gff3-py

https://travis-ci.org/hotdogee/gff3-py.png?branch=master

Manipulate genomic features and validate the syntax and reference sequence of your GFF3 files.

Free software: BSD license
Documentation: https://gff3-py.readthedocs.org.

Features

Simple data structures: Parses a GFF3 file into a structure composed of simple python dict and list.
Validation: Validates the GFF3 syntax on parse, and saves the error messages in the parsed structure.
Best effort parsing: Despite any detected errors, continue to parse the whole file and make as much sense to it as possible.
Uses the python logging library to log error messages with support for custom loggers.
Parses embeded or external FASTA sequences to check bounds and number of N s.
Check and correct the phase for CDS features.
Tree traversal methods ancestors and descendants returns a simple list in Breadth-first search order.
Transfer children and parents using the adopt and adopted methods.
Test for overlapping features using the overlap method.
Remove a feature and its associated features using the remove method.
Write the modified structure to a GFF3 file using the write mthod.

Quick Start

An example that just parses a GFF3 file named annotations.gff and validates it using an external FASTA file named annotations.fa looks like:

# validate.py
# ============
from gff3 import Gff3

# initialize a Gff3 object
gff = Gff3()
# parse GFF3 file and do syntax checking, this populates gff.lines and gff.features
# if an embedded ##FASTA directive is found, parse the sequences into gff.fasta_embedded
gff.parse('annotations.gff')
# parse the external FASTA file into gff.fasta_external
gff.parse_fasta_external('annotations.fa')
# Check seqid, bounds and the number of Ns in each feature using one or more reference sources
gff.check_reference(allowed_num_of_n=0, feature_types=['CDS'])
# Checks whether child features are within the coordinate boundaries of parent features
gff.check_parent_boundary()
# Calculates the correct phase and checks if it matches the given phase for CDS features
gff.check_phase()

A more feature complete GFF3 validator with a command line interface which also generates validation report in MarkDown is available under examples/gff_valid.py

The following example demonstrates how to filter, tranverse, and modify the parsed gff3 lines list.

Change features with type exon to pseudogenic_exon and type transcript to pseudogenic_transcript if the feature has an ancestor of type pseudogene
If a pseudogene feature overlaps with a gene feature, move all of the children from the pseudogene feature to the gene feature, and remove the pseudogene feature.

# fix_pseudogene.py
# =================
from gff3 import Gff3
gff = Gff3('annotations.gff')
type_map = {'exon': 'pseudogenic_exon', 'transcript': 'pseudogenic_transcript'}
pseudogenes = [line for line in gff.lines if line['line_type'] == 'feature' and line['type'] == 'pseudogene']
for pseudogene in pseudogenes:
    # convert types
    for line in gff.descendants(pseudogene):
        if line['type'] in type_map:
            line['type'] = type_map[line['type']]
    # find overlapping gene
    overlapping_genes = [line for line in gff.lines if line['line_type'] == 'feature' and line['type'] == 'gene' and gff.overlap(line, pseudogene)]
    if overlapping_genes:
        # move pseudogene children to overlapping gene
        gff.adopt(pseudogene, overlapping_genes[0])
        # remove pseudogene
        gff.remove(pseudogene)
gff.write('annotations_fixed.gff')

License

timeu/gff3-py

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