#!/usr/bin/env python3
"""Module containing the IntraBasePairCorrelation class and the command line interface."""
import argparse
from itertools import product
import numpy as np
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_dna.utils.loader import read_series
from biobb_dna.utils import constants
[docs]class IntraBasePairCorrelation(BiobbObject):
"""
| biobb_dna IntraBasePairCorrelation
| Calculate correlation between all intra-base pairs of a single sequence and for a single helical parameter.
Args:
input_filename_shear (str): Path to .ser file with data for helical parameter 'shear'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_shear.ser>`_. Accepted formats: ser (edam:format_2330).
input_filename_stretch (str): Path to .ser file with data for helical parameter 'stretch'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stretch.ser>`_. Accepted formats: ser (edam:format_2330).
input_filename_stagger (str): Path to .ser file with data for helical parameter 'stagger'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_stagger.ser>`_. Accepted formats: ser (edam:format_2330).
input_filename_buckle (str): Path to .ser file with data for helical parameter 'buckle'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_buckle.ser>`_. Accepted formats: ser (edam:format_2330).
input_filename_propel (str): Path to .ser file with data for helical parameter 'propel'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_propel.ser>`_. Accepted formats: ser (edam:format_2330).
input_filename_opening (str): Path to .ser file with data for helical parameter 'opening'. File type: input. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/data/correlation/canal_output_opening.ser>`_. Accepted formats: ser (edam:format_2330).
output_csv_path (str): Path to directory where output is saved. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/correlation/intra_bpcorr_ref.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/correlation/intra_bpcorr_ref.jpg>`_. Accepted formats: jpg (edam:format_3579).
properties (dict):
* **sequence** (*str*) - (None) Nucleic acid sequence for 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).
* **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.intrabp_correlations.intrabpcorr import intrabpcorr
intrabpcorr(
input_filename_shear='path/to/input/shear.ser',
input_filename_stretch='path/to/input/stretch.ser',
input_filename_stagger='path/to/input/stagger.ser',
input_filename_buckle='path/to/input/buckle.ser',
input_filename_propel='path/to/input/propel.ser',
input_filename_opening='path/to/input/opening.ser',
output_csv_path='path/to/output/file.csv',
output_jpg_path='path/to/output/plot.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_filename_shear, input_filename_stretch,
input_filename_stagger, input_filename_buckle,
input_filename_propel, input_filename_opening,
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_filename_shear': input_filename_shear,
'input_filename_stretch': input_filename_stretch,
'input_filename_stagger': input_filename_stagger,
'input_filename_buckle': input_filename_buckle,
'input_filename_propel': input_filename_propel,
'input_filename_opening': input_filename_opening
},
'out': {
'output_csv_path': output_csv_path,
'output_jpg_path': output_jpg_path
}
}
self.properties = properties
self.sequence = properties.get("sequence", None)
self.seqpos = properties.get("seqpos", None)
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`HelParCorrelation <intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` 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!")
# check seqpos
if self.seqpos is not None:
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="bpcorrelation_")
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
# read input
shear = read_series(
self.io_dict["in"]["input_filename_shear"], usecols=self.seqpos)
stretch = read_series(
self.io_dict["in"]["input_filename_stretch"], usecols=self.seqpos)
stagger = read_series(
self.io_dict["in"]["input_filename_stagger"], usecols=self.seqpos)
buckle = read_series(
self.io_dict["in"]["input_filename_buckle"], usecols=self.seqpos)
propel = read_series(
self.io_dict["in"]["input_filename_propel"], usecols=self.seqpos)
opening = read_series(
self.io_dict["in"]["input_filename_opening"], usecols=self.seqpos)
if self.seqpos is None:
# drop first and last columns
shear = shear[shear.columns[1:-1]]
stretch = stretch[stretch.columns[1:-1]]
stagger = stagger[stagger.columns[1:-1]]
buckle = buckle[buckle.columns[1:-1]]
propel = propel[propel.columns[1:-1]]
opening = opening[opening.columns[1:-1]]
labels = [
f"{i+1}_{self.sequence[i:i+1]}" for i in range(1, len(shear.columns) + 1)]
corr_index = [
f"{self.sequence[i:i+2]}" for i in range(1, len(shear.columns) + 1)]
else:
labels = [f"{i+1}_{self.sequence[i:i+1]}" for i in self.seqpos]
corr_index = [f"{self.sequence[i:i+2]}" for i in self.seqpos]
# rename duplicated subunits
shear.columns = labels
stretch.columns = labels
stagger.columns = labels
buckle.columns = labels
propel.columns = labels
opening.columns = labels
# set names to each dataset
shear.name = "shear"
stretch.name = "stretch"
stagger.name = "stagger"
buckle.name = "buckle"
propel.name = "propel"
opening.name = "opening"
# get correlation between neighboring basepairs among all helical parameters
results = {}
datasets = [shear, stretch, stagger, buckle, propel, opening]
for ser1, ser2 in product(datasets, datasets):
ser2_shifted = ser2.shift(axis=1)
ser2_shifted[labels[0]] = ser2[labels[-1]]
if (
ser1.name in constants.hp_angular and ser2.name in constants.hp_angular):
method = self.circular
elif (
(
ser1.name in constants.hp_angular and not (
ser2.name in constants.hp_angular)
) or (
ser2.name in constants.hp_angular and not (
ser1.name in constants.hp_angular)
)
):
method = self.circlineal
else:
method = "pearson"
corr_data = ser1.corrwith(ser2_shifted, method=method)
corr_data.index = corr_index
results[f"{ser1.name}/{ser2.name}"] = corr_data
result_df = pd.DataFrame.from_dict(results)
result_df.index = corr_index
# save csv data
result_df.to_csv(self.io_dict["out"]["output_csv_path"])
# create heatmap
cmap = plt.get_cmap("bwr").copy()
bounds = [-1, -.8, -.6, -.4, -.2, .2, .4, .6, .8, 1]
num = cmap.N
norm = mpl.colors.BoundaryNorm(bounds, num)
cmap.set_bad(color="gainsboro")
fig, ax = plt.subplots(
1,
1,
dpi=300,
figsize=(7.5, 5),
tight_layout=True)
im = ax.imshow(result_df, cmap=cmap, norm=norm, aspect='auto')
plt.colorbar(im, ticks=[-1, -.8, -.6, -.4, -.2, .2, .4, .6, .8, 1])
# axes
xlocs = np.arange(len(result_df.columns))
_ = ax.set_xticks(xlocs)
_ = ax.set_xticklabels(result_df.columns.to_list(), rotation=90)
ylocs = np.arange(len(result_df.index))
_ = ax.set_yticks(ylocs)
_ = ax.set_yticklabels(result_df.index.to_list())
ax.set_title(
"Correlation for neighboring basepairs "
"and pairs of helical parameters")
fig.tight_layout()
fig.savefig(
self.io_dict['out']['output_jpg_path'],
format="jpg")
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] @staticmethod
def circular(x1, x2):
x1 = x1 * np.pi / 180
x2 = x2 * np.pi / 180
diff_1 = np.sin(x1 - x1.mean())
diff_2 = np.sin(x2 - x2.mean())
num = (diff_1 * diff_2).sum()
den = np.sqrt((diff_1 ** 2).sum() * (diff_2 ** 2).sum())
return num / den
[docs] @staticmethod
def circlineal(x1, x2):
x2 = x2 * np.pi / 180
rc = np.corrcoef(x1, np.cos(x2))[1, 0]
rs = np.corrcoef(x1, np.sin(x2))[1, 0]
rcs = np.corrcoef(np.sin(x2), np.cos(x2))[1, 0]
num = (rc ** 2) + (rs ** 2) - 2 * rc * rs * rcs
den = 1 - (rcs ** 2)
correlation = np.sqrt(num / den)
if np.corrcoef(x1, x2)[1, 0] < 0:
correlation *= -1
return correlation
[docs]def intrabpcorr(
input_filename_shear: str, input_filename_stretch: str,
input_filename_stagger: str, input_filename_buckle: str,
input_filename_propel: str, input_filename_opening: str,
output_csv_path: str, output_jpg_path: str,
properties: dict = None, **kwargs) -> int:
"""Create :class:`HelParCorrelation <intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` class and
execute the :meth:`launch() <intrabp_correlations.intrabpcorr.IntraBasePairCorrelation.launch>` method."""
return IntraBasePairCorrelation(
input_filename_shear=input_filename_shear,
input_filename_stretch=input_filename_stretch,
input_filename_stagger=input_filename_stagger,
input_filename_buckle=input_filename_buckle,
input_filename_propel=input_filename_propel,
input_filename_opening=input_filename_opening,
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 .ser file from Canal output and calculate correlation between base pairs of the corresponding sequence.',
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_filename_shear', required=True,
help='Path to ser file for helical parameter shear. Accepted formats: ser.')
required_args.add_argument('--input_filename_stretch', required=True,
help='Path to ser file for helical parameter stretch. Accepted formats: ser.')
required_args.add_argument('--input_filename_stagger', required=True,
help='Path to ser file for helical parameter stagger. Accepted formats: ser.')
required_args.add_argument('--input_filename_buckle', required=True,
help='Path to ser file for helical parameter buckle. Accepted formats: ser.')
required_args.add_argument('--input_filename_propel', required=True,
help='Path to ser file for helical parameter propel. Accepted formats: ser.')
required_args.add_argument('--input_filename_opening', required=True,
help='Path to ser file for helical parameter opening. Accepted formats: ser.')
required_args.add_argument('--output_csv_path', required=True,
help='Path to output file. Accepted formats: csv.')
required_args.add_argument('--output_jpg_path', required=True,
help='Path to output plot. Accepted formats: jpg.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
intrabpcorr(
input_filename_shear=args.input_filename_shear,
input_filename_stretch=args.input_filename_stretch,
input_filename_stagger=args.input_filename_stagger,
input_filename_buckle=args.input_filename_buckle,
input_filename_propel=args.input_filename_propel,
input_filename_opening=args.input_filename_opening,
output_csv_path=args.output_csv_path,
output_jpg_path=args.output_jpg_path,
properties=properties)
if __name__ == '__main__':
main()