Usage Python Package¶
The CLI - Command Line Interface¶
Usage: c3pred [OPTIONS]
Console script for c3pred.
Options:
-s, --sequence TEXT If the input is a FASTA protein string, please use this flag
-u, --uniprot TEXT If the input is a UniProtKB accession number, please use this flag
-g, --igem TEXT If the input is a iGEM Registry ID, please use this flag
--help Show this message and exit.
How to use C3Pred in a Python script¶
Example Python script:
from c3pred.c3pred import *
# predict using sequence string
example_1 = predict_fasta("AGYLLGKINLKALAALAKKIL")
# predict using sequence string
example_2 = predict_uniprot("Q86FU0")
# predict using sequence string
example_3 = predict_igem("BBa_K2660000")
The functions predict_fasta(), :predict_uniprot(), predict_igem() return a “Results” object:
Results object attributes:
sequence: | str - sequence string |
---|---|
activity: | float - activity score |
activity_class: | str - classification for activity (“low/none”/”medium”/”high”) |
description: | str - description of the sequence (if available for Uniprot ID, iGEM ID) |
error: | boolean - describes whether the prediction was successful |
error_type: | str - if an error occured, the error message is stored here |