ParseGFF

class yoda_powers.bio.ParseGFF(filename)

Bases: object

Parser of GFF3 file write in python. return an object iterable contain GFFRecord()

line in GFF3 return:

Example

>>> scaffold_44     prediction      gene    46      6942    0       +       .       ID=gene_1;Name=jgi.p|Mycfi2|180833;portal_id=Mycfi2;proteinId=180833;transcriptId=180833
>>> GFFRecord(seqid='scaffold_44', source='prediction', type='gene', start=46, end=6942, score=0.0, strand='+', phase=None,
>>>             attributes={'portal_id': 'Mycfi2', 'transcriptId': '180833', 'proteinId': '180833', 'Name': 'jgi.p|Mycfi2|180833', 'ID': 'gene_1'}, seq=None, len=6896)

GFFRecord has attributes can acces with record.value (ex: record.seqid):

attribute	infos
seqid	first column of gff3
source	second column of gff3
type	third column of gff3 contain type
start	start position
end	end position
score	score
strand	DNA brin
phase	phase
attributes	dict() with key corresponding to GFFAttributes
seq	if fasta load can add sequence but by default = None
len	size of sequence

Example

>>> objGFF = ParseGFF(gffFile)
>>> for record in objGFF.parseGFF3():
>>>     print(record.seqid)
>>>     if record.type == "mRNA" :
>>>             transcriptID = record.attributes["transcriptId"]

Methods Summary

parseGFF3()	A minimalistic GFF3 format parser.
parseGFFAttributes(self, attributeString)	Parse the GFF3 attribute column and return a dict

Methods Documentation

parseGFF3()

A minimalistic GFF3 format parser. Yields objects that contain info about a single GFF3 feature.

Supports transparent gzip decompression.

static parseGFFAttributes(self, attributeString)

Parse the GFF3 attribute column and return a dict