GTF.py is a simple module for reading GTF and GFF files

GTF.py

#!/usr/bin/env python
"""
GTF.py
Kamil Slowikowski
December 24, 2013

Read GFF/GTF files. Works with gzip compressed files and pandas.

    http://useast.ensembl.org/info/website/upload/gff.html

LICENSE

This is free and unencumbered software released into the public domain.
Anyone is free to copy, modify, publish, use, compile, sell, or
distribute this software, either in source code form or as a compiled
binary, for any purpose, commercial or non-commercial, and by any
means.

In jurisdictions that recognize copyright laws, the author or authors
of this software dedicate any and all copyright interest in the
software to the public domain. We make this dedication for the benefit
of the public at large and to the detriment of our heirs and
successors. We intend this dedication to be an overt act of
relinquishment in perpetuity of all present and future rights to this
software under copyright law.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
OTHER DEALINGS IN THE SOFTWARE.

For more information, please refer to <http://unlicense.org/>
"""


from collections import defaultdict
import gzip
import pandas as pd
import re


GTF_HEADER  = ['seqname', 'source', 'feature', 'start', 'end', 'score',
               'strand', 'frame']
R_SEMICOLON = re.compile(r'\s*;\s*')
R_COMMA     = re.compile(r'\s*,\s*')
R_KEYVALUE  = re.compile(r'(\s+|\s*=\s*)')


def dataframe(filename):
    """Open an optionally gzipped GTF file and return a pandas.DataFrame.
    """
    # Each column is a list stored as a value in this dict.
    result = defaultdict(list)

    for i, line in enumerate(lines(filename)):
        for key in line.keys():
            # This key has not been seen yet, so set it to None for all
            # previous lines.
            if key not in result:
                result[key] = [None] * i

        # Ensure this row has some value for each column.
        for key in result.keys():
            result[key].append(line.get(key, None))

    return pd.DataFrame(result)


def lines(filename):
    """Open an optionally gzipped GTF file and generate a dict for each line.
    """
    fn_open = gzip.open if filename.endswith('.gz') else open

    with fn_open(filename) as fh:
        for line in fh:
            if line.startswith('#'):
                continue
            else:
                yield parse(line)


def parse(line):
    """Parse a single GTF line and return a dict.
    """
    result = {}

    fields = line.rstrip().split('\t')

    for i, col in enumerate(GTF_HEADER):
        result[col] = _get_value(fields[i])

    # INFO field consists of "key1=value;key2=value;...".
    infos = [x for x in re.split(R_SEMICOLON, fields[8]) if x.strip()]

    for i, info in enumerate(infos, 1):
        # It should be key="value".
        try:
            key, _, value = re.split(R_KEYVALUE, info, 1)
        # But sometimes it is just "value".
        except ValueError:
            key = 'INFO{}'.format(i)
            value = info
        # Ignore the field if there is no value.
        if value:
            result[key] = _get_value(value)

    return result


def _get_value(value):
    if not value:
        return None

    # Strip double and single quotes.
    value = value.strip('"\'')

    # Return a list if the value has a comma.
    if ',' in value:
        value = re.split(R_COMMA, value)
    # These values are equivalent to None.
    elif value in ['', '.', 'NA']:
        return None

    return value

Thank you so much. I am very impressed by your code.
I am new to Linux/Unix though. Could you let me know a Linux terminal command to execute your code interacting with the gtf.gz file?
It will be greatly appreciated! Thank you.

Hi @sallyey

To use this code, you'll need Python 2.

Check which version you have installed by running:

python --version

Copy the code into a file called GTF.py.

In a new Python script in the same folder as GTF.py, you can write:

import GTF
df = GTF.dataframe("filename.gtf")

Hi, thank you so much for your prompt response.
I did save your code as GTF.py and I also created a new file, init_gtf.py, including the last two commands:
import GTF
df = GTF.dataframe("myfilename.gtf.gz")

And I run the codes with a linux command: python init_gtf.py
But, after the init_gtf.py is complete with running, I was not able to see any result.
Could you advise me how I can see the result from your code?

My goal is to count how many genes are annotated in my gtf.gz file, and I found your code for the reference.
Since I am not familiar with both linux and python, I am struggling a lot.
Please advise me. I really do appreciate your time and efforts.
Thank you so much!

@sallyey You might consider asking for help on https://www.biostars.org

There, many people ask for help and provide answers every day. Hundreds of people will see your question, and some of them might offer suggestions.

Make sure you describe your problem, your goals, what you have tried, and what went wrong. The more information you provide, the more likely it is that other people will understand what you are hoping to do.

Good luck!

Thanks so much!