Documentation corrections

Each file has been check in order to correct possible misspellings in
their documentation.

MEvoLib/Align/__init__.py

@@ -79,7 +79,7 @@ def get_alignment ( binary, infile, infile_format, args = 'default',
     """
     Align the sequences of the input file using the alignment tool and arguments
     given. The resultant alignment is returned as a Bio.Align.MultipleSeqAlign
-    object and saved in the ouput file (if provided). If 'infile' or 'outfile'
+    object and saved in the output file (if provided). If 'infile' or 'outfile'
     contain a relative path, the current working directory will be used to get
     the absolute path. If the output file already exists, the old file will be
     overwritten without any warning.
@@ -96,7 +96,7 @@ def get_alignment ( binary, infile, infile_format, args = 'default',
         infile_format  ( string )
             Input file format.
         args  ( Optional[string] )
-            Keyword or arguments to use in the call of the aligment tool,
+            Keyword or arguments to use in the call of the alignment tool,
             excluding infile and outfile arguments.  By default, 'default'
             arguments are used.
         outfile  ( Optional[string] )
@@ -105,7 +105,7 @@ def get_alignment ( binary, infile, infile_format, args = 'default',
             Output file format. By default, FASTA format.
         **kwargs  ( Optional[dict] )
             Keyworded arguments required to execute alignment tools not included
-            in the current version of MEvoLib. It is neccesary to pass a list
+            in the current version of MEvoLib. It is necessary to pass a list
             of supported infile formats under "informats" key, and the infile
             argument (e.g. "-in") with "incmd" key.
 

MEvoLib/Cluster/Genes.py

@@ -126,7 +126,7 @@ def _normalization ( record, refseq_record, alignment_bin ) :
     SeqIO.write([refseq_record, record], tmpfile.name, 'fasta')
     alignment = Align.get_alignment(alignment_bin, tmpfile.name, 'fasta')
     # Get the normalized sequence by removing the sites that correspond to gaps
-    # introduced in the reference sequence during the alingment process
+    # introduced in the reference sequence during the alignment process
     record_seq = ''.join((x  for i, x in enumerate(alignment[1])
                                  if alignment[0][i] != '-'))
     return ( Seq(record_seq, alignment[1].seq.alphabet),
@@ -168,7 +168,7 @@ def get_features ( ) :
 def map_seqs ( record_list, feature_filter = None, ref_seq = None,
                alignment_bin = None ) :
     """
-    Gene splicing of the sequences at 'record_list'. By defautl, the gene
+    Gene splicing of the sequences at 'record_list'. By default, the gene
     location is extracted from the feature list of each sequence. If there is no
     list, that sequence is classified as "unprocessable" or, if a reference
     sequence is given, the reference features are used to extract the different

MEvoLib/Cluster/PRD.py

@@ -177,7 +177,7 @@ def map_seqs ( record_list, tree_file, file_format, subset_size, overlapping,
             further_decomp += output[1]
         start = end
         to_process = len(further_decomp[start:])
-    # Remove all the temporal files created for the multirpocessing stage
+    # Remove all the temporal files created for the multiprocessing stage
     for file_path in further_decomp :
         os.remove(file_path)
     record_dict = {record.id: record  for record in record_list}

MEvoLib/Cluster/__init__.py

@@ -90,11 +90,11 @@ def get_subsets ( method, seqfile, fileformat = 'genbank', *extra_args ) :
     mapseqs_func = _METHOD_TO_FUNC[method_key]
     filepath = get_abspath(seqfile)
     if ( method_key in ['prd', 'genes'] ) :
-        # Non data-driven (throught input slicing) parallelizable methods
+        # Non data-driven (through input slicing) parallelizable methods
         seq_list = (x  for x in SeqIO.parse(filepath, fileformat))
         set_dict = mapseqs_func(seq_list, *extra_args)
     else :
-        # Data-driven (throught input slicing) parallelizable methods
+        # Data-driven (through input slicing) parallelizable methods
         manager = multiprocessing.Manager()
         seq_list = manager.list([x  for x in SeqIO.parse(filepath, fileformat)])
         num_seqs = len(seq_list)

MEvoLib/Data/rCRS.py

@@ -10,7 +10,7 @@
 # File :  rCRS.py
 # Last version :  v1.0 ( 05/Feb/2016 )
 # Description :  Human mitochondrial DNA revised Cambridge Reference Sequence
-#       (rCRS)'s filepath and Bio.SeqRecord object.
+#       (rCRS)'s file path and Bio.SeqRecord object.
 #-------------------------------------------------------------------------------
 # Historical report :
 #

MEvoLib/Fetch/BioSeqs.py

@@ -512,7 +512,7 @@ def update ( self, email ) :
     def write ( self, bioseqs_file ) :
         """
         Save all sequences stored at the BioSeqs object in the 'bioseqs_file'
-        (in genbank format). A file with a detailed report of the sequences will
+        (in GENBANK format). A file with a detailed report of the sequences will
         be created replacing the extension of 'bioseqs_file' by ".rep". If
         'bioseqs_file' contains a relative path, the current working directory
         will be used to get the absolute path. If any file already exists, it

MEvoLib/Fetch/PhyTrees.py

@@ -245,7 +245,7 @@ def join ( self, new_phytrees ) :
     def write ( self, phytrees_file ) :
         """
         Save all trees stored at the PhyTrees object in the 'phytrees_file' (in
-        newick format). A file with a detailed report of the trees will be
+        NEWICK format). A file with a detailed report of the trees will be
         created replacing the extension of 'phytrees_file' by ".rep". If
         'phytrees_file' contains a relative path, the current working directory
         will be used to get the absolute path. If any file already exists, it

MEvoLib/Inference/_FastTree.py

@@ -76,7 +76,7 @@ def gen_args ( args, infile_path, bootstraps ) :
     if ( '-log' not in argument_list ) :
         log_tmpfile = tempfile.NamedTemporaryFile(delete=False)
         argument_list += ['-log', log_tmpfile.name]
-    # Add the bootstrapping generation option if 'boostraps' is greater than 0
+    # Add the bootstrapping generation option if 'bootstraps' is greater than 0
     if ( bootstraps > 0 ) :
         argument_list += ['-boot', str(bootstraps)]
     # Add the input file option

MEvoLib/Inference/_RAxML.py

@@ -83,7 +83,7 @@ def gen_args ( args, infile_path, bootstraps ) :
                          '-w', tmpdir_path] + KEYWORDS[args]
     else : # args not in KEYWORDS
         argument_list = [arg  for arg in args.split(' ')]
-    # Add the bootstrapping generation option if 'boostraps' is greater than 0
+    # Add the bootstrapping generation option if 'bootstraps' is greater than 0
     if ( bootstraps > 0 ) :
         argument_list += ['-N', str(bootstraps)]
     # Add the input file option

MEvoLib/Inference/__init__.py

@@ -83,7 +83,7 @@ def get_phylogeny ( binary, infile, infile_format, args = 'default',
     """
     Infer the phylogeny from the input alignment using the phylogenetic
     inference tool and arguments given. The resultant phylogeny is returned as a
-    Bio.Phylo.BaseTree object and saved in the ouput file (if provided). If
+    Bio.Phylo.BaseTree object and saved in the output file (if provided). If
     'infile' or 'outfile' contain a relative path, the current working directory
     will be used to get the absolute path. If the output file already exists,
     the old file will be overwritten without any warning.

MEvoLib/PhyloAssemble/__init__.py

@@ -83,7 +83,7 @@ def get_consensus_tree ( binary, infile, infile_format, args = 'default',
     """
     Calculate the consensus tree of the input trees file with the given
     arguments. The resultant consensus tree is returned as a Bio.Phylo.BaseTree
-    object and saved in the ouput file (if provided). If 'infile' or 'outfile'
+    object and saved in the output file (if provided). If 'infile' or 'outfile'
     contain a relative path, the current working directory will be used to get
     the absolute path. If the output file already exists, the old file will be
     overwritten without any warning.

MEvoLib/_py3k/__init__.py

@@ -106,7 +106,7 @@ def _is_int_or_long ( value ) :
 
         Returns :
             bool
-                True if value is instance of interger or long, False otherwise.
+                True if value is instance of integer or long, False otherwise.
         """
         return ( isinstance(value, (int, long)) )
 

README

@@ -7,14 +7,13 @@ evolution.
 
 The documentation file with further details on how to use our library is
 included in the release as "manual.pdf" and can be downloaded from our website
-(http://zaramit.org/documents/MEvoLib_manual.pdf).
+( http://zaramit.org/documents/MEvoLib_manual.pdf ).
 
 This MEvoLib package is open source software made available under the GNU
 General Public License terms. Please see the LICENSE file for further details.
 
 If you use MEvoLib in work contributing to a scientific publication, you can
-refer to the DOI: 10.5281/zenodo.46011
-(https://zenodo.org/badge/latestdoi/20347/JAlvarezJarreta/MEvoLib)
+refer to the latest DOI at https://zenodo.org/badge/latestdoi/20347/JAlvarezJarreta/MEvoLib .
 
 
 > INSTALLATION :

setup.py

@@ -180,4 +180,4 @@ def run(self):
     setup(**setup_args)
 finally:
     del sys.path[0]
-    os.chdir(old_path)
+    os.chdir(old_path)