Database-comparator 1.0.1

Bioinformatics tool for compering large sequence files

Database_comparator

A program for searching and analyzing databases using various algorithms.

Table of Contents

• Overview

• Installation

• Configuration file

  • Syntax of configuration file

  • Inserting configuration file to program

• Usage

  • Exact match

  • Aligner

  • BLAST

  • Hamming distances

Overview

The program is for comparing and analyzing databases using various methods.

It utilizes the provided configuration to perform exact matching, sequence alignment,

BLAST searches, and calculates Hamming distances between sequences. The class allows for exporting the results to

different file formats, such as Excel, CSV, and Markdown.

Configuration of program is given by config_file.txt

Installation

# Example installation command

pip install Database_comparator

Configuration file

# Databases

QUERY HEDIMED__230620_Hedimed_1_22_basic--table_EF_predelana.xlsx part3



DB Databases/Nakayama.csv CDR3b [Clone/SequenceID, Epitope]

DB Databases/McPAS-TCR-filtred.csv CDR3.beta.aa [PubMed.ID, Pathology, Additional.study.details]

DB Databases/vdjdb.csv cdr3 [antigen.gene, antigen.species, mhc.a, gene]

DB Databases/TCRdb_all_sequnces.csv AASeq [TCRDB_project_ID, RunId, cloneFraction]



# Smith–Waterman algorithm

SWA_tolerance 0.9

SWA_gap_score -1000

SWA_mismatch_score 0

SWA_match_score 1



# Blastp Algorithm

BLAST_e_value 0.05

BLAST_database_name clip_seq_db

BLAST_output_name blastp_output.txt



# Hamming distance

HD_max_distance 1



# Multiprocessing

number_of_processors 3

Syntax of config file:

# QUERY - query database 

QUERY >Name of query database< >Name of column with sequence<



# DB - Databases with the data we want to analyze

DB >Name of data database< >Name of column with sequence< >identifiers of sequence<



# SWA_tolerance - tolerance of Smith Waterman algorithm (score/max_score)

SWA_tolerance >float<



# Smith Waterman scoring

SWA_gap_score >int<

SWA_mismatch_score >int<

SWA_match_score >int<



BLAST_e_value >float<

BLAST_database_name >the name of the blast database that will be created if needed<

BLAST_output_name >name of output file<



HD_max_distance >Maximum Hamming distance(int)<



number_of_processors >number of processors for multprocessing(int)<

Inserting config file to program:

from Database_comparator import db_compare



cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)

Usage

from Database_comparator import db_compare



cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)



# Modules

db_exact_match = db.exact_match # Used fot exact match search

db_aligner = db.aligner # Used for Smith Waterman algorithm

db_blast = db.blast # Used for BLAST search

db_hamming = db.hamming_distances # Used for finding Hamming distances between sequences

# Exporting results

from Database_comparator import db_compare



cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)



# Data computing....



db.export_data_frame(output_file="Results.xlsx", data_format="xlsx")

db.export_data_frame(output_file="Results.csv", data_format="csv")

Exact match

from Database_comparator import db_compare



cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)



# Program will search in single database for exact match with query database

db.exact_match.exact_match_search_in_single_database(database_index=0)

#Multiprocessing

db.exact_match.exact_match_search_in_single_database(database_index=0, parallel=True)

db.exact_match.exact_match_search_in_single_database_MULTIPROCESSING(database_index=0)

# Program will search all given databases for exact match with query database

db.exact_match.exact_match_search_in_all_databases()



# User can also use multiprocessing

db.exact_match.exact_match_search_in_all_databases(parallel=True)

# or

db.exact_match.exact_match_search_in_all_databases_MULTIPROCESSING()

Aligner

from Database_comparator import db_compare



cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)



#Single core

db.aligner.smithWatermanAlgorithm_match_search_in_single_database(database_index=0)

db.aligner.smithWatermanAlgorithm_match_search_in_all_databases()



#Multiprocessing

db.aligner.smithWatermanAlgorithm_match_search_in_single_database(database_index=0, parallel=True)

db.aligner.smithWatermanAlgorithm_match_search_in_single_database_MULTIPROCESSING()

db.aligner.smithWatermanAlgorithm_match_search_in_all_databases(parallel=True)

db.aligner.smithWatermanAlgorithm_match_search_in_all_databases_MULTIPROCESSING()

BLAST

from Database_comparator import db_compare

cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)

# Info about BLAST

db.blast.blast_database_info()



# Making BLAST database

db.blast.blast_make_database(name="BLAST_Database")



db.blast.blast_search_for_match_in_database() #Query is input database

db.blast.analyze_matches_in_database() #BLAST output will be analyzed with aligner



# User can also use this function.

db.blast.blast_search_and_analyze_matches_in_database()

Hamming distances

from Database_comparator import db_compare

cfg_file = 'path_to_config_file.txt'

db = db_compare.DB_comparator(cfg_file)



db.hamming_distances.find_hamming_distances_for_single_database(database_index=0)

db.hamming_distances.find_hamming_distances_for_all_databases()



# User can also do this

db.hamming_distances.find_hamming_distances_for_single_database(database_index=0, analyze=False)

db.hamming_distances.analyze_single_hamming_matrix(database_index=0)



db.hamming_distances.find_hamming_distances_for_all_databases(analyze=False)

db.hamming_distances.analyze_all_hamming_matrices()



# Hamming matrices are stored in >hamming_matrices_for_all_databases<

db_matrices = db.hamming_distances.hamming_matrices_for_all_databases