to the LOCUS id in a GenBank record.
+ \item[name] -- A ``common'' name/id for the sequence -- a string. In some cases this will be the same as the accession number, but it could also be a clone name. I think of this as being analogous to the LOCUS id in a GenBank record.
\item[description] -- A human readable description or expressive name for the sequence -- a string.
\item[letter\_annotations] -- Holds per-letter-annotations using a (restricted) dictionary of additional information about the letters in the sequence. The keys are the name of the information, and the information is contained in the value as a Python sequence (i.e. a list, tuple or string) with the same length as the sequence itself. This is often used for quality scores (e.g. Section~\ref{sec:FASTQ-filtering-example}) or secondary structure information (e.g. from Stockholm/PFAM alignment files).
- \item[annotations] -- A dictionary of additional information about the sequence. The keys are the name of the information, and the information is contained in the value. This allows the addition of more ``unstructed'' information to the sequence.
+ \item[annotations] -- A dictionary of additional information about the sequence. The keys are the name of the information, and the information is contained in the value. This allows the addition of more ``unstructured'' information to the sequence.
\item[features] -- A list of \verb|SeqFeature| objects with more structured information about the features on a sequence (e.g. position of genes on a genome, or domains on a protein sequence). The structure of sequence features is described below in Section~\ref{sec:seq_features}.
@@ -1735,12 +1735,12 @@ \subsection{Locations}
The complication in dealing with locations comes in the positions themselves. In biology many times things aren't entirely certain (as much as us wet lab biologists try to make them certain!). For instance, you might do a dinucleotide priming experiment and discover that the start of mRNA transcript starts at one of two sites. This is very useful information, but the complication comes in how to represent this as a position. To help us deal with this, we have the concept of fuzzy positions. Basically there are five types of fuzzy positions, so we have five classes do deal with them:
\begin{description}
- \item[ExactPosition] -- As its name suggests, this class represents a position which is specified as exact along the sequence. This is represented as just a a number, and you can get the position by looking at the \verb|position| attribute of the object.
+ \item[ExactPosition] -- As its name suggests, this class represents a position which is specified as exact along the sequence. This is represented as just a number, and you can get the position by looking at the \verb|position| attribute of the object.
\item[BeforePosition] -- This class represents a fuzzy position
that occurs prior to some specified site. In GenBank/EMBL notation,
this is represented as something like \verb|`<13'|, signifying that
- the real position is located somewhere less then 13. To get
+ the real position is located somewhere less than 13. To get
the specified upper boundary, look at the \verb|position|
attribute of the object.
@@ -1826,7 +1826,7 @@ \subsection{Locations}
Notice that this just gives you back the position attributes of the fuzzy locations.
-Similary, to make it easy to create a position without worrying about fuzzy positions, you can just pass in numbers to the \verb|FeaturePosition| constructors, and you'll get back out \verb|ExactPosition| objects:
+Similarly, to make it easy to create a position without worrying about fuzzy positions, you can just pass in numbers to the \verb|FeaturePosition| constructors, and you'll get back out \verb|ExactPosition| objects:
%cont-doctest
\begin{verbatim}
@@ -6232,7 +6232,7 @@ \subsection{HSP}
\item We've also got the matching range of the query and hit sequences. The
slice notation we're using here is an indication that the range is displayed
using Python's indexing style (zero-based, half open). The number inside the
- parenthesis denotes the strand. In this case, both sequences have the plust
+ parenthesis denotes the strand. In this case, both sequences have the plus
strand.
\item Some quick statistics are available: the e-value and bitscore.
\item There is information about the HSP fragments. Ignore this for now; it will
@@ -6338,7 +6338,7 @@ \subsection{HSP}
Fragments: 1 (? columns)
\end{verbatim}
-Some of the outputs you may have alredy guessed. We have the query and hit IDs
+Some of the outputs you may have already guessed. We have the query and hit IDs
and descriptions and the sequence coordinates. Values for evalue and bitscore is
`?' as BLAT HSPs do not have these attributes. But The biggest difference here
is that you don't see any sequence alignments displayed. If you look closer, PSL
@@ -6419,7 +6419,7 @@ \subsection{HSP}
Take a look at the hit coordinate of the HSP above. In the \verb|Hit range:| field,
we see that the coordinate is \verb|[54233104:54264463]|. But looking at the
table rows, we see that not the entire region spanned by this coordinate matches
-our query. Specificallly, the intervening region spans from \verb|54233122| to
+our query. Specifically, the intervening region spans from \verb|54233122| to
\verb|54264420|.
Why then, is the query coordinates seem to be contiguous, you ask? This is
@@ -6547,7 +6547,7 @@ \section{A note about standards and conventions}
For example, one tools might use one-based coordinates, while the other uses
zero-based coordinates. Or, one program might reverse the start and end
coordinates if the strand is minus, while others don't. In short, these often
-creates unecessary mess that we must deal with.
+creates unnecessary mess that we must deal with.
We realize this problem ourselves and we intend to address it in
\verb|Bio.SearchIO|. After all, one of the goals of \verb|Bio.SearchIO| is to
@@ -6700,7 +6700,7 @@ \section{Dealing with large search output files with indexing}
\section{Writing and converting search output files}
\label{sec:searchio-write}
-It is occasionally useful to be able to manipulate search results from an ouput
+It is occasionally useful to be able to manipulate search results from an output
file and write it again to a new file. \verb|Bio.SearchIO| provides a
\verb|write| function that lets you do exactly this. It takes as its arguments
an iterable returning \verb|QueryResult| objects, the output filename to write
@@ -7194,7 +7194,7 @@ \section{ELink: Searching for related items in NCBI Entrez}
['19304878']
\end{verbatim}
-The \verb+"LinkSetDb"+ key contains the search results, stored as a list consisting of one item for each target database. In our search results, we only find hits in the PubMed database (although sub-diveded into categories):
+The \verb+"LinkSetDb"+ key contains the search results, stored as a list consisting of one item for each target database. In our search results, we only find hits in the PubMed database (although sub-divided into categories):
\begin{verbatim}
>>> len(record[0]["LinkSetDb"])
@@ -14447,7 +14447,7 @@ \subsection{Converting SFF files}
\label{sec:SeqIO-sff-conversion}
If you work with 454 (Roche) sequence data, you will probably have access
-to the raw data as an Standard Flowgram Format (SFF) file. This contains
+to the raw data as a Standard Flowgram Format (SFF) file. This contains
the sequence reads (called bases) with quality scores and the original
flow information.
View
18 NEWS
@@ -28,7 +28,7 @@ different ways. The "pdb-atom" format determines the sequence as it appears in
the structure based on the atom coordinate section of the file (via Bio.PDB,
so NumPy is currently required for this). Alternatively, you can use the
"pdb-seqres" format to read the complete protein sequence as it is listed in
-the the PDB header, if available.
+the PDB header, if available.
The Bio.SeqUtils module how has a seq1 function to turn a sequence using three
letter amino acid codes into one using the more common one letter codes. This
@@ -208,12 +208,12 @@ would only return alignments for the first query sequence.
The Bio.AlignIO "phylip" parser and writer now treat a dot/period in the
sequence as an error, in line with the official PHYLIP specification. Older
-verions of our code didn't do anything special with this character. Also,
+versions of our code didn't do anything special with this character. Also,
support for "phylip-relaxed" has been added which allows longer record names
as used in RAxML and PHYML.
Of potential interest to anyone subclassing Biopython objects, any remaining
-"old syle" Python classes have been switched to "new style" classes. This
+"old style" Python classes have been switched to "new style" classes. This
allows things like defining properties.
Bio.HMM's Viterbi algorithm now expects the initial probabilities explicitly.
@@ -273,7 +273,7 @@ their element type and IUPAC mass. (The new features that use these
attributes won't be included in Biopython until the next release, though, so
stay tuned.)
-The nodetype hierachy in the Bio.SCOP.Cla.Record class is now a dictionary
+The nodetype hierarchy in the Bio.SCOP.Cla.Record class is now a dictionary
(previously it was a list of key,value tuples) to better match the standard.
Many thanks to the Biopython developers and community for making this release
@@ -311,16 +311,16 @@ Bio.SeqIO can now read, write and index IMGT files. These are a variant of
the EMBL sequence text file format with longer feature indentation.
Bio.SeqIO now supports protein EMBL files (used in the EMBL patents database
-file epo_prt.dat) - perviously we only expected nucleotide EMBL files.
+file epo_prt.dat) - previously we only expected nucleotide EMBL files.
The Bio.Seq translation methods and function will now accept an arbitrary
CodonTable object (for those of you working on very unusual organisms).
The SeqFeature object now supports len(feature) giving the length consistent
with the existing extract method. Also, it now supports iteration giving the
-coordindate (with respect to the parent sequence) of each letter within the
+coordinate (with respect to the parent sequence) of each letter within the
feature (in frame aware order), and "in" which allows you to check if a
-(parent based) coordindate is within the feature location.
+(parent based) coordinate is within the feature location.
Bio.Entrez will now try to download any missing NCBI DTD files and cache them
in the user's home directory.
@@ -585,7 +585,7 @@ optimisations (e.g. FASTQ to FASTA, and interconverting FASTQ variants).
New function Bio.SeqIO.index() allows indexing of most sequence file formats
(but not alignment file formats), allowing dictionary like random access to
all the entries in the file as SeqRecord objects, keyed on the record id.
-This is epecially useful for very large sequencing files, where all the
+This is especially useful for very large sequencing files, where all the
records cannot be held in memory at once. This supplements the more flexible
but memory demanding Bio.SeqIO.to_dict() function.
@@ -1234,7 +1234,7 @@ Dec 17, 2002: Biopython 1.10
pairwise2 replaces fastpairwise and pairwise
removed deprecated Sequence.py package
minor bug fix in File.SGMLStripper
- added Scripts/debug/debug_blast_parser.py to diagnoze blast parsing errors
+ added Scripts/debug/debug_blast_parser.py to diagnose blast parsing errors
IPI supported by SwissProt/SProt.py parser
large speedup for kmeans
new registry framework for generic access to databases and parsers
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2  Tests/test_GAQueens.py
@@ -333,7 +333,7 @@ def _find_best_region(self, genome, make_best_larger = 1):
best_fitness = [start_index, start_index + region_size,
region_fitness]
- # get the the two regions and return 'em
+ # get the two regions and return 'em
best_region = genome[best_fitness[0]:best_fitness[1]]
rest_region = genome[0:best_fitness[0]] + genome[best_fitness[1]:]
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2  Tests/test_SearchIO_model.py
@@ -394,7 +394,7 @@ def test_hsp_filter(self):
# test hsps in hit11
self.assertTrue(all([hsp in filtered['hit1'] for hsp in
[hsp111, hsp112, hsp114]]))
- # test hsps in in hit31
+ # test hsps in hit31
self.assertTrue(all([hsp in filtered['hit3'] for hsp in
[hsp311, hsp312]]))
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