daler / gffutils

GFF and GTF file manipulation and interconversion

http://daler.github.io/gffutils

daler/gffutils Issues

Update an entry and retain children
Closed a month ago3
Value of Target attribute gains quotes when it shouldn't in round trip manipulation
Updated 2 months ago4
FeatureDB.update on disk db very slow
Closed 2 months ago2
Suggestion: Drop support for python < 3.7 and add support for newer python verison
Closed 2 months ago
How to get closest features?
Closed 2 months ago1
gffutils-cli incompatability with argh >= 0.30.0
Updated 7 months ago
create_db() does not parse directives from GFF files starting in v0.11.0
Updated 8 months ago3
Field separators in quoted attributes cause error
Updated 10 months ago3
merge_strategy='create_unique' not always creating unique id's
Updated a year ago2
Map transcript coordinates to genome coordinates
Updated a year ago3
Sqlite3.OptimizedUnicode deprecation warning
Closed a year ago1
Please remove 'nose' dependencies from tests: nose is not maintained and doesn't work any more on many systems
Closed a year ago1
how to save the modified gff to the disk
Closed a year ago2
Handling of multi-line features with same ID
Closed a year ago3
How to get all the gene ids of the read gff file
Closed a year ago1
Inconsistent behaviour of trailing semicolon
Closed a year ago1
gtf_extract command not found with conda installation
Closed a year ago4
How to create database for GRCh38_latest_genomic.gtf.gz?
Closed 2 years ago4
Better handling of merged components
Closed a year ago2
introns = G.interfeatures(exons) gives 0 introns. is it because exon gives unnamed_exon?
Closed a year ago2
"ValueError: The ID field ID has more than one value" when updating database.
Closed a year ago2
Apologies - delete me!
Closed a year ago
db.parents(id) stops at level 2?
Updated a year ago
SyntaxError when importing gffutils using python 2.7.15
Closed 2 years ago2
Updating db with intergenic space features
Closed 2 years ago9
bedtools object by pybedtools_integration.to_bedtool: pybedtools.merge automatically substracts start position by one
Closed 2 years ago1
Same IDs for gene_id and transcript_id
Closed 2 years ago3
Repair canonical_transcripts
Closed 2 years ago2
Proper way to sort/order features after merge?
Closed 2 years ago2
`id_spec` default can be misleading
Closed 2 years ago3
Bug: New merge method does not have "ignore_strand" argument => merge=True throws error
Closed 2 years ago2
create_db sqlite3.InterfaceError (small genome)
Closed 2 years ago3
Inconsistent Ordering of exon_number attribute in introns
Closed 2 years ago2
Import of introns fails
Closed 2 years ago2
Missing docstring entry
Closed 2 years ago1
How to get all chromsome names and featuretypes
Closed 2 years ago1
AttributeError: 'FeatureDB' object has no attribute 'strand'
Closed 2 years ago1
Tasmanian devil transcriptome is not loading in the database
Closed 2 years ago2
sort_attribute_values -- how to keep the exons in numerical order
Closed 2 years ago2
Can't get children from NCBI GFF (may be user error)
Closed 2 years ago13
change IDs in a GFF3
Closed 2 years ago1
Feature.sequence misses last base
Closed 3 years ago1
Is it possible to create a db only for one chromosome?
Closed 4 years ago2
Introducing new attributes and values from data file
Closed 4 years ago10
Update conda and pypi
Closed 4 years ago1
inspect.py vs inspection.py?
Closed 4 years ago1
Generating New Parent Attributes from gene_ID
Closed 4 years ago1
No all features are written to file
Closed 4 years ago1
creating a file with gene/transcript from exon only lines
Closed 4 years ago1
AttributeError: module 'gffutils' has no attribute 'pybedtools_integration'
Closed 5 years ago1