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

Project description

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.encodeText biotext.aminocode.encodetext biotext.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.
biotext.aminocode.decodeText biotext.aminocode.decodetext biotext.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.
biotext.aminocode.encodeFile biotext.aminocode.encodefile biotext.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.
biotext.aminocode.decodeFile biotext.aminocode.decodefile biotext.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.
biotext. dnabits.encodeText biotext.dnabits.encodetext biotext. dnabits.et Encodes a string with DNAbits. text: natural language text string to be encoded. encode text in string format.
biotext.dnabits.decodeText biotext.dnabits.decodetext biotext.dnabits.dt Decodes a string with reverse DNAbits. text: text string encoded using the encodefile function to be decode. decode text in string format.
biotext.dnabits.encodeFile biotext.dnabits.encodefile biotext.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.
biotext.dnabits.decodeFile biotext.dnabits.decodefile biotext.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.
biotext.fastatools.list2SeqRecord biotext.fastatools.list2seqrecord biotext.fastatools.list2bioSeqRecord biotext.fastatools.list2bioseqrecord biotext.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.
biotext.fastatools.fastaRead biotext.fastatools.fastaread Uses biopython to import a FASTA file. input_file_name: input fasta file name. list of SeqRecord.
biotext.fastatools.fastaWrite biotext.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.
biotext.fastatools.getHeader biotext.fastatools.getheader Extracts the header from a list of SeqRecord. records: list of SeqRecord. list with headers.
biotext.fastatools.getSeq biotext.fastatools.getseq Extracts the string from a list of SeqRecord. records: list of SeqRecord. list with sequences.
biotext.fastatools.removePattern biotext.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.
biotext.fastatools.clustalOmega biotext.fastatools.clustalomega biotext.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.
biotext.fastatools.getCons biotext.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>

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