Metadata-Version: 1.1
Name: gtfparse
Version: 0.2.3
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| |Coverage Status|
        
        gtfparse
        ========
        
        Parsing tools for GTF (gene transfer format) files.
        
        Example usage
        =============
        
        Parsing all rows of a GTF file into a Pandas DataFrame
        ------------------------------------------------------
        
        .. code:: 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
        --------------------------------------------------
        
        .. code:: 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"
            }
        
        .. |Build Status| image:: https://travis-ci.org/openvax/gtfparse.svg?branch=master
           :target: https://travis-ci.org/openvax/gtfparse
        .. |Coverage Status| image:: https://coveralls.io/repos/openvax/gtfparse/badge.svg?branch=master&service=github
           :target: https://coveralls.io/github/openvax/gtfparse?branch=master
        
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
