biotex 1.0.0.0
The biotext library offers resources to support text mining strategy using bioinformatics tool

BioTEX
=======
The biotex 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/biotex-tools/>.

Installation
------------
To install aminocode through `pip`::

      pip install biotex


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
   :widths: auto
   :stub-columns: 1
   :delim: -

   biotex.aminocode.encodeText  biotex.aminocode.encodetext  biotex.aminocode.et-Encodes a string with AMINOcode.-text: natural language text string to be encoded;  detailing: details in coding. 'd' for details in digits. 'p' for details on the punctuation. 'dp' or 'pd' for both.-encode text in string format.
   biotex.aminocode.decodeText  biotex.aminocode.decodetext  biotex.aminocode.dt-Decodes a string with reverse AMINOcode.-text: text string encoded using the encodefile function to be decode;  detailing: details used in the text to be decoded. 'd' for details in digits. 'p' for details on the punctuation. 'dp' or 'pd' for both.-decode text in string format.
   biotex.aminocode.encodeFile  biotex.aminocode.encodefile  biotex.aminocode.ef-Encodes a text file or a list of strings with AMINOcode.-input_file_name: text file name or list of string. It can also be used in a list of SeqRecord, in which case the function will automatically extract the headers to do the encoding;  output_file_name: the name for the output file. If not defined, the result will only be returned as a variable;  detailing: same as in the encodetext function;  header_format: format for the headers of the generated FASTA. It can be 'number+originaltext', 'number' or 'originaltext'. 'number' is a count of the lines in the input file. Blank lines are considered in the count, but are not added to the FASTA file. 'originaltext' is the input text itself;  verbose: if True displays progress.-list of SeqRecord*;  If defined output_file_name a file will be saved.
   biotex.aminocode.decodeFile  biotex.aminocode.decodefile  biotex.aminocode.df-Decodes a fasta file or a list of SeqRecord with the reverse amino acid.-input_file_name: file name or list of SeqRecord;  output_file_name: the name for the output file. If not defined, the result will only be returned as a variable;  detailing: same as in the decodetext function;  verbose: if True displays progress;  output: string list. If defined output_file_name a file will be saved.-string list;  if defined output_file_name a file will be saved.
   biotex. dnabits.encodeText   biotex.dnabits.encodetext  biotex. dnabits.et-Encodes a string with DNAbits.-text: natural language text string to be encoded.-encode text in string format.
   biotex.dnabits.decodeText  biotex.dnabits.decodetext  biotex.dnabits.dt-Decodes a string with reverse DNAbits.-text: text string encoded using the encodefile function to be decode.-decode text in string format.
   biotex.dnabits.encodeFile   biotex.dnabits.encodefile  biotex.dnabits.ef-Encodes a text file or a list of strings with DNAbits.-input_file_name: text file name or list of string. It can also be used in a list of SeqRecord, in which case the function will automatically extract the headers to do the encoding;  output_file_name: the name for the output file. If not defined, the result will only be returned as a variable;  header_format: format for the headers of the generated FASTA. It can be 'number+originaltext', 'number' or 'originaltext'. 'number' is a count of the lines in the input file. Blank lines are considered in the count, but are not added to the FASTA file. 'originaltext' is the input text itself;  verbose: if True displays progress.-list of SeqRecord.  if defined output_file_name a file will be saved.
   biotex.dnabits.decodeFile  biotex.dnabits.decodefile  biotex.dnabits.df-Decodes a text file or a list of SeqRecord with reverse DNAbits.-input_file_name: file name or list of SeqRecord;  output_file_name: the name for the output file. If not defined, the result will only be returned as a variable;  verbose: if True displays progress.-string list;  if defined output_file_name a file will be saved.
   biotex.fastatools.list2SeqRecord  biotex.fastatools.list2seqrecord  biotex.fastatools.list2bioSeqRecord  biotex.fastatools.list2bioseqrecord  biotex.fastatools.list2fasta-Converts a list of strings to a list of SeqRecord, a biopython object that holds Biological sequences and information about it.-seq: list of biological sequences in string format;  header: list of headers in string format, if set to "None" the headers will be automatically defined with an increasing number.-list of SeqRecord.
   biotex.fastatools.fastaRead  biotex.fastatools.fastaread-Uses biopython to import a FASTA file.-input_file_name: input fasta file name.-list of SeqRecord.
   biotex.fastatools.fastaWrite  biotex.fastatools.fastawrite-Create a file using a list of SeqRecord.-records: list of SeqRecord;  output_file_name: output fasta file name.-a file is saved with the defined name.
   biotex.fastatools.getHeader  biotex.fastatools.getheader-Extracts the header from a list of SeqRecord.-records: list of SeqRecord.-list with headers.
   biotex.fastatools.getSeq  biotex.fastatools.getseq-Extracts the string from a list of SeqRecord.-records: list of SeqRecord.-list with sequences.
   biotex.fastatools.removePattern  biotex.fastatools.removepattern-Removes patterns from a SeqRecord range based on regular expression.-records: list of SeqRecord;  rex: regular expression.-list of SeqRecord with removal applied.
   biotex.fastatools.clustalOmega  biotex.fastatools.clustalomega  biotex.fastatools.clustalo-Uses the Clustal Omega to align the strings in a FASTA file.-input_file_name: input FASTA file name.-list with strings aligned in string format.
   biotex.fastatools.getCons  biotex.fastatools.getcons-Save a temporary file with the sequences from the list of SeqRecord, apply the clustalo function and obtain alignment consensus.-records: SeqRecord.list.-consensus for alignment in string format.

\*SeqRecord: Biopython object to store biological sequences and its information, as described in <https://biopython.org/DIST/docs/api/Bio.SeqRecord.SeqRecord-class.html>