Metadata-Version: 2.1
Name: mkprobe
Version: 0.1.0
Summary: Rebuild contigs from serie of contiguous kmers formatted in fasta
Home-page: https://github.com/bio2m/mkprobe
Author: Benoit Guibert
Author-email: contact <contact@bio2m.fr>
License: GPLv3
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3
Classifier: Natural Language :: English
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENCE.md

# mkprobe

## Description

Build contigs from a suite of contiguous kmers as fasta format

kmers of input fasta file : 
```
ATCG	             kmer 1
 TCGC	             kmer 2
  CGCT	             kmer 3
   GCTA	             kmer 4
      CTAT     	     kmer 5
       TATG          kmer 6
        ATGG  	     kmer 7
```
contigs of output
```
ATCGCTA	             contig 1
      CTATGG         contig 2
```

## Installation

No dependency required.

```
# with pip (recommended)
pip install mkprobe

# or github
git clone ....
```



## Examples


```
# All in a single output fasta file
mkprobe path/to/fasta/files/*  -o result.fa

# All in a single output TSV file
mkprobe path/to/fasta/files/*  -o result.tsv

# in separated files
for file in path/to/fasta/files/*
do
  mkprobe $file -o  output/$(basename $file}
done
```

**Nota**: when several files are given at input, mkprobe add the name of the file (minus extension) to headers.


## Usage

```
usage: main.py [-h] [-o OUTPUT] [-v] [files ...]

positional arguments:
  files                 fasta files

options:
  -h, --help            show this help message and exit
  -o OUTPUT, --output OUTPUT
                        output file name, by default at fasta. If extension 
                        is 'tsv', output will be a tabuled file
  -v, --version         show program's version number and exit
```
