Metadata-Version: 2.1
Name: readcomb
Version: 0.0.2
Summary: Fast detection of recombinant reads in BAMs
Home-page: https://github.com/ness-lab/readcomb
License: GNU GPLV3+
Description: # `Readcomb` - fast detection of recombinant reads in BAMs
        
        ## What is it?
        
        Readcomb is a hybrid command line script and Python module for the filtering and classification of bam sequences based on their phase change properties. 
        
        ## Installation
        
        ``` Python
        pip install readcomb
        ```
        
        ## Dependencies
        - [cyvcf2](https://brentp.github.io/cyvcf2/) - Fast retrieval and filtering of vcf files and vcf objects written in C
        - [pysam](https://pysam.readthedocs.io/en/latest/api.html) - Interface for SAM and BAM files and provides SAM and BAM objects
        - [pandas](https://pandas.pydata.org/) - Support for data tables
        - [tqdm](https://tqdm.github.io/) - Provides updating progress bars for command line programs
        - [samtools](http://www.htslib.org/)
        
        # Usage:
        
        ## bamprep 
        Command line preprocessing script for bam files
        ```bash
        
        ```
        
        Optional parameters:
        
        - 
        
        ## vcfprep
        Command line preprocessing script for vcf files
        ```bash
        readcomb-vcfprep --vcf [vcf_filepath] --out [output_filepath]
        ```
        
        Optional arguments
        - `--snps_only`, Keep only SNPs
        - `--indels_only`, Keep only indels
        - `--no_hets`, Remove heterozygote calls
        - `--min_GQ [quality]`, Minimum genotype quality at both sites (default is 30)
        
        ## filter
        Command line multiprocessing script for identification of bam sequences with phase changes
        ```bash
        readcomb-filter --bam [bam_filepath] --vcf [vcf_filepath]
        ```
        
        Optional arguments:
        - `-p, --processes [processes]`, Number of processes available for filter (default is 4)
        - `-m, --mode [phase_change|no_match]`, Filtering mode (default phase_change)
        - `-l, --log [log_filepath]`, Filename for log metric output
        - `-o, --out [output_filepath]`, File to write filtered output to (default recomb_diagnosis)
        
        ## classification
        Python module for detailed classification of sequences containing phase changes
        ```python
        from readcomb.classification import rc
        
        # generate list of bam read pairs
        pairs = rc.pairs_creation(bam_filepath, vcf_filepath)
        
        # call each of the pairs to analyse and classify them
        # map and lambda function
        map(lambda x:x.call(), pairs)
        
        # or use a for loop
        for pair in pairs:
            pair.call() 
        
        # get classification of first read pair
        pairs[0].classify
        # > gene_conversion
        ```
        ## License
        
        GNU General Public License v3 (GPLv3+)
        
        ## Development
        
        Currently in alpha
        
        [Source code](https://github.com/ness-lab/readcomb)
        
        [Development repo](https://github.com/ness-lab/recombinant-reads)
Platform: UNKNOWN
Classifier: License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.5
Classifier: Development Status :: 3 - Alpha
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
