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Arkadiy-Garber / FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
GNU Affero General Public License v3.0
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No protein sequence for Cyc2 #47

Open EvaP29 opened 1 week ago

EvaP29 commented 1 week ago

Hey ! Thank for your tool :)

I am looking for gene involved in iron oxydation in genomes and MAGs. When Cyc2 is found there are not proteins sequences associated. It is the only gene for which it is noted as "empty" in protein_sequence column in geneSummary outputs. Is not normal ? if not, why do I always get this result ?

Thanks,

Eva

sheaster commented 1 week ago

Hi I also have this issue - seeing "EMPTY" for protein_sequence for cyc2.

edit: looking a little deeper in issues i found this: https://github.com/Arkadiy-Garber/FeGenie/issues/45#issue-2340642584

i'll just parse the HMM_results. thanks!

Arkadiy-Garber commented 5 days ago

Hi Shea and Eva,

Thanks for your interest in FeGenie, and apologies for this bug/issue.

Shea correctly identified a similar issue in a different issue thread: https://github.com/Arkadiy-Garber/FeGenie/issues/45#issue-2340642584

This is a bug that is slated to be fixed sometime within the next few weeks. In the meantime, please consider that Cyc2 identification as correct. FeGenie has an issue fetching the protein sequence for that from the raw output files, but you can find that sequence in the protein predictions (InputSeq.fa-proteins.faa) if you use the locus tag assigned to Cyc2 in the FeGenie summary CSV file.

Thanks, Arkadiy