Source code for samsifter.tools.filter_read_pmds
# -*- coding: utf-8 -*-
"""Wrapper for PMDtools ancient read filter functionality.
.. moduleauthor:: Florian Aldehoff <faldehoff@student.uni-tuebingen.de>
"""
""" custom libraries """
from samsifter.models.filter import FilterItem
from samsifter.models.parameter import (FilterParameter, FilterThreshold)
""" global variables """
TEXT = "[PMDtools] Filter reads by PMDS"
DESC = "Filtering reads by their post-mortem degradation score."
[docs]def item():
"""Create item representing this tool in list and tree views.
Returns
-------
FilterItem
Item for use in item-based list and tree views.
"""
item = FilterItem(text=TEXT, desc=DESC)
item.set_command('pmdtools_mod --writesamfield --header')
item.add_parameter(FilterThreshold(
text="min. PMDS",
desc="minimum post-mortem degradation score (PMDS)",
cli_name="--threshold",
default=3,
minimum=-10,
maximum=10,
precision=0,
required=True,
active=True
))
item.add_parameter(FilterParameter(
text="verbose",
desc="print additional information to STDERR",
cli_name="--verbose",
default=True,
active=True
))
item.add_parameter(FilterParameter(
text="statistics",
desc="output summarizing statistics to STDERR",
cli_name="--stats",
default=False
))
return item