Package: 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/>.InstallationTo install aminocode throughpip:pip install biotexTested PlatformsPython:3.7.4Windows (64bits):10Ubuntu (64bits)18.04.1 LTSRequired external librariesnumpypandasscipyscikit-learnmatplotlibunidecodebiopythonsweepFunctionsFunction NameDescriptionInputOutputbiotex.aminocode.encodeText  biotex.aminocode.encodetext  biotex.aminocode.etEncodes 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.dtDecodes 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.efEncodes 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.dfDecodes 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.etEncodes 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.dtDecodes 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.efEncodes 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.dfDecodes 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.list2fastaConverts 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.fastareadUses biopython to import a FASTA file.input_file_name: input fasta file name.list of SeqRecord.biotex.fastatools.fastaWrite  biotex.fastatools.fastawriteCreate 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.getheaderExtracts the header from a list of SeqRecord.records: list of SeqRecord.list with headers.biotex.fastatools.getSeq  biotex.fastatools.getseqExtracts the string from a list of SeqRecord.records: list of SeqRecord.list with sequences.biotex.fastatools.removePattern  biotex.fastatools.removepatternRemoves 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.clustaloUses 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.getconsSave 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>