Does what is says on the tin... it parses GTF (GFFv2) files...
Tries to do it fast as well...
You probably don't want to use this! Instead, you're probably better off with HTSeq's GTF Parser, or BioPython, or in fact anything more tested...!
pip install git+https://github.com/krooijers/gtfparser>>> from gtfparser import GTFParser
>>> fn = "gencode.v26lift37.basic.annotation.gtf"
>>> fn = "/data/zfs/references/human/hg19/transcriptome/gencode_v26/gencode.v26lift37.basic.annotation.gtf"
>>> gtf = GTFParser(fn)
>>> gtfiter = iter(gtf)
>>> gf = next(gtfiter)
>>> gf.iv
GenomicInterval(chrom='chr1', start=11868, end=14409, strand='+')
>>> gf.iv.end > gf.iv.start
True
>>> gf.feature
'gene'
>>> gf.attr
{'gene_type': 'transcribed_unprocessed_pseudogene', 'gene_name': 'DDX11L1', 'havana_gene': 'OTTHUMG00000000961.2_2', 'level': '2', 'remap_status': 'full_contig', 'gene_id': 'ENSG00000223972.5_2', 'remap_target_status': 'overlap', 'remap_num_mappings': '1'}
>>> gf.source
'HAVANA'
>>> print(gf)
GenomicFeature(feature='transcript', source='HAVANA', iv=GenomicInterval(chrom='chr1', start=11868, end=14409, strand='+'), score='.', frame='.', attrstr='gene_id "ENSG00000223972.5_2"; transcript_id "ENST00000456328.2_1"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-002"; level 2; transcript_support_level 1; tag "basic"; havana_gene "OTTHUMG00000000961.2_2"; havana_transcript "OTTHUMT00000362751.1_1"; remap_num_mappings 1; remap_status "full_contig"; remap_target_status "overlap";\n')
# let's have some fun while we're at it:
>>> from collections import Counter
>>> exoncounter = Counter()
>>> for exon in filter(lambda gf: gf.feature == "exon", gtfiter):
... assert exon.feature == "exon"
... assert "transcript_id" in exon.attr
... tid = exon.attr["transcript_id"]
... exoncounter[tid] += 1
>>> print(exoncounter.most_common(15))
[('ENST00000589042.5_3', 363), ('ENST00000591111.5_3', 313), ('ENST00000342992.10_3', 312), ('ENST00000615779.5_1', 312), ('ENST00000342175.11_1', 191), ('ENST00000359218.10_1', 191), ('ENST00000460472.6_3', 191), ('ENST00000618972.4_2', 183), ('ENST00000397345.7_1', 182), ('ENST00000427231.6_1', 182), ('ENST00000603639.5_1', 180), ('ENST00000604864.5_1', 180), ('ENST00000454784.8_2', 172), ('ENST00000409198.5_2', 150), ('ENST00000172853.14_2', 149)]No joke (it's TTN):
grep "ENST00000589042.5_3" gencode.v26lift37.basic.annotation.gtf | awk '$3 == "exon"' | wc -l363
StepVector, a package to handle data or features spanning (genomic) ranges efficiently.
No warranty whatsoever.
Feedback, bug reports and fixes (in the form of well-formatted pull requests) are much appreciated.