from collections import namedtuple from agalma import config from agalma import database import biolite.database from biolite import diagnostics from biolite import report from biolite import utils from biolite import wrappers from biolite import workflows from biolite.pipeline import Pipeline from biolite.pipeline import BasePipeline pipe = Pipeline('orthofinder', "Pipeline for executing orthofinder") pipe.add_arg('load_ids', nargs='+', metavar='LOAD_ID', help=""" Specifies which datasets to analyze; A space delimited list of run_id's corresponding to the load runs that populated the database""") pipe.add_arg('--seq_type', '-t', metavar='TYPE', default='protein', help=""" Choose whether comparisons are based on 'nucleotide', 'protein', or 'masked_protein' sequences.""") pipe.add_arg( '--genome_type', '-g', nargs="+", metavar='TYPE', default=['nuclear'], help=""" Select sequences with genome type: nuclear, mitochondrial, and/or plastid.""") pipe.add_arg( '--molecule_type', '-m', nargs="+", metavar='TYPE', default=['protein-coding'], help="""
import biolite.database from biolite import diagnostics from biolite import report from biolite import utils from biolite import wrappers from biolite import workflows from biolite.pipeline import Pipeline pipe = Pipeline("homologize", __doc__) ### ARGUMENTS ### pipe.add_arg( "load_ids", nargs="+", metavar="LOAD_ID", help=""" Specifies which datasets to analyze; A space delimited list of run_id's corresponding to the load runs that populated the database""", ) pipe.add_arg( "--seq_type", "-t", metavar="TYPE", default="protein", help=""" Choose whether comparisons are based on 'nucleotide', 'protein', or 'masked_protein' sequences.""", ) pipe.add_arg(