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.
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.encode_string |
Encodes a string with AMINOcode. |
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|
biotext.aminocode.decode_string |
Decodes a string with AMINOcode reverse. |
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biotext.aminocode.encode_list |
Encodes all strings in a list with AMINOcode. |
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|
biotext.aminocode.decode_list |
Decodes all strings in a list with reverse AMINOcode. |
|
|
biotext.dnabits.encode_string |
Encodes a string with DNAbits. |
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biotext.dnabits.decode_string |
Decodes a string with DNAbits reverse. |
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biotext.dnabits.encode_list |
Encodes all strings in a list with DNAbits. |
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biotext.dnabits.decode_list |
Decodes all strings in a list with reverse DNAbits. |
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create_seqrecord_list |
Creates a list of SeqRecord*SeqRecord* from a string list. |
|
|
biotext.fastatools.import_fasta |
Uses biopython to import a FASTA file. |
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biotext.fastatools.export_fasta |
Creates a file using a SeqRecord*SeqRecord* list. |
|
A file is saved with the defined name. |
biotext.fastatools.get_header |
Get the header from all items in a list of SeqRecord*SeqRecord*. |
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biotext.fastatools.get_seq |
Get the sequences from all items in a list of SeqRecord*SeqRecord*. |
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biotext.fastatools.remove_pattern |
Removes patterns from a SeqRecord* range based on regular expression. |
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biotext.fastatools.run_clustalo |
Uses the Clustal Omega to align the strings in a FASTA file. |
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biotext.fastatools.get_consensus |
Applies clustalo and obtain alignment consensus. |
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biotext.fastatools.fasta_to_mat |
Performs a vectorization of a list of SeqRecord* using the SWeeP. |
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biotext.treetools.mat_to_tree |
Creates a dendrogram in newick format from a matrix. |
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|
*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>.
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