Metadata-Version: 1.0
Name: biotext
Version: 2.4.1.2
Summary: The biotext library offers resources to support text mining strategy using bioinformatics tool
Home-page: https://github.com/diogomachado-bioinfo/biotext
Author: Diogo de J. S. Machado
Author-email: diogomachado.bioinfo@gmail.com
License: UNKNOWN
Description: Biotext
        =======
        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
        ---------------
        .. csv-table::
           :header: "Function Name", "Description", "Input", "Output"
           :stub-columns: 1
        
           "biotext.aminocode.encode_string", "Encodes a string with AMINOcode.","input_string \: string:
            Natural language text string to be encoded.
           detail \: string:
            Set details in coding. 'd' for details in digits; 'p' for details on the punctuation; 'dp' or 'pd' for both.", "encoded_string \: string
            Encoded text."
           "biotext.aminocode.decode_string", "Decodes a string with AMINOcode reverse.", "input_string \: string:
            Text string encoded with AMINOcode.
           detail \: string:
            Set details in coding. 'd' for details in digits; 'p' for details on the punctuation; 'dp' or 'pd' for both.", "decoded_string \: string
            Decoded text."
           "biotext.aminocode.encode_list ", "Encodes all strings in a list with AMINOcode.", "string_list \: list
            List of string to be encoded.
           detail \: string
             Set details in coding. 'd' for details in digits; 'p' for details on the punctuation; 'dp' or 'pd' for both.
           verbose \: bool
            If True displays progress.", "encoded_list \: list
            List with all encoded text in string format."
           "biotext.aminocode.decode_list", "Decodes all strings in a list with reverse AMINOcode.", "string_list \: list
            List of string encoded with aminocode.
           detail \: string
            Set details in coding. 'd' for details in digits; 'p' for details on the punctuation; 'dp' or 'pd' for both.
           verbose \: bool
            If True displays progress.", "decoded_list \: list of string
             List with all decoded text."
           "biotext.dnabits.encode_string", "Encodes a string with DNAbits.","input_string \: string:
            Natural language text string to be encoded.", "encoded_string \: string
            Encoded text."
           "biotext.dnabits.decode_string", "Decodes a string with DNAbits reverse.", "input_string \: string:
            Text string encoded with AMINOcode.", "decoded_string \: string
            Decoded text."
           "biotext.dnabits.encode_list ", "Encodes all strings in a list with DNAbits.", "string_list \: list
            List of string to be encoded.
           verbose \: bool
            If True displays progress.", "encoded_list \: list
            List with all encoded text in string format."
           "biotext.dnabits.decode_list", "Decodes all strings in a list with reverse DNAbits.", "string_list \: list
            List of string encoded with aminocode.
           verbose \: bool
            If True displays progress.", "decoded_list \: list of string
             List with all decoded text."
           "create_seqrecord_list", "Creates a list of SeqRecord*SeqRecord* from a string list.", "seq_list \: list of string
            List of biological sequences in string format.
           header \: list of string
            List of headers in string format, if set to 'None' the headers will be automatically defined with numbers in increasing order.", "seqrecord_list \: list of SeqRecord*
            List of SeqRecord*."
           "biotext.fastatools.import_fasta", "Uses biopython to import a FASTA file.", "input_file_name \: string (valid file name)
            Input fasta file name.", "seqrecord_list \: list of SeqRecord*
            List of SeqRecord* imported from file."
           "biotext.fastatools.export_fasta", "Creates a file using a SeqRecord*SeqRecord* list.", "seqrecord_list \: list of SeqRecord*
            List of SeqRecord*.
           output_file_name \: string
            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_list \: list of SeqRecord*
            List of SeqRecord*.", "header_list \: list 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_list \: list of SeqRecord*
            List of SeqRecord*.", "seq_list \: list of string
            List of all sequences extracted from input."
           "biotext.fastatools.remove_pattern", "Removes patterns from a SeqRecord* range based on regular expression.", "seq_list \: list of SeqRecord*
            List of SeqRecord*.
           rex \: string
            regular expression.", "seq_list \: list 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_name \: string (valid file name)
            Input fasta file name.", "alignment \: MultipleSeqAlignment**
            Alignment result."
           "biotext.fastatools.get_consensus", "Applies clustalo and obtain alignment consensus.", "seqrecord_list \: list of SeqRecord*
            List of SeqRecord*.", "consensus \: string
            Alignment consensus.
           alignment \: list 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_list \: list of string
            List of strings in FASTA format.", "mat \: ndarray***
            Matrix with the generated vectors."
           "biotext.treetools.mat_to_tree", "Creates a dendrogram in newick format from a matrix.", "mat \: ndarray***
            Matrix.
           ids \: list of string
            List with line identifiers in mat.
           method \: string
            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.", "tree \: string
            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>.
        
        \*\*\*numpy.ndarray: Numpy object to represent array, as described in <https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html>.
Platform: UNKNOWN
