Parsing GTF file - Help!
I have data from gencode which looks like this:
chr1 ENSEMBL gene 17369 17436 . - . gene_id "ENSG00000278267.1"; gene_type "miRNA"; gene_status "KNOWN"; gene_name "MIR6859-1"; level 3;
chr1 ENSEMBL gene 30366 30503 . + . gene_id "ENSG00000274890.1"; gene_type "miRNA"; gene_status "KNOWN"; gene_name "MIR1302-2"; level 3;
chr1 ENSEMBL gene 157784 157887 . - . gene_id "ENSG00000222623.1"; gene_type "snRNA"; gene_status "KNOWN"; gene_name "RNU6-1100P"; level 3;
I have tried using gffutils, but I get an error with this code:
import gffutils
db = gffutils.create_db("sRNA.gene.gtf", dbfn='sRNA.gene.gtf.db')
print(list(db.featuretypes()))
# ['CDS', 'exon', 'gene', 'start_codon', 'stop_codon', 'transcript']
# Here's how to write genes out to file
with open('sRNA.gene.gtf', 'w') as fout:
for gene in db.features_of_type('gene'):
fout.write(str(gene) + '\n')
Where it says
ImportError: cannot import name 'feature'.
Can someone please offer suggestions on the best way to parse such GTF files?
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Hello espop23!
It appears that your post has been cross-posted to another site: https://www.reddit.com/r/bioinformatics/comments/3rvn3g/help_parsing_gtf_file/
This is typically not recommended as it runs the risk of annoying people in both communities.
If I use your example GTF file and your example code, it works -- with the exception that the list of featuretypes is ['gene'] since only gene features are in your example GTF.
Can you provide a minimal example (complete code and input) that reproduces the error?
More generally, what is your end goal? It may not be necessary to create a database. For example, you can use gffutils just for parsing a GTF file (with the
gffutils.FeatureIteratorclass).Last, see some hints at A: GFFutils very slow at creating database file. Any Idea why..? for using GENCODE GTF files which now already include features for genes and transcripts.