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biotext-2.4.1.3
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The biotext library offers resources to support text mining strategy using bioinformatics tool
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | biotext-2.4.1.3 |
| نام | biotext |
| نسخه کتابخانه | 2.4.1.3 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Diogo de J. S. Machado |
| ایمیل نویسنده | diogomachado.bioinfo@gmail.com |
| آدرس صفحه اصلی | https://github.com/diogomachado-bioinfo/biotext |
| آدرس اینترنتی | https://pypi.org/project/biotext/ |
| مجوز | - |
Biotext
=======
The biotext library offers resources to support text mining strategy using bioinformatics tool.
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>.
نحوه نصب
نصب پکیج whl biotext-2.4.1.3:
pip install biotext-2.4.1.3.whl
نصب پکیج tar.gz biotext-2.4.1.3:
pip install biotext-2.4.1.3.tar.gz