#!/usr/bin/env python3
"""Module containing the HelParAverages class and the command line interface."""
import shutil
import argparse
from pathlib import Path
import matplotlib.pyplot as plt
import pandas as pd
from biobb_dna.utils import constants
from biobb_dna.utils.loader import read_series
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools.file_utils import launchlogger
from biobb_common.tools import file_utils as fu
from biobb_common.configuration import settings
[docs]class HelParAverages(BiobbObject):
"""
| biobb_dna HelParAverages
| Load .ser file for a given helical parameter and read each column corresponding to a base calculating average over each one.
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/dna/canal_output_shift.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/dna/shift_avg.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/dna/shift_avg.jpg>`_. Accepted formats: jpg (edam:format_3579).
properties (dict):
* **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 *seqpos* option).
* **helpar_name** (*str*) - (Optional) helical parameter name.
* **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.
* **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.
Examples:
This is a use example of how to use the building block from Python::
from biobb_dna.dna.dna_averages import dna_averages
prop = {
'helpar_name': 'twist',
'seqpos': [1,2],
'sequence': 'GCAT'
}
dna_averages(
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
}
}
# Properties specific for BB
self.properties = properties
self.sequence = properties.get("sequence", None)
self.stride = properties.get(
"stride", 1000)
self.seqpos = 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:`HelParAverages <dna.averages.HelParAverages>` 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:
ser_name = Path(
self.io_dict['in']['input_ser_path']).name.lower()
if hp.lower() in ser_name:
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 constants.hp_basepairs:
self.baselen = 1
elif self.helpar_name.lower() in constants.hp_singlebases:
self.baselen = 0
if self.helpar_name in constants.hp_angular:
self.hp_unit = "Degrees"
else:
self.hp_unit = "Angstroms"
# check seqpos
if self.seqpos is not None:
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")
# Creating temporary folder
self.tmp_folder = fu.create_unique_dir(prefix="averages_")
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
# Copy input_file_path1 to temporary folder
shutil.copy(self.io_dict['in']['input_ser_path'], self.tmp_folder)
# read input .ser file
ser_data = read_series(
self.io_dict['in']['input_ser_path'],
usecols=self.seqpos)
if self.seqpos is None:
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+1+self.baselen]}"
for i in range(len(ser_data.columns) - self.baselen)]
else:
sequence = self.sequence
xlabels = [
f"{sequence[i:i+1+self.baselen]}"
for i in self.seqpos]
# rename duplicated subunits
while any(ser_data.columns.duplicated()):
ser_data.columns = [
name if not duplicated else name + "_dup"
for duplicated, name
in zip(ser_data.columns.duplicated(), ser_data.columns)]
# write output files for all selected bases
means = ser_data.mean(axis=0).iloc[:len(xlabels)]
stds = ser_data.std(axis=0).iloc[:len(xlabels)]
# save plot
fig, axs = plt.subplots(1, 1, dpi=300, tight_layout=True)
axs.errorbar(
means.index,
means.to_numpy(),
yerr=stds.to_numpy(),
marker="o",
capsize=5)
axs.set_xticks(means.index)
axs.set_xticklabels(xlabels, rotation=90)
axs.set_xlabel(
"Sequence Base Pair "
f"{'Step' if self.baselen==1 else ''}")
axs.set_ylabel(f"{self.helpar_name.capitalize()} ({self.hp_unit})")
axs.set_title(
"Base Pair "
f"{'Step' if self.baselen==1 else ''} "
f"Helical Parameter: {self.helpar_name.capitalize()}")
fig.savefig(
self.io_dict['out']['output_jpg_path'],
format="jpg")
# save table
dataset = pd.DataFrame({
f"Base Pair {'Step' if self.baselen==1 else ''}": xlabels,
"mean": means.to_numpy(),
"std": stds.to_numpy()})
dataset.to_csv(
self.io_dict['out']['output_csv_path'],
index=False)
plt.close()
# Remove temporary file(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
self.tmp_folder
])
self.remove_tmp_files()
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def dna_averages(
input_ser_path: str, output_csv_path: str, output_jpg_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`HelParAverages <dna.dna_averages.HelParAverages>` class and
execute the :meth:`launch() <dna.dna_averages.HelParAverages.launch>` method."""
return HelParAverages(input_ser_path=input_ser_path,
output_csv_path=output_csv_path,
output_jpg_path=output_jpg_path,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description='Load helical parameter file and calculate average values for each base pair.',
formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_ser_path', required=True,
help='Helical parameter input ser file path. Accepted formats: ser.')
required_args.add_argument('--output_csv_path', required=True,
help='Path to output csv file. Accepted formats: csv.')
required_args.add_argument('--output_jpg_path', required=True,
help='Path to output jpg file. Accepted formats: jpg.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
dna_averages(
input_ser_path=args.input_ser_path,
output_csv_path=args.output_csv_path,
output_jpg_path=args.output_jpg_path,
properties=properties)
if __name__ == '__main__':
main()