#!/usr/bin/env python3
"""Module containing the AverageStiffness class and the command line interface."""
from pathlib import Path
from typing import Optional
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
from biobb_dna.utils import constants
from biobb_dna.utils.common import _from_string_to_list
from biobb_dna.utils.loader import read_series
[docs]
class AverageStiffness(BiobbObject):
"""
| biobb_dna AverageStiffness
| Calculate average stiffness constants for each base pair of a trajectory's series.
| Calculate the average stiffness constants for each base pair of a trajectory's series. The input is a .ser file with the helical parameter values for each base/basepair. The output is a .csv file with the average stiffness constants for each base pair and a .jpg file with a plot of the average stiffness constants for each base pair.
Args:
input_ser_path (str): Path to .ser file for helical parameter. File is expected to be a table, with the first column being an index and the rest the helical parameter values for each base/basepair. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/stiffness/canal_output_roll.ser>`_. Accepted formats: ser (edam:format_2330).
output_csv_path (str): Path to .csv file where output is saved. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffavg_roll.csv>`_. Accepted formats: csv (edam:format_3752).
output_jpg_path (str): Path to .jpg file where output is saved. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/stiffness/stiffavg_roll.jpg>`_. Accepted formats: jpg (edam:format_3579).
properties (dict):
* **KT** (*float*) - (0.592186827) Value of Boltzmann temperature factor.
* **sequence** (*str*) - (None) Nucleic acid sequence corresponding to the input .ser file. Length of sequence is expected to be the same as the total number of columns in the .ser file, minus the index column (even if later on a subset of columns is selected with the *usecols* option).
* **helpar_name** (*str*) - (None) helical parameter name.
* **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
Examples:
This is a use example of how to use the building block from Python::
from biobb_dna.stiffness.average_stiffness import average_stiffness
prop = {
'helpar_name': 'twist',
'sequence': 'GCAT',
}
average_stiffness(
input_ser_path='/path/to/twist.ser',
output_csv_path='/path/to/table/output.csv',
output_jpg_path='/path/to/table/output.jpg',
properties=prop)
Info:
* wrapped_software:
* name: In house
* license: Apache-2.0
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(
self,
input_ser_path,
output_csv_path,
output_jpg_path,
properties=None,
**kwargs,
) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"in": {
"input_ser_path": input_ser_path,
},
"out": {
"output_csv_path": output_csv_path,
"output_jpg_path": output_jpg_path,
},
}
self.properties = properties
self.sequence = properties.get("sequence")
self.KT = properties.get("KT", 0.592186827)
self.seqpos = [
int(elem) for elem in _from_string_to_list(properties.get("seqpos", None))
]
self.helpar_name = properties.get("helpar_name", None)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs]
@launchlogger
def launch(self) -> int:
"""Execute the :class:`AverageStiffness <stiffness.average_stiffness.AverageStiffness>` object."""
# Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# check sequence
if self.sequence is None or len(self.sequence) < 2:
raise ValueError("sequence is null or too short!")
# get helical parameter from filename if not specified
if self.helpar_name is None:
for hp in constants.helical_parameters:
if (
hp.lower()
in Path(self.stage_io_dict["in"]["input_ser_path"]).name.lower()
):
self.helpar_name = hp
if self.helpar_name is None:
raise ValueError(
"Helical parameter name can't be inferred from file, "
"so it must be specified!"
)
else:
if self.helpar_name not in constants.helical_parameters:
raise ValueError(
"Helical parameter name is invalid! "
f"Options: {constants.helical_parameters}"
)
# get base length and unit from helical parameter name
if self.helpar_name.lower() in ["roll", "tilt", "twist"]:
self.hp_unit = "kcal/(mol*degree²)"
scale = 1.0
else:
self.hp_unit = "kcal/(mol*Ų)"
scale = 10.6
# check seqpos
if self.seqpos:
if (max(self.seqpos) > len(self.sequence) - 2) or (min(self.seqpos) < 1):
raise ValueError(
f"seqpos values must be between 1 and {len(self.sequence) - 2}"
)
if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
raise ValueError("seqpos must be a list of at least two integers")
else:
self.seqpos = None # type: ignore
# read input .ser file
ser_data = read_series(
self.stage_io_dict["in"]["input_ser_path"], usecols=self.seqpos
)
if not self.seqpos:
ser_data = ser_data[ser_data.columns[1:-1]]
# discard first and last base(pairs) from sequence
sequence = self.sequence[1:]
xlabels = [f"{sequence[i:i+2]}" for i in range(len(ser_data.columns))]
else:
sequence = self.sequence
xlabels = [f"{sequence[i:i+2]}" for i in self.seqpos]
# calculate average stiffness
cov = ser_data.cov()
stiff = np.linalg.inv(cov) * self.KT
avg_stiffness = np.diag(stiff) * scale
# save plot
fig, axs = plt.subplots(1, 1, dpi=300, tight_layout=True)
axs.plot(range(len(xlabels)), avg_stiffness, "-o")
axs.set_xticks(range(len(xlabels)))
axs.set_xticklabels(xlabels)
axs.set_xlabel("Sequence Base Pair")
axs.set_ylabel(f"{self.helpar_name.capitalize()} ({self.hp_unit})")
axs.set_title(
"Base Pair Helical Parameter Stiffness: " f"{self.helpar_name.capitalize()}"
)
fig.savefig(self.stage_io_dict["out"]["output_jpg_path"], format="jpg")
# save table
dataset = pd.DataFrame(
data=avg_stiffness, index=xlabels, columns=[f"{self.helpar_name}_stiffness"]
)
dataset.to_csv(self.stage_io_dict["out"]["output_csv_path"])
plt.close()
# Copy files to host
self.copy_to_host()
# Remove temporary file(s)
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]
def average_stiffness(
input_ser_path: str,
output_csv_path: str,
output_jpg_path: str,
properties: Optional[dict] = None,
**kwargs,
) -> int:
"""Create :class:`AverageStiffness <stiffness.average_stiffness.AverageStiffness>` class and
execute the :meth:`launch() <stiffness.average_stiffness.AverageStiffness.launch>` method."""
return AverageStiffness(**dict(locals())).launch()
average_stiffness.__doc__ = AverageStiffness.__doc__
main = AverageStiffness.get_main(average_stiffness, "Calculate average stiffness constants for each base pair of a trajectory's series.")
if __name__ == '__main__':
main()