gff3-py

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.

1. Change features with type exon to pseudogenic_exon and type transcript to pseudogenic_transcript if the feature has an ancestor of type pseudogene
2. 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')