Metadata-Version: 2.1
Name: contig tools
Version: 0.3.6
Summary: Utility package to parse multi fasta files resulting from de novo assembly
Home-page: UNKNOWN
Author: Anthony Underwood
Author-email: au3@sanger.ac.uk
License: MIT
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} ...
        
        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/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
        
        2. 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](https://gitlab.com/antunderwood/contig_tools)
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.7
Description-Content-Type: text/markdown
