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Utility package to parse multi fasta files resulting from de novo assembly

Project description

# Contig Tools
## Installation
```
pip3 install contig-tools
```

## Usage
```
usage: contig-tools [-h] [-v] {filter,metrics,check_metrics} ...

A package to maniuplate and assess contigs arising from de novo assemblies


positional arguments:
{filter,metrics,check_metrics}
The following commands are available. Type
contig_tools <COMMAND> -h for more help on a specific
commands
filter Filter contigs based on either length and/or coverage
metrics Print contig metrics
check_metrics check contig metrics

optional arguments:
-h, --help show this help message and exit
-v, --version display the version number
```

## Examples
**filter contigs**
```
contig-tools filter -l 500 -c 3 -f contigs.fasta
```

**print contig metrics**
```
contig-tools metrics -f contig_tools/tests/test_data/test.fas
contig-tools metrics -f contig_tools/tests/test_data/test.fas -o json
```
**check if contigs meet conditions based on conditions enoded in a yaml file**

example yaml file
```
N50 score:
condition_type: gt
condition_value: 10
Largest contig:
condition_type: gt
condition_value: 15
Total length:
condition_type: lt_gt
condition_value:
- 100
- 50
```
example command
```
contig-tools check_metrics -f contigs.fasta -y conditions.yml
```
metrics that can be checked are
- Number of contigs
- Number of contigs > 500bp
- Total length
- %GC
- Largest contig
- N50 score

conditions that can be used are
- gt => greater than
- lt => less than
- lt_gt => less than and greater than

## code
Code can be found [here](https://gitlab.com/antunderwood/contig_tools)

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