Version Compatibility

Reference examples tested with: gffutils 0.13+, gffread 0.12+, gtfparse 2.x, pyranges 0.1+ (or 1.0+ - see note), AGAT 1.4+.

Before using code patterns, verify installed versions match. If versions differ:

• CLI: <tool> --version then <tool> --help to confirm flags
• Python: pip show <package> then help(module.function) to check signatures

Two version landmines specific to this skill: (1) gtfparse changed its return type - older releases returned a pandas DataFrame, gtfparse >=2.x returns a polars DataFrame by default; pass result_type='pandas' before chaining pandas idioms (.copy(), boolean masks). (2) pyranges has a major-version API split - pyranges 0.x and the 1.0 rewrite differ in method names and attribute access; check import pyranges; pyranges.version before pasting code. gffutils stores 1-based coordinates while pyranges stores 0-based - their start fields differ by one by design. If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt rather than retrying.

GTF/GFF Handling

"Pull these features (or their sequences) out of my annotation, convert it, or find out why my counts are wrong." -> Treat the file as a serialized gene-model tree: walk gene->transcript->exon/CDS, derive implicit features, and reconcile coordinate and namespace conventions before trusting any number.

• CLI: gffread in.gtf -T -o out.gtf (convert), gffread -w tx.fa -g genome.fa in.gtf (FASTA), agatconvertsp_gxf2gxf.pl (sanitize)
• Python: gffutils.createdb(...) then db.children(gene, featuretype='exon') (tree query); gtfparse.readgtf(..., resulttype='pandas') / pyranges.readgtf(...) (dataframe)

The Single Most Important Modern Insight -- A GTF/GFF3 Is a Serialized Gene-Model Tree, Not a Table of Intervals

Almost every painful bug here comes from the file looking like a CSV while behaving like a tree, or from a coordinate/provenance mismatch the tools never warn about - and every one of these failures is silent: nothing throws, the wrong answer just propagates. Three load-bearing facts the tutorials skip:

1. The coordinate conversion is asymmetric. GTF/GFF3 are 1-based fully inclusive [start, end]; BED (and pyranges-internal) are 0-based half-open [start-1, end). Convert to BED by subtracting 1 from the start only - the end is unchanged (the inclusive 1-based end and the exclusive 0-based end are the same integer). Doing start-1 AND end-1 shifts the feature one base left and is the classic over-correction: invisible in coverage/overlap, catastrophic in CDS translation (a one-base frameshift garbles the protein). gffutils keeps 1-based, pyranges stores 0-based, so their start fields differ by one correctly - never "fix" that discrepancy.

1. The all-zero count matrix. featureCounts/htseq-count match a read to a feature by string equality on the chromosome name, so chr1 != 1 != NC_000001.11 produces a perfectly well-formed matrix of zeros with no error or warning - the only signal is ~0% assigned in the summary. Same bug one altitude up: gene-ID version suffixes (ENSG00000223972.5 vs ENSG00000223972) silently drop rows on an annotation join. Audit every cross-file key (chromosomes between BAM/GTF/FASTA, gene IDs between GTF/count-matrix/annotation) by set intersection, never by eye, before any count or join.

1. phase is not frame, and the stop codon is a 3-bp ghost. Phase (column 8) is the strand-aware count of bases to trim from the segment's transcriptional 5' end to reach the next codon (0/1/2) - recompute it on any CDS edit (AGAT/gffread do; hand-editing coordinates without fixing phase frameshifts the translation). GTF (Ensembl/GENCODE) excludes the stop codon from CDS; GenBank/GFF3 often include it - so a CDS length off by exactly 3 nt (or a protein +/-1 stop) between two sources is a convention mismatch, not a bug.

Tool Taxonomy

Decision Tree by Scenario

Walk the Gene Tree and Derive Introns (gffutils)

Goal: Traverse gene -> transcript -> exon and reconstruct features (introns) that the file does not store explicitly.

Approach: Build a SQLite DB once (disabling gene/transcript inference when those lines already exist, for a ~100x speedup), then query children ordered by position and synthesize introns from the exon gaps.

import gffutils

# disable_infer_* is GTF-only and applies when gene/transcript lines ALREADY exist (modern GENCODE/Ensembl) -> ~100x faster
db = gffutils.create_db('annotation.gtf', 'annotation.db', force=True,
                        disable_infer_genes=True, disable_infer_transcripts=True,
                        merge_strategy='create_unique')

gene = db['ENSG00000141510']                                    # gffutils returns 1-based coords (raw record)
for tx in db.children(gene, featuretype=['mRNA', 'transcript'], order_by='start'):
    exons = list(db.children(tx, featuretype='exon', order_by='start'))
    introns = list(db.interfeatures(exons, new_featuretype='intron'))   # introns are not stored - derived from exon gaps
    print(tx.id, len(exons), 'exons', len(introns), 'introns')

A modern GTF without disableinfer triggers the slow inference/merge machinery; an older* minimal GTF lacking gene/transcript lines needs inference ON so gffutils reconstructs the envelopes. Match the flag to the file. introns, UTRs (exon - CDS), and TSS are derived, not stored - never infer biological absence from a missing feature line.

Convert Formats and Extract Sequences (gffread)

gffread is genome-aware and respects the stop-codon convention, so it is the safe path for sequence extraction (naive coordinate math is not).

gffread annotation.gff3 -T -o annotation.gtf            # GFF3 -> GTF2 (default output is GFF3)
gffread -w transcripts.fa -g genome.fa annotation.gtf   # spliced exon (mature transcript) FASTA
gffread -x cds.fa         -g genome.fa annotation.gtf   # spliced CDS nucleotide FASTA
gffread -y proteins.fa    -g genome.fa annotation.gtf   # translated-CDS protein FASTA
gffread annotation.gtf -C -o coding.gtf                 # keep only coding transcripts

-g needs the genome FASTA (gffread auto-creates the .fai). -w/-x/-y splice the segments per transcript, so they handle multi-exon models correctly - do not concatenate exon FASTAs by hand.

Convert GTF to BED with the Right Coordinate Shift

Goal: Emit a BED of a chosen feature type for bedtools, without the off-by-one frameshift.

Approach: Parse to a pandas frame, filter to the feature type, subtract 1 from the start only, leave the end untouched.

import gtfparse

df = gtfparse.read_gtf('annotation.gtf', result_type='pandas')   # gtfparse >=2.x defaults to POLARS - force pandas
genes = df[df['feature'] == 'gene'].copy()
genes['start'] = genes['start'] - 1                              # 1-based inclusive -> 0-based half-open: START ONLY
bed = genes[['seqname', 'start', 'end', 'gene_id', 'score', 'strand']]
bed.to_csv('genes.bed', sep='\t', header=False, index=False)

For TSS/promoter derivation (strand-aware: + strand TSS = start, - strand TSS = end), route to proximity-operations - the promoter window is an imposed definition, not an annotated feature.

Sanitize a Malformed File First (AGAT)

When a file lacks ##gff-version 3, has non-Sequence-Ontology types, is missing gene/exon/UTR lines, has duplicate IDs, or mixes conventions, sanitize it once rather than coding around it:

agat_convert_sp_gxf2gxf.pl -g messy.gff3 -o clean.gff3   # adds missing ID/Parent + features, fixes dup IDs, recomputes phase, sorts
agat_convert_sp_gff2gtf.pl -g clean.gff3 -o clean.gtf    # GFF3 -> GTF (collapses level1->gene, level2->transcript)

AGAT makes decisions (which convention to standardize to, how to derive missing features) - usually a feature, but when a source's exact encoding must be preserved (e.g. auditing a submission), inspect what it changed rather than trusting blindly.

Per-Method Failure Modes

Over-correcting the coordinate conversion

Trigger: subtracting 1 from both start and end when converting to BED. Mechanism: only the start representation differs; the inclusive 1-based end equals the exclusive 0-based end. Symptom: every feature shifted one base left; invisible in coverage, frameshifts CDS translation. Fix: start-1, end unchanged.

Comparing coordinates across gffutils and pyranges

Trigger: asserting equality on start fields from both libraries in one script. Mechanism: gffutils keeps 1-based, pyranges stores 0-based. Symptom: an off-by-one that looks like a bug; "fixing" it introduces a real error. Fix: confirm each library's convention; expect the difference.

All-zero count matrix (seqid mismatch)

Trigger: BAM aligned to chr1, GTF annotated with 1. Mechanism: counters match reads to features by chromosome-name string equality. Symptom: well-formed matrix of zeros, no error; ~0% assigned in the summary. Fix: intersect the BAM @SQ/idxstats chromosome set with the GTF column-1 set programmatically; remap one namespace, re-confirm.

Dropped rows on a gene-ID join

Trigger: count matrix keyed ENSG... joined to annotation keyed ENSG....5. Mechanism: exact string match on a versioned vs unversioned ID. Symptom: join returns a dataframe but rows vanish / annotation is NA. Fix: strip .\d+$ on both sides for matching; keep the version in the stored annotation for provenance.

CDS length off by exactly 3

Trigger: comparing CDS/protein length across two sources, or translating after a convention-flipping conversion. Mechanism: GTF excludes the stop codon from CDS; GenBank/GFF3 often include it. Symptom: length differs by 3 nt / 1 aa; protein does/does not end in *. Fix: suspect the convention before debugging code; extract CDS with gffread/AGAT, which know it.

Editing CDS coordinates without recomputing phase

Trigger: trimming/merging/lifting CDS coordinates, leaving column 8 as-is. Mechanism: phase is a static integer; the chain of per-segment phases depends on cumulative coding length. Symptom: downstream translation (gffread -y, table2asn, EMBL) frameshifts or rejects. Fix: treat a CDS edit + phase recompute as one atomic operation; let AGAT/gffread recompute.

gffutils pathologically slow on a modern GTF

Trigger: createdb on a GENCODE/Ensembl GTF without the infer flags. Mechanism: gffutils infers gene/transcript envelopes and runs the merge machinery. Symptom: createdb hangs for many minutes. Fix: disableinfergenes=True, disableinfertranscripts=True when those lines already exist (~100x faster).

Quantitative Thresholds

Common Errors

References

• Pertea G, Pertea M. 2020. GFF Utilities: GffRead and GffCompare. F1000Research 9:304.
• Stovner EB, Saetrom P. 2020. PyRanges: efficient comparison of genomic intervals in Python. Bioinformatics 36:918-919.
• Dale R. gffutils: GFF and GTF file manipulation and interconversion. Software, https://github.com/daler/gffutils (no journal publication).
• Dainat J. AGAT: Another Gff Analysis Toolkit to handle annotations in any GTF/GFF format. Zenodo. doi:10.5281/zenodo.3552717.
• Rubinsteyn A, et al. gtfparse: parsing tools for GTF (gene transfer format) files. Software, https://github.com/openvax/gtfparse (no journal publication).
• Liao Y, Smyth GK, Shi W. 2014. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30:923-930.
• Anders S, Pyl PT, Huber W. 2015. HTSeq - a Python framework to work with high-throughput sequencing data. Bioinformatics 31:166-169.

Related Skills

• bed-file-basics - BED format and the coordinate conversion this skill feeds into
• interval-arithmetic - Set operations on the features extracted here
• proximity-operations - Strand-aware TSS/promoter derivation from extracted features
• rna-quantification/featurecounts-counting - Consumes the GTF/GFF features; the seqid/strand landmines live there
• genome-annotation/functional-annotation - Downstream of feature/sequence extraction from the annotation
• genome-annotation/annotation-qc - Judges whether the annotation this skill parses is sound
• differential-expression/de-results - Map gene coordinates back to DE results