Coverage for biobb_dna/dna/dna_timeseries.py: 80%
110 statements
« prev ^ index » next coverage.py v7.5.1, created at 2024-05-07 09:06 +0000
1#!/usr/bin/env python3
3"""Module containing the HelParTimeSeries class and the command line interface."""
4import argparse
5import shutil
6import zipfile
7from pathlib import Path
9import pandas as pd
10import matplotlib.pyplot as plt
11from biobb_dna.utils import constants
12from biobb_dna.utils.loader import read_series
13from biobb_common.generic.biobb_object import BiobbObject
14from biobb_common.configuration import settings
15from biobb_common.tools import file_utils as fu
16from biobb_common.tools.file_utils import launchlogger
19class HelParTimeSeries(BiobbObject):
20 """
21 | biobb_dna HelParTimeSeries
22 | Created time series and histogram plots for each base pair from a helical parameter series file.
24 Args:
25 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).
26 output_zip_path (str): Path to output .zip files where data is saved. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_dna/master/biobb_dna/test/reference/dna/timeseries_output.zip>`_. Accepted formats: zip (edam:format_3987).
27 properties (dict):
28 * **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).
29 * **bins** (*int*) - (None) Bins for histogram. Parameter has same options as matplotlib.pyplot.hist.
30 * **helpar_name** (*str*) - (Optional) helical parameter name.
31 * **stride** (*int*) - (1000) granularity of the number of snapshots for plotting time series.
32 * **seqpos** (*list*) - (None) list of sequence positions (columns indices starting by 0) to analyze. If not specified it will analyse the complete sequence.
33 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
34 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
36 Examples:
37 This is a use example of how to use the building block from Python::
39 from biobb_dna.dna.dna_timeseries import dna_timeseries
41 prop = {
42 'helpar_name': 'twist',
43 'seqpos': [1,2,3,4,5],
44 'sequence': 'GCAACGTGCTATGGAAGC',
45 }
46 dna_timeseries(
47 input_ser_path='/path/to/twist.ser',
48 output_zip_path='/path/to/output/file.zip'
49 properties=prop)
50 Info:
51 * wrapped_software:
52 * name: In house
53 * license: Apache-2.0
54 * ontology:
55 * name: EDAM
56 * schema: http://edamontology.org/EDAM.owl
58 """
60 def __init__(self, input_ser_path, output_zip_path,
61 properties=None, **kwargs) -> None:
62 properties = properties or {}
64 # Call parent class constructor
65 super().__init__(properties)
66 self.locals_var_dict = locals().copy()
68 # Input/Output files
69 self.io_dict = {
70 'in': {
71 'input_ser_path': input_ser_path,
72 },
73 'out': {
74 'output_zip_path': output_zip_path
75 }
76 }
78 self.properties = properties
79 self.sequence = properties.get("sequence", None)
80 self.bins = properties.get("bins", "auto")
81 self.stride = properties.get(
82 "stride", 10)
83 self.seqpos = properties.get(
84 "seqpos", None)
85 self.helpar_name = properties.get(
86 "helpar_name", None)
88 # get helical parameter from filename if not specified
89 if self.helpar_name is None:
90 for hp in constants.helical_parameters:
91 if hp.lower() in Path(input_ser_path).name.lower():
92 self.helpar_name = hp
93 if self.helpar_name is None:
94 raise ValueError(
95 "Helical parameter name can't be inferred from file, "
96 "so it must be specified!")
97 else:
98 if self.helpar_name not in constants.helical_parameters:
99 raise ValueError(
100 "Helical parameter name is invalid! "
101 f"Options: {constants.helical_parameters}")
103 # get base length and unit from helical parameter name
104 if self.helpar_name.lower() in constants.hp_singlebases:
105 self.baselen = 0
106 else:
107 self.baselen = 1
108 if self.helpar_name in constants.hp_angular:
109 self.hp_unit = "Degrees"
110 else:
111 self.hp_unit = "Angstroms"
113 # Check the properties
114 self.check_properties(properties)
115 self.check_arguments()
117 @launchlogger
118 def launch(self) -> int:
119 """Execute the :class:`HelParTimeSeries <dna.dna_timeseries.HelParTimeSeries>` object."""
121 # Setup Biobb
122 if self.check_restart():
123 return 0
124 self.stage_files()
126 # check sequence
127 if self.sequence is None or len(self.sequence) < 2:
128 raise ValueError("sequence is null or too short!")
130 # check seqpos
131 if self.seqpos is not None:
132 if (max(self.seqpos) > len(self.sequence) - 2) or (min(self.seqpos) < 1):
133 raise ValueError(
134 f"seqpos values must be between 1 and {len(self.sequence) - 2}")
135 if not (isinstance(self.seqpos, list) and len(self.seqpos) > 1):
136 raise ValueError(
137 "seqpos must be a list of at least two integers")
139 # Creating temporary folder
140 self.tmp_folder = fu.create_unique_dir(prefix="timeseries_")
141 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
143 # Copy input_ser_path to temporary folder
144 shutil.copy(self.io_dict['in']['input_ser_path'], self.tmp_folder)
146 # read input .ser file
147 ser_data = read_series(
148 self.io_dict['in']['input_ser_path'],
149 usecols=self.seqpos)
150 if self.seqpos is None:
151 ser_data = ser_data[ser_data.columns[1:-1]]
152 # discard first and last base(pairs) from sequence
153 sequence = self.sequence[1:]
154 subunits = [
155 f"{i+1}_{sequence[i:i+1+self.baselen]}"
156 for i in range(len(ser_data.columns))]
157 else:
158 sequence = self.sequence
159 subunits = [
160 f"{i+1}_{sequence[i:i+1+self.baselen]}"
161 for i in self.seqpos]
162 ser_data.columns = subunits
164 # write output files for all selected bases (one per column)
165 zf = zipfile.ZipFile(
166 Path(self.io_dict["out"]["output_zip_path"]), "w")
167 for col in ser_data.columns:
168 # unstack columns to prevent errors from repeated base pairs
169 column_data = (
170 ser_data[[col]]
171 .unstack()
172 .dropna()
173 .reset_index(drop=True))
174 column_data.name = col
175 fu.log(f"Computing base number {col}...")
177 # column series
178 series_colfn = f"series_{self.helpar_name}_{col}"
179 column_data.to_csv(
180 Path(self.tmp_folder) / f"{series_colfn}.csv")
181 # save table
182 zf.write(
183 Path(self.tmp_folder) / f"{series_colfn}.csv", arcname=f"{series_colfn}.csv")
185 fig, axs = plt.subplots(1, 1, dpi=300, tight_layout=True)
186 reduced_data = column_data.iloc[::self.stride]
187 axs.plot(reduced_data.index, reduced_data.to_numpy())
188 axs.set_xlabel("Time (Snapshots)")
189 axs.set_ylabel(f"{self.helpar_name.capitalize()} ({self.hp_unit})")
190 axs.set_title(
191 f"Helical Parameter vs Time: {self.helpar_name.capitalize()} "
192 "(base pair "
193 f"{'step' if self.baselen==1 else ''} {col})")
194 fig.savefig(
195 Path(self.tmp_folder) / f"{series_colfn}.jpg", format="jpg")
196 # save plot
197 zf.write(
198 Path(self.tmp_folder) / f"{series_colfn}.jpg", arcname=f"{series_colfn}.jpg")
199 plt.close()
201 # columns histogram
202 hist_colfn = f"hist_{self.helpar_name}_{col}"
203 fig, axs = plt.subplots(1, 1, dpi=300, tight_layout=True)
204 ybins, x, _ = axs.hist(column_data, bins=self.bins)
205 pd.DataFrame({self.helpar_name: x[:-1], "density": ybins}).to_csv(
206 Path(self.tmp_folder) / f"{hist_colfn}.csv",
207 index=False)
208 # save table
209 zf.write(
210 Path(self.tmp_folder) / f"{hist_colfn}.csv",
211 arcname=f"{hist_colfn}.csv")
213 axs.set_ylabel("Density")
214 axs.set_xlabel(f"{self.helpar_name.capitalize()} ({self.hp_unit})")
215 fig.savefig(
216 Path(self.tmp_folder) / f"{hist_colfn}.jpg",
217 format="jpg")
218 # save plot
219 zf.write(
220 Path(self.tmp_folder) / f"{hist_colfn}.jpg",
221 arcname=f"{hist_colfn}.jpg")
222 plt.close()
223 zf.close()
225 # Remove temporary file(s)
226 self.tmp_files.extend([
227 self.stage_io_dict.get("unique_dir"),
228 self.tmp_folder
229 ])
230 self.remove_tmp_files()
232 self.check_arguments(output_files_created=True, raise_exception=False)
234 return 0
237def dna_timeseries(
238 input_ser_path: str, output_zip_path: str,
239 properties: dict = None, **kwargs) -> int:
240 """Create :class:`HelParTimeSeries <dna.dna_timeseries.HelParTimeSeries>` class and
241 execute the :meth:`launch() <dna.dna_timeseries.HelParTimeSeries.launch>` method."""
243 return HelParTimeSeries(
244 input_ser_path=input_ser_path,
245 output_zip_path=output_zip_path,
246 properties=properties, **kwargs).launch()
249def main():
250 """Command line execution of this building block. Please check the command line documentation."""
251 parser = argparse.ArgumentParser(description='Created time series and histogram plots for each base pair from a helical parameter series file.',
252 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
253 parser.add_argument('--config', required=False,
254 help='Configuration file')
256 required_args = parser.add_argument_group('required arguments')
257 required_args.add_argument('--input_ser_path', required=True,
258 help='Helical parameter input ser file path. Accepted formats: ser.')
259 required_args.add_argument('--output_zip_path', required=True,
260 help='Path to output directory.')
262 args = parser.parse_args()
263 args.config = args.config or "{}"
264 properties = settings.ConfReader(config=args.config).get_prop_dic()
266 dna_timeseries(
267 input_ser_path=args.input_ser_path,
268 output_zip_path=args.output_zip_path,
269 properties=properties)
272if __name__ == '__main__':
273 main()