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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