embl-api-validator is deleting gene for single exon/CDS features

[Asutu]

Hi,

when running embl-api-validator version 1.1.265 with the -fix flag it seems that the validator is removing the gene feature from the embl flat file if the gene has a single exon/CDS feature.

For example, running:

java -jar embl-api-validator-1.1.265.jar -r -fix -prefix fixed.2 my_flatfile.embl

the first line of the fixed.2_VAL_FIXES.txt is:

FIX: Deleted gene associated with "CDS" feature with location "complement(54086..54850)" [my_flatfile.embl,  line: 324 of my_flatfile.embl]

looking at the original flat file I have:

FT   CDS             complement(join(45260..45365,47660..47683,47851..47988,
FT                   48031..48038))
FT                   /locus_tag="XXXX_LOCUS7"
FT                   /codon_start=1
FT                   /note="source:maker"
FT                   /note="ID:C00000000006"
FT                   /transl_table=1
FT   gene            complement(54086..54850)
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /note="source:maker"
FT                   /note="ID:G00000000007"
FT                   /standard_name="ccme"
FT   mRNA            complement(54086..54850)
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /note="source:maker"
FT                   /note="ID:T00000000007"
FT                   /db_xref="PFAM:PF03100"
FT                   /db_xref="InterPro:IPR004329"
FT                   /standard_name="ccme"
FT                   /product="Cytochrome c-type biogenesis protein CcmE"
FT   exon            complement(54086..54850)
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /note="source:maker"
FT                   /note="ID:E00000000034"
FT   CDS             complement(54086..54850)
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /codon_start=1
FT                   /note="source:maker"
FT                   /note="ID:C00000000007"
FT                   /transl_table=1
FT   gene            58057..63744
FT                   /locus_tag="XXXX_LOCUS9"

in the file generate by embl-api-validator the gene feature for the locus XXXX_LOCUS8 is missing:

FT   exon            complement(48031..48038)
FT                   /locus_tag="XXXX_LOCUS7"
FT                   /note="source:maker"
FT                   /note="ID:E00000000033"
FT   mRNA            complement(54086..54850)
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /standard_name="ccme"
FT                   /product="Cytochrome c-type biogenesis protein CcmE"
FT                   /note="source:maker"
FT                   /note="ID:T00000000007"
FT                   /db_xref="PFAM:PF03100"
FT                   /db_xref="InterPro:IPR004329"
FT   exon            complement(54086..54850)
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /note="source:maker"
FT                   /note="ID:E00000000034"
FT   CDS             complement(54086..54850)
FT                   /codon_start=1
FT                   /transl_table=1
FT                   /locus_tag="XXXX_LOCUS8"
FT                   /note="source:maker"
FT                   /note="ID:C00000000007"
FT   gene            58057..63744
FT                   /locus_tag="XXXX_LOCUS9"

What is the rationale behind this?

Thanks,
Pedro

[sholt6]

Hi Pedro,

Please note that the EMBL flatfile validator is about to be deprecated and no longer provides the most up-to-date version of our validation.
Please look into using Webin-CLI:
https://ena-docs.readthedocs.io/en/latest/cli.html

If you would like to discuss this further, open a ticket by sending an email to datasubs@ebi.ac.uk

Best wishes,
Sam