Deep Codon Mutation Analyser (DCMA)
DCMA analyses each column of codons within .fasta files, from a target file, generating a report with all possible mutations listed.
Installation
pip install dcmaExamples
Usage
Command Line
usage: run-dcma [-h] [--reportName REPORTNAME] [--reportPath REPORTPATH]
[--searchKP SEARCHKP] [--debug]
TARGET REPORTTYPE
Analyse mutation on all nucleotide alignment .fasta files from a target.
positional arguments:
TARGET Target .fasta file to be analysed.
REPORTTYPE Output report file type.
optional arguments:
-h, --help show this help message and exit
--reportName REPORTNAME
Output report custom file name.
--reportPath REPORTPATH
Output report custom file path.
--searchKP SEARCHKP Custom keyphrase to detect searchable sequences.
--debug Turn debug messages on.Python
import dcma.core as solver
target_path = 'example.fasta'
report_name = 'myrep'
report_type = 'all' # 'xls', 'csv' or 'all'
report_path = 'results-folder' # optional
solver.set_debug_mode(True) # optional
# results[0] -> polarity results dataframe
# results[1] -> alerts dataframe
results = solver.run(target_path)
# option 1: export to the current folder
solver.export(results, report_type, report_name)
# option 2: export to custom folder
solver.export(results, report_type, report_name, report_path)
