makeTxDbFromGRanges dropping a lot of transcripts

[Rohit-Satyam]

Hi @hpages

I have stumbled upon a peculiar case where the makeTxDbFromGRanges function is dropping a lot of transcripts

## Deifne release of annotation
x=49

## Import GFF
  txdb<-paste0("https://toxodb.org/common/downloads/release-",x,"/TgondiiME49/gff/data/ToxoDB-",x,"_TgondiiME49.gff") %>% txdbmaker::makeTxDbFromGFF(format = "gff3")

Warning message:
In makeTxDbFromGRanges(gr, metadata = metadata) :
  The following transcripts were dropped because their exon ranks could
  not be inferred (either because the exons are not on the same
  chromosome/strand or because they are not separated by introns):
  TGME49_200010-t26_1, TGME49_200110-t26_1, TGME49_200130-t26_1,
  TGME49_200230-t26_1, TGME49_200240-t26_1, TGME49_200250-t26_1,
  TGME49_200260-t26_1, TGME49_200270-t26_1, TGME49_200280-t26_1,
  TGME49_200290-t26_1, TGME49_200295-t26_1, TGME49_200300-t26_1,
  TGME49_200310-t26_1, TGME49_200320-t26_1, TGME49_200330-t26_1,
  TGME49_200340-t26_1, TGME49_200350-t26_1, TGME49_200360-t26_1,
  TGME49_200370-t26_1, TGME49_200375-t26_1, TGME49_200385-t26_1,
  TGME49_200400-t26_1, TGME49_200410-t26_1, TGME49_200430-t26_1,
  TGME49_200440-t26_1, TGME49_200450-t26_1, TGME49_200460-t26_1,
  TGME49_200470-t26_1, TGME49_200480-t26_1, TGME49_200590-t26_1,
  TGME49_200595-t26_1, TGME49_200600-t26_1, TGME49_200700-t26_1,
  TGME49_201100-t26_1, TGME49_201110-t26_1, TGME49_201120-t26_1,
  TGME49_201130-t26 [... truncated]

Only the release 49 annotation is problematic for this parasite. Having a look at the GFF file, I am still unable to understand why the makeTxDbFromGRanges will discard TGME49_200010-t26_1 in release 49 but will have no issue with TGME49_200010.R447 in release 68? is it because mRNA field is missing from the GFF?

## Release 49
TGME49_chrXII	VEuPathDB	gene	2245476	2249210	.	-	.	ID=TGME49_200010;description=hypothetical protein
TGME49_chrXII	VEuPathDB	protein_coding_gene	2245476	2249210	.	-	.	ID=TGME49_200010-t26_1;Parent=TGME49_200010;description=hypothetical protein
TGME49_chrXII	VEuPathDB	exon	2245476	2247209	.	-	.	ID=exon_TGME49_200010-t26_1-E2;Parent=TGME49_200010-t26_1
TGME49_chrXII	VEuPathDB	exon	2247554	2249210	.	-	.	ID=exon_TGME49_200010-t26_1-E1;Parent=TGME49_200010-t26_1
TGME49_chrXII	VEuPathDB	CDS	2246111	2247209	.	-	1	ID=TGME49_200010-t26_1-p1-CDS2;Parent=TGME49_200010-t26_1;protein_source_id=TGME49_200010-t26_1-p1
TGME49_chrXII	VEuPathDB	CDS	2247554	2247696	.	-	0	ID=TGME49_200010-t26_1-p1-CDS1;Parent=TGME49_200010-t26_1;protein_source_id=TGME49_200010-t26_1-p1
TGME49_chrXII	VEuPathDB	three_prime_UTR	2245476	2246110	.	-	.	ID=utr_TGME49_200010-t26_1_1;Parent=TGME49_200010-t26_1
TGME49_chrXII	VEuPathDB	five_prime_UTR	2247697	2249210	.	-	.	ID=utr_TGME49_200010-t26_1_2;Parent=TGME49_200010-t26_1

## Release 68
TGME49_chrXII	VEuPathDB	protein_coding_gene	2245476	2248187	.	-	.	ID=TGME49_200010;Name=GRA20;description=dense granule protein GRA20;ebi_biotype=protein_coding
TGME49_chrXII	VEuPathDB	mRNA	2245476	2248187	.	-	.	ID=TGME49_200010.R447;Parent=TGME49_200010;description=dense granule protein GRA20;gene_ebi_biotype=protein_coding
TGME49_chrXII	VEuPathDB	exon	2245476	2247209	.	-	.	ID=exon_TGME49_200010.R447-E2;Parent=TGME49_200010.R447;gene_id=TGME49_200010
TGME49_chrXII	VEuPathDB	exon	2247554	2248187	.	-	.	ID=exon_TGME49_200010.R447-E1;Parent=TGME49_200010.R447;gene_id=TGME49_200010
TGME49_chrXII	VEuPathDB	CDS	2246111	2247209	.	-	1	ID=TGME49_200010.P447-CDS2;Parent=TGME49_200010.R447;gene_id=TGME49_200010;protein_source_id=TGME49_200010.P447
TGME49_chrXII	VEuPathDB	CDS	2247554	2247696	.	-	0	ID=TGME49_200010.P447-CDS1;Parent=TGME49_200010.R447;gene_id=TGME49_200010;protein_source_id=TGME49_200010.P447
TGME49_chrXII	VEuPathDB	three_prime_UTR	2245476	2246110	.	-	.	ID=utr_TGME49_200010.R447_1;Parent=TGME49_200010.R447
TGME49_chrXII	VEuPathDB	five_prime_UTR	2247697	2248187	.	-	.	ID=utr_TGME49_200010.R447_2;Parent=TGME49_200010.R447