topiary.cli_scripts

topiary.cli_scripts.alignment_to_ancestors

Command line interface to pipeline.alignment_to_ancestors

topiary.cli_scripts.alignment_to_ancestors.main(argv=None)

topiary.cli_scripts.bootstrap_reconcile

Command line interface to pipeline.bootstrap_reconcile

topiary.cli_scripts.bootstrap_reconcile.main(argv=None)

topiary.cli_scripts.check_installed

Check for installed packages on command line.

topiary.cli_scripts.check_installed.main(argv=None)

topiary.cli_scripts.create_report

Command line interface to reports.create_report

topiary.cli_scripts.create_report.main(argv=None)

topiary.cli_scripts.dataframe_from_fasta

Create a topiary dataframe from a fasta file.

topiary.cli_scripts.dataframe_from_fasta.dataframe_from_fasta(fasta, out='topiary-dataframe.csv', description='unknown', species='unknown', overwrite=False)

Create a topiary dataframe from a fasta file.

Parameters:

• fasta (str) – fasta file to read.

• out (str, default="topiary-dataframe.csv") – output file for the dataframe.

• description (str, default="unknown") – placeholder for ‘name’ column in the dataframe if not parsed from fasta.

• species (str, default="unknown") – placeholder for ‘species’ column in the dataframe.

• overwrite (bool, default=False) – whether or not to overwrite an existing output file.

Returns:

topiary dataframe.

Return type:

pandas.DataFrame

topiary.cli_scripts.dataframe_from_fasta.main(argv=None)

Main function for the script.

topiary.cli_scripts.fasta_into_dataframe

Command line interface to topiary.io.alignments.read_fasta_into

topiary.cli_scripts.fasta_into_dataframe.main(argv=None)

topiary.cli_scripts.seed_to_alignment

Command line interface to pipeline.seed_to_alignment

topiary.cli_scripts.seed_to_alignment.main(argv=None)