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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

source code: https://gitlab.com/antunderwood/contig_tools

Usage

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

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


positional arguments:
  {filter,metrics,check_metrics,co_located}
                        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
    co_located          check to see if two or more loci are found on the same
                        contig.

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/contigs_for_checks.fas
contig-tools metrics -f contig_tools/tests/test_data/contigs_for_checks.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

check if a two or more loci are co-located

Make a fasta query file with the 2 or more loci you want to see if they are co-located e.g

>gene1
GCAGCTAGCGACTGCGAC.....
>gene2
CTACGTAGGACACGACTA....

There are two options

  1. Search a single genome file for the co-location of loci

    contig-tools co_located -q queries.fas -f /path/to/single/genome/contigs.fas
    

or

  1. Search a list of genomes for the co-location of loci Make a text file with paths to genomes e.g

    /path/to/single/genome1.fas
    /path/to/single/genome1.fas
    ....
    

    and then run the command

    contig-tools co_located -q queries.fas -l /path/to/single/genome_list_file.txt
    

    If you have muliple cores on the computer you are running this on you can process the search in parallel using the -n <NUMBER PARALLEL PROCESSES>.

    If you only want to write out genomes where the queries are co-located use the -y options

code

Code can be found here

Project details


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