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https://github.com/bibymaths/pattern_fasta
A Perl script to match marker sequences. Supports efficient file handling and regex-based searches, with benchmarking for memory and runtime performance.
https://github.com/bibymaths/pattern_fasta
dna-sequences pattern-matching perl regex
Last synced: 14 days ago
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A Perl script to match marker sequences. Supports efficient file handling and regex-based searches, with benchmarking for memory and runtime performance.
- Host: GitHub
- URL: https://github.com/bibymaths/pattern_fasta
- Owner: bibymaths
- License: mit
- Created: 2023-01-23T16:15:36.000Z (about 2 years ago)
- Default Branch: main
- Last Pushed: 2025-01-18T20:31:41.000Z (23 days ago)
- Last Synced: 2025-01-18T21:25:30.198Z (23 days ago)
- Topics: dna-sequences, pattern-matching, perl, regex
- Language: Perl
- Homepage:
- Size: 14.8 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# Read Pattern Tool
## Overview
This Perl script matches marker sequences from Illumina reads (lengths: 40, 60, 80, 100) to the partial hg38 reference genome. It calculates how many of these markers appear in chromosome 1 of hg38. Results include matched sequences, runtime, and memory benchmarks.
## Features
- Supports `.fasta.gz` input files to save memory and time.
- Matches sequences using regex for global counts of matches.
- Handles different Illumina read lengths and query sizes.
- Outputs matched markers to `MatchedMarkers.txt`.
- Benchmarks runtime and memory usage.
## Prerequisites
### Windows
- Install Perl or ActiveState Perl.
- Optional: Install Valgrind for benchmarking.
### MacOS/Linux
- Perl is pre-installed in most distributions.
- Optional: Use `/usr/bin/time` for benchmarking.
## Installation
Clone the repository and place the following files in the same directory:
1. This script (`read_pattern.pl`)
2. Reference genome file (`hg38_partial.fasta.gz`)
3. Illumina read files:
- `illumina_reads_40.fasta.gz`
- `illumina_reads_60.fasta.gz`
- `illumina_reads_80.fasta.gz`
- `illumina_reads_100.fasta.gz`
## Usage
### Windows
Run the script using any Perl-compatible IDE or command line:
```bash
perl read_pattern.pl
```
### MacOS/Linux
#### Basic Usage:
```bash
perl read_pattern.pl
```
#### Benchmarking:
```bash
/usr/bin/time -l perl read_pattern.pl # MacOS
/usr/bin/time -v perl read_pattern.pl # Linux
```
## Input Options
1. Select an Illumina read file:
- 1: `illumina_reads_40.fasta.gz`
- 2: `illumina_reads_60.fasta.gz`
- 3: `illumina_reads_80.fasta.gz`
- 4: `illumina_reads_100.fasta.gz`
2. Select a query size for read length = 100:
- 1: 1,000 queries
- 2: 10,000 queries
- 3: 100,000 queries
- 4: 1,000,000 queries
## Output
- Matched marker sequences are written to `MatchedMarkers.txt`.
- The script prints the total number of matches to the console.
## Benchmarking Details
| Read Length | Query Size | Markers Found | Runtime | Memory Usage |
|-------------|------------|---------------|----------|--------------|
| 40 | 1,000 | 511 | 2.94 min | 334 MB |
| 60 | 1,000 | 446 | 3.27 min | 336 MB |
| 80 | 1,000 | 415 | 3.83 min | 337.5 MB |
| 100 | 1,000 | 439 | 3.23 min | 341 MB |
| 100 | 10,000 | 4,280 | 33 min | 341 MB |
## Error Handling
- Validates `.fasta.gz` file paths.
- Prompts for re-execution if invalid options are entered.
## Author
**Abhinav Mishra**
[email protected]
## License
This project is licensed under the MIT License.