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
Function Name, Description, Input, Output |
|||
|---|---|---|---|
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>
1 maintainer
Release files for biotex 1.0.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| biotex-1.0.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Release files / biotex-1.0.0.0-py3-none-any.whl
| Download URL | biotex-1.0.0.0-py3-none-any.whl |
|---|---|
| Size | 17.1 kB |
| Tags | Python 3 |
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