Skip to main content

Rebuild contigs from serie of contiguous kmers formatted in fasta

Project description

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

mkprobe-0.1.0.tar.gz (15.8 kB view details)

Uploaded Source

Built Distribution

mkprobe-0.1.0-py3-none-any.whl (16.2 kB view details)

Uploaded Python 3

File details

Details for the file mkprobe-0.1.0.tar.gz.

File metadata

  • Download URL: mkprobe-0.1.0.tar.gz
  • Upload date:
  • Size: 15.8 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.11.2

File hashes

Hashes for mkprobe-0.1.0.tar.gz
Algorithm Hash digest
SHA256 546db7c36934b1b6276a74e93e3dc71dcc1b743a90b0d4dfc2ce6c60a63c27e4
MD5 b1caa5f87d00dfe330a4cdc12118a27e
BLAKE2b-256 8eb4945a4a8c21b13cefbeace3c37554b04426989b4c4ea8896e183f26e9fbfd

See more details on using hashes here.

File details

Details for the file mkprobe-0.1.0-py3-none-any.whl.

File metadata

  • Download URL: mkprobe-0.1.0-py3-none-any.whl
  • Upload date:
  • Size: 16.2 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/5.1.1 CPython/3.11.2

File hashes

Hashes for mkprobe-0.1.0-py3-none-any.whl
Algorithm Hash digest
SHA256 e5d879fe71209ac8c4687fe265d7562b4c2007b6055f64805a89868ae7cc53d8
MD5 e594b0d63ce3c90901ce180b22f6a4f1
BLAKE2b-256 2bb9b34d5167d0b806f427cf8c2322189e7b6c5e87471c0a480733eb2a1b71e5

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page