Metadata-Version: 2.1
Name: gtfparse
Version: 1.2.1
Summary: GTF Parsing
Home-page: https://github.com/openvax/gtfparse
Author: Alex Rubinsteyn
License: http://www.apache.org/licenses/LICENSE-2.0.html
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/">
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        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
        
        # 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("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
        
        df = read_gtf(
            "stringtie-output.gtf",
            column_converters={"FPKM": float})
        
        gene_fpkms = {
            gene_name: fpkm
            for (gene_name, fpkm, feature)
            in zip(df["gene_name"], df["FPKM"], df["feature"])
            if feature == "gene"
        }
        ```
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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
Description-Content-Type: text/markdown
