biotext 2.4.1.0

The biotext library offers resources to support text mining strategy using bioinformatics tool

The biotext library offers resources to support text mining strategy using bioinformatics tool.

Stand alone tools based on library are available at link <https://sourceforge.net/projects/biotext-tools/>.

Installation

To install aminocode through pip:

pip install biotext

Tested Platforms

• Python:

• 3.7.4

• Windows (64bits):

• 10

• Ubuntu (64bits)

• 18.04.1 LTS

Required external libraries

• numpy

• pandas

• scipy

• scikit-learn

• matplotlib

• unidecode

• biopython

• sweep

Functions

Function Name	Description	Input	Output
biotext.aminocode.encode_string	Encodes a string with AMINOcode.	input_stringstring: Natural language text string to be encoded. detailstring: Set details in coding. ‘d’ for details in digits; ‘p’ for details on the punctuation; ‘dp’ or ‘pd’ for both.	encoded_stringstring Encoded text.
biotext.aminocode.decode_string	Decodes a string with AMINOcode reverse.	input_stringstring: Text string encoded with AMINOcode. detailstring: Set details in coding. ‘d’ for details in digits; ‘p’ for details on the punctuation; ‘dp’ or ‘pd’ for both.	decoded_stringstring Decoded text.
biotext.aminocode.encode_list	Encodes all strings in a list with AMINOcode.	string_listlist List of string to be encoded. detailstring Set details in coding. ‘d’ for details in digits; ‘p’ for details on the punctuation; ‘dp’ or ‘pd’ for both. verbosebool If True displays progress.	encoded_listlist List with all encoded text in string format.
biotext.aminocode.decode_list	Decodes all strings in a list with reverse AMINOcode.	string_listlist List of string encoded with aminocode. detailstring Set details in coding. ‘d’ for details in digits; ‘p’ for details on the punctuation; ‘dp’ or ‘pd’ for both. verbosebool If True displays progress.	decoded_listlist of string List with all decoded text.
biotext.dnabits.encode_string	Encodes a string with DNAbits.	input_stringstring: Natural language text string to be encoded.	encoded_stringstring Encoded text.
biotext.dnabits.decode_string	Decodes a string with DNAbits reverse.	input_stringstring: Text string encoded with AMINOcode.	decoded_stringstring Decoded text.
biotext.dnabits.encode_list	Encodes all strings in a list with DNAbits.	string_listlist List of string to be encoded. verbosebool If True displays progress.	encoded_listlist List with all encoded text in string format.
biotext.dnabits.decode_list	Decodes all strings in a list with reverse DNAbits.	string_listlist List of string encoded with aminocode. verbosebool If True displays progress.	decoded_listlist of string List with all decoded text.
create_seqrecord_list	Creates a list of SeqRecord*SeqRecord* from a string list.	seq_listlist of string List of biological sequences in string format. headerlist of string List of headers in string format, if set to ‘None’ the headers will be automatically defined with numbers in increasing order.	seqrecord_listlist of SeqRecord* List of SeqRecord*.
biotext.fastatools.import_fasta	Uses biopython to import a FASTA file.	input_file_namestring (valid file name) Input fasta file name.	seqrecord_listlist of SeqRecord* List of SeqRecord* imported from file.
biotext.fastatools.export_fasta	Creates a file using a SeqRecord*SeqRecord* list.	seqrecord_listlist of SeqRecord* List of SeqRecord*. output_file_namestring Output fasta file name.	A file is saved with the defined name.
biotext.fastatools.get_header	Get the header from all items in a list of SeqRecord*SeqRecord*.	seqrecord_listlist of SeqRecord* List of SeqRecord*.	header_listlist of string List of all headers extracted from input.
biotext.fastatools.get_seq	Get the sequences from all items in a list of SeqRecord*SeqRecord*.	seqrecord_listlist of SeqRecord* List of SeqRecord*.	seq_listlist of string List of all sequences extracted from input.
biotext.fastatools.remove_pattern	Removes patterns from a SeqRecord* range based on regular expression.	seq_listlist of SeqRecord* List of SeqRecord*. rexstring regular expression.	seq_listlist of SeqRecord* List of SeqRecord* with removal applied.
biotext.fastatools.run_clustalo	Uses the Clustal Omega to align the strings in a FASTA file.	input_file_namestring (valid file name) Input fasta file name.	alignmentMultipleSeqAlignment** Alignment result.
biotext.fastatools.get_consensus	Applies clustalo and obtain alignment consensus.	seqrecord_listlist of SeqRecord* List of SeqRecord*.	consensusstring Alignment consensus. alignmentlist of string List of sequences with alignment gaps.
biotext.fastatools.fasta_to_mat	Performs a vectorization of a list of SeqRecord* using the SWeeP.	seq_listlist of string List of strings in FASTA format.	matndarray*** Matrix with the generated vectors.
biotext.treetools.mat_to_tree	Creates a dendrogram in newick format from a matrix.	matndarray*** Matrix. idslist of string List with line identifiers in mat. methodstring Method to create the dendrogram. Available options are ‘complete’, scipy library implementation, and ‘nj’ (neighbor joining), skbio library implementation. The default is the ‘complete’ method.	treestring tree: dendrogram in newick format.

*Bio.SeqRecord.SeqRecord: Biopython object to store biological sequences and its information, as described in <https://biopython.org/docs/1.76/api/Bio.SeqRecord.html> **Bio.Align.MultipleSeqAlignment: Biopython object to store biological multiple sequence alignment, as described in <https://biopython.org/docs/1.76/api/Bio.Align.html> ***ndarray: Numpy object to represent array, as described in https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html