diff --git a/MEvoLib/Align/__init__.py b/MEvoLib/Align/__init__.py index 90a6251..ed4a543 100644 --- a/MEvoLib/Align/__init__.py +++ b/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. diff --git a/MEvoLib/Cluster/Genes.py b/MEvoLib/Cluster/Genes.py index a339723..b0f0432 100644 --- a/MEvoLib/Cluster/Genes.py +++ b/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 diff --git a/MEvoLib/Cluster/PRD.py b/MEvoLib/Cluster/PRD.py index 7862307..fcd9f2f 100644 --- a/MEvoLib/Cluster/PRD.py +++ b/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} diff --git a/MEvoLib/Cluster/__init__.py b/MEvoLib/Cluster/__init__.py index aa12063..8131fcc 100644 --- a/MEvoLib/Cluster/__init__.py +++ b/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) diff --git a/MEvoLib/Data/rCRS.py b/MEvoLib/Data/rCRS.py index 1b33893..15e5064 100644 --- a/MEvoLib/Data/rCRS.py +++ b/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 : # diff --git a/MEvoLib/Fetch/BioSeqs.py b/MEvoLib/Fetch/BioSeqs.py index df5bc25..6bd94e0 100644 --- a/MEvoLib/Fetch/BioSeqs.py +++ b/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 diff --git a/MEvoLib/Fetch/PhyTrees.py b/MEvoLib/Fetch/PhyTrees.py index fa2efd3..a063339 100644 --- a/MEvoLib/Fetch/PhyTrees.py +++ b/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 diff --git a/MEvoLib/Inference/_FastTree.py b/MEvoLib/Inference/_FastTree.py index a41d41d..b75d4a2 100644 --- a/MEvoLib/Inference/_FastTree.py +++ b/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 diff --git a/MEvoLib/Inference/_RAxML.py b/MEvoLib/Inference/_RAxML.py index f93be26..0ecc5bb 100644 --- a/MEvoLib/Inference/_RAxML.py +++ b/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 diff --git a/MEvoLib/Inference/__init__.py b/MEvoLib/Inference/__init__.py index 71a7620..55b3039 100644 --- a/MEvoLib/Inference/__init__.py +++ b/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. diff --git a/MEvoLib/PhyloAssemble/__init__.py b/MEvoLib/PhyloAssemble/__init__.py index 78f2157..f094365 100644 --- a/MEvoLib/PhyloAssemble/__init__.py +++ b/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. diff --git a/MEvoLib/_py3k/__init__.py b/MEvoLib/_py3k/__init__.py index 1660795..b48fe92 100644 --- a/MEvoLib/_py3k/__init__.py +++ b/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)) ) diff --git a/README b/README index d7bda08..fc7a014 100644 --- a/README +++ b/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 : diff --git a/setup.py b/setup.py index a129919..39ee3fb 100644 --- a/setup.py +++ b/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) \ No newline at end of file