Metadata-Version: 2.1
Name: igblast_parser
Version: 0.0.3
Summary: Parser of Igblast results into a csv file
Home-page: https://github.com/aerijman/igblast-parser
Author: Ariel Erijman & Brd Langhorst
Author-email: aerijman@fredhutch.org
License: UNKNOWN
Description: ## Simple parser of igblast results
        
        [Igblast](https://github.com/ncbi/igblast) allows to view the matches to the germline V, D and J genes, details at rearrangement junctions and a lot more (see [documentation](https://ncbi.github.io/igblast/)).  
        
        The output includes a lot of information in a format that can't be directly used in statistical analyses.  
        
        This simple script parses igblast output into a csv formatted table, easy to understand and ready to include in a statistical analysis.
        
        
        ### Installation
        
        pip install igblast-parser
        conda install -c bioconda igblast-parser
        
        python setup.py install
        
        ### Usage
        
        docs
        
        While docs are not ready:
        
        Command line executable in unix-like systems:
        ```bash
        	cat <igblast.output> | igblast-parser
        ``` 
        Pipe is not obligatory as the input could be specified with the argument `--in`   
        
        optional argument: `--out` to specify the prefix of the output csv file   
        ```bash
        	igblast-parser --in <igblast.output> --out <parser_output>
        ```
        
        In interactive python or script
        ```python
        	f_in = open('igblast.output','r')
        
        	# dictionary with UMI as primary key and multiple keys/UMI
        	d = igblast_parse(f)
        
        	# pandas provides very nice tables
         	import pandas
        	df = pandas.DataFrame(d).T
        ```
        
        
        
Platform: UNKNOWN
Requires-Python: >=3.6
Description-Content-Type: text/markdown
