We developed Incremental Protein Search highly inspired by iBlast(https://github.com/vtsynergy/iBLAST).
Incremental Protein Search is a tool designed to merge protein search results. It operates in two modes: default and extension, supporting .m8 and .m8e files respectively. The tool can be run locally, via Docker, or using Singularity.
To view a tutorial example, please visit the following link:
https://github.com/EESI/Incremental-Protein-Search/tree/main/examples
Usage: ./run_merge.sh [MODE] [INPUT_FILE1] [INPUT_FILE2] [OUTPUT_FILE] [OPTIONAL_PARAMETERS]
Modes:
--default Use default mode for .m8 files
--extension Use extension mode for .m8e files
Arguments:
INPUT_FILE1 Path to the first input file
INPUT_FILE2 Path to the second input file
OUTPUT_FILE Path to the output merged file
Optional Parameters (for default mode only):
PARAM1 First integer parameter (e.g., sequence length)
PARAM2 Second integer parameter (e.g., sequence length)$ python utils/fasta_length_calculator.py <fasta_file_path>
$ ./run_merge.sh --default source/blastp_astral_scope_result2.m8 source/blastp_astral_scope_result3.m8 source/merge_blastp_astral_scope_result23.m8 6205115 6211928
$ ./run_merge.sh --extension source/blastp_astral_scope_result2.m8e source/blastp_astral_scope_result3.m8e source/merge_blastp_astral_scope_result23.m8e
$ docker pull comhyunwoo/incremental-protein-search:latest
$ docker run --rm -v /home/user/data:/app/data comhyunwoo/incremental-protein-search:latest --default /app/data/blastp_astral_scope_result2.m8 /app/data/blastp_astral_scope_result3.m8 /app/data/merge_blastp_astral_scope_result23.m8 6205115 6211928
$ docker run --rm -v /home/user/data:/app/data comhyunwoo/incremental-protein-search:latest --extension /app/data/blastp_astral_scope_result2.m8e /app/data/blastp_astral_scope_result3.m8e /app/data/merge_blastp_astral_scope_result23.m8e
$ singularity pull docker:https://comhyunwoo/incremental-protein-search:latest
$ singularity exec -B /home/user/data:/app/data incremental-protein-search_latest.sif /bin/bash -c "cd /app/Incremental-Protein-Search && ./run_merge.sh --default /app/data/blastp_astral_scope_result2.m8 /app/data/blastp_astral_scope_result3.m8 /app/data/merge_blastp_astral_scope_result23.m8 6205115 6211928"
$ singularity exec -B /home/user/data:/app/data incremental-protein-search_latest.sif /bin/bash -c "cd /app/Incremental-Protein-Search && ./run_merge.sh --extension /app/data/blastp_astral_scope_result2.m8e /app/data/blastp_astral_scope_result3.m8e /app/data/merge_blastp_astral_scope_result23.m8e"
This tool is particularly useful in protein sequence analysis workflows, especially when dealing with large datasets. The incremental search approach can significantly improve efficiency in processing and analyzing protein data. Its flexibility in execution methods (local, Docker, Singularity) makes it adaptable to various computational environments, from personal workstations to high-performance computing clusters.