interbp_correlations package

Correlation functions for inter-base pairs.

Submodules

interbp_correlations.interhpcorr module

Module containing the InterHelParCorrelation class and the command line interface.

class interbp_correlations.interhpcorr.InterHelParCorrelation(input_filename_shift, input_filename_slide, input_filename_rise, input_filename_tilt, input_filename_roll, input_filename_twist, output_csv_path, output_jpg_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna InterHelParCorrelation
Calculate correlation between helical parameters for a single inter-base pair.
Calculate correlation between helical parameters for a single inter-base pair.
Parameters:

  • input_filename_shift (str) – Path to .csv file with data for helical parameter ‘shift’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_slide (str) –

    Path to .csv file with data for helical parameter ‘slide’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_rise (str) –

    Path to .csv file with data for helical parameter ‘rise’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_tilt (str) –

    Path to .csv file with data for helical parameter ‘tilt’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_roll (str) –

    Path to .csv file with data for helical parameter ‘roll’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_twist (str) –

    Path to .csv file with data for helical parameter ‘twist’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • output_csv_path (str) –

    Path to directory where output is saved. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

  • output_jpg_path (str) –

    Path to .jpg file where output is saved. File type: output. Sample file. Accepted formats: jpg (edam:format_3579).

  • properties (dict) –

    • basepair (str) - (None) Name of basepair analyzed.

    • 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.interbp_correlations.interhpcorr import interhpcorr

prop = {
    'basepair': 'AA',
}
interhpcorr(
    input_filename_shift='path/to/shift.csv',
    input_filename_slide='path/to/slide.csv',
    input_filename_rise='path/to/rise.csv',
    input_filename_tilt='path/to/tilt.csv',
    input_filename_roll='path/to/roll.csv',
    input_filename_twist='path/to/twist.csv',
    output_csv_path='path/to/output/file.csv',
    output_jpg_path='path/to/output/file.jpg',
    properties=prop)
Info:
static circlineal(x1, x2)[source]
static circular(x1, x2)[source]
get_corr_method(corrtype1, corrtype2)[source]
launch() → int[source]

Execute the InterHelParCorrelation object.

interbp_correlations.interhpcorr.interhpcorr(input_filename_shift: str, input_filename_slide: str, input_filename_rise: str, input_filename_tilt: str, input_filename_roll: str, input_filename_twist: str, output_csv_path: str, output_jpg_path: str, properties: dict | None = None, **kwargs) → int[source]
biobb_dna InterHelParCorrelation
Calculate correlation between helical parameters for a single inter-base pair.
Calculate correlation between helical parameters for a single inter-base pair.
Parameters:

  • input_filename_shift (str) –

    Path to .csv file with data for helical parameter ‘shift’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_slide (str) –

    Path to .csv file with data for helical parameter ‘slide’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_rise (str) –

    Path to .csv file with data for helical parameter ‘rise’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_tilt (str) –

    Path to .csv file with data for helical parameter ‘tilt’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_roll (str) –

    Path to .csv file with data for helical parameter ‘roll’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • input_filename_twist (str) –

    Path to .csv file with data for helical parameter ‘twist’. File type: input. Sample file. Accepted formats: csv (edam:format_3752).

  • output_csv_path (str) –

    Path to directory where output is saved. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

  • output_jpg_path (str) –

    Path to .jpg file where output is saved. File type: output. Sample file. Accepted formats: jpg (edam:format_3579).

  • properties (dict) –

    • basepair (str) - (None) Name of basepair analyzed.

    • 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.interbp_correlations.interhpcorr import interhpcorr

prop = {
    'basepair': 'AA',
}
interhpcorr(
    input_filename_shift='path/to/shift.csv',
    input_filename_slide='path/to/slide.csv',
    input_filename_rise='path/to/rise.csv',
    input_filename_tilt='path/to/tilt.csv',
    input_filename_roll='path/to/roll.csv',
    input_filename_twist='path/to/twist.csv',
    output_csv_path='path/to/output/file.csv',
    output_jpg_path='path/to/output/file.jpg',
    properties=prop)
Info:

interbp_correlations.interseqcorr module

Module containing the InterSequenceCorrelation class and the command line interface.

class interbp_correlations.interseqcorr.InterSequenceCorrelation(input_ser_path, output_csv_path, output_jpg_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna InterSequenceCorrelation
Calculate correlation between all base pairs of a single sequence and for a single helical parameter.
Calculate correlation between all base pairs of a single sequence and for a single helical parameter.
Parameters:

  • input_ser_path (str) –

    Path to .ser file with data for single helical parameter. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • output_csv_path (str) –

    Path to directory where output is saved. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

  • output_jpg_path (str) –

    Path to .jpg file where output is saved. File type: output. Sample file. 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).

    • helpar_name (str) - (None) helical parameter name to add to plot title.

    • 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.interbp_correlations.interseqcorr import interseqcorr

prop = {
    "helpar_name": "helpar",
    "sequence": "CGTAATCG"
}
interseqcorr(
    input_ser_path='path/to/input/file.ser',
    output_csv_path='path/to/output/file.csv',
    output_jpg_path='path/to/output/plot.jpg',
    properties=prop)
Info:
static circular(x1, x2)[source]
launch() → int[source]

Execute the HelParCorrelation object.

interbp_correlations.interseqcorr.interseqcorr(input_ser_path: str, output_csv_path: str, output_jpg_path: str, properties: dict | None = None, **kwargs) → int[source]
biobb_dna InterSequenceCorrelation
Calculate correlation between all base pairs of a single sequence and for a single helical parameter.
Calculate correlation between all base pairs of a single sequence and for a single helical parameter.
Parameters:

  • input_ser_path (str) –

    Path to .ser file with data for single helical parameter. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • output_csv_path (str) –

    Path to directory where output is saved. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

  • output_jpg_path (str) –

    Path to .jpg file where output is saved. File type: output. Sample file. 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).

    • helpar_name (str) - (None) helical parameter name to add to plot title.

    • 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.interbp_correlations.interseqcorr import interseqcorr

prop = {
    "helpar_name": "helpar",
    "sequence": "CGTAATCG"
}
interseqcorr(
    input_ser_path='path/to/input/file.ser',
    output_csv_path='path/to/output/file.csv',
    output_jpg_path='path/to/output/plot.jpg',
    properties=prop)
Info:

interbp_correlations.interbpcorr module

Module containing the InterBasePairCorrelation class and the command line interface.

class interbp_correlations.interbpcorr.InterBasePairCorrelation(input_filename_shift, input_filename_slide, input_filename_rise, input_filename_tilt, input_filename_roll, input_filename_twist, output_csv_path, output_jpg_path, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna InterBasePairCorrelation
Calculate correlation between all base pairs of a single sequence and for a single helical parameter.
Calculate correlation between neighboring base pairs and pairs of helical parameters.
Parameters:

  • input_filename_shift (str) –

    Path to .ser file with data for helical parameter ‘shift’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_slide (str) –

    Path to .ser file with data for helical parameter ‘slide’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_rise (str) –

    Path to .ser file with data for helical parameter ‘rise’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_tilt (str) –

    Path to .ser file with data for helical parameter ‘tilt’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_roll (str) –

    Path to .ser file with data for helical parameter ‘roll’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_twist (str) –

    Path to .ser file with data for helical parameter ‘twist’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • output_csv_path (str) –

    Path to directory where output is saved. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

  • output_jpg_path (str) –

    Path to .jpg file where output is saved. File type: output. Sample file. 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.

    • 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.interbp_correlations.interbpcorr import interbpcorr

interbpcorr(
    input_filename_shift='path/to/input/shift.ser',
    input_filename_slide='path/to/input/slide.ser',
    input_filename_rise='path/to/input/slide.ser',
    input_filename_tilt='path/to/input/tilt.ser',
    input_filename_roll='path/to/input/roll.ser',
    input_filename_twist='path/to/input/twist.ser',
    output_csv_path='path/to/output/file.csv',
    output_jpg_path='path/to/output/plot.jpg',
    properties=prop)
Info:
static circlineal(x1, x2)[source]
static circular(x1, x2)[source]
launch() → int[source]

Execute the HelParCorrelation object.

interbp_correlations.interbpcorr.interbpcorr(input_filename_shift: str, input_filename_slide: str, input_filename_rise: str, input_filename_tilt: str, input_filename_roll: str, input_filename_twist: str, output_csv_path: str, output_jpg_path: str, properties: dict | None = None, **kwargs) → int[source]
biobb_dna InterBasePairCorrelation
Calculate correlation between all base pairs of a single sequence and for a single helical parameter.
Calculate correlation between neighboring base pairs and pairs of helical parameters.
Parameters:

  • input_filename_shift (str) –

    Path to .ser file with data for helical parameter ‘shift’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_slide (str) –

    Path to .ser file with data for helical parameter ‘slide’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_rise (str) –

    Path to .ser file with data for helical parameter ‘rise’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_tilt (str) –

    Path to .ser file with data for helical parameter ‘tilt’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_roll (str) –

    Path to .ser file with data for helical parameter ‘roll’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • input_filename_twist (str) –

    Path to .ser file with data for helical parameter ‘twist’. File type: input. Sample file. Accepted formats: ser (edam:format_2330).

  • output_csv_path (str) –

    Path to directory where output is saved. File type: output. Sample file. Accepted formats: csv (edam:format_3752).

  • output_jpg_path (str) –

    Path to .jpg file where output is saved. File type: output. Sample file. 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.

    • 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.interbp_correlations.interbpcorr import interbpcorr

interbpcorr(
    input_filename_shift='path/to/input/shift.ser',
    input_filename_slide='path/to/input/slide.ser',
    input_filename_rise='path/to/input/slide.ser',
    input_filename_tilt='path/to/input/tilt.ser',
    input_filename_roll='path/to/input/roll.ser',
    input_filename_twist='path/to/input/twist.ser',
    output_csv_path='path/to/output/file.csv',
    output_jpg_path='path/to/output/plot.jpg',
    properties=prop)
Info: