Metadata-Version: 1.1
Name: gtfparse
Version: 0.2.1
Summary: GTF Parsing
Home-page: https://github.com/hammerlab/gtfparse
Author: Alex Rubinsteyn
Author-email: UNKNOWN
License: http://www.apache.org/licenses/LICENSE-2.0.html
Description-Content-Type: UNKNOWN
Description: [![Build Status](https://travis-ci.org/openvax/gtfparse.svg?branch=master)](https://travis-ci.org/openvax/gtfparse) [![Coverage Status](https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github)](https://coveralls.io/github/openvax/gtfparse?branch=master)
        <a href="https://pypi.python.org/pypi/gtfparse/">
            <img src="https://img.shields.io/pypi/v/gtfparse.svg?maxAge=1000" alt="PyPI" />
        </a>
        
        gtfparse
        ========
        Parsing tools for GTF (gene transfer format) files.
        
        # Example usage
        
        ## Parsing all rows of a GTF file into a Pandas DataFrame
        
        ```python
        from gtfparse import read_gtf_as_dataframe
        
        # returns GTF with essential columns such as "feature", "seqname", "start", "end"
        # alongside the names of any optional keys which appeared in the attribute column
        df = read_gtf_as_dataframe("gene_annotations.gtf")
        
        # filter DataFrame to gene entries on chrY
        df_genes = df[df["feature"] == "gene"]
        df_genes_chrY = df_genes[df_genes["seqname"] == "Y"]
        ```
        
        
        ## Getting gene FPKM values from a StringTie GTF file
        
        ```python
        from gtfparse import read_gtf_as_dict
        
        gtf_dict = read_gtf_as_dict(
            "stringtie-output.gtf",
            column_converters={"FPKM": float})
        
        gene_fpkms = {
            gene_name: fpkm
            for (gene_name, fpkm, feature)
            in zip(gtf_dict["gene_name"], gtf_dict["FPKM"], gtf_dict["feature"])
            if feature == "gene"
        }
        ```
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
