Suggestion: Download along with sequence metadata

[ChongLC]

Dear developer,

I just have a suggestion here. Sequence metadata usually is quite useful for data analysis for the downloaded sequence. Perhaps, you may consider adding that feature.

Looking forward to the feature.

Best regards,
Chong

[StuntsPT]

Hello @ChongLC ,
What kind of metadata do you have in mind? It might be possible, depending on what you mean.

Best,
Francisco

[ChongLC]

Dear Franciso,

Perhaps the record from genpept (.gp)? Although from my side, I would like to have the details (source/organism information) of the sequences. While downloading a huge dataset at once, it is hard to deep mine the souce/organism information of each sequence.

Best regards,
Chong

[StuntsPT]

Dear Chong,

Sorry about the delay. I somehow missed the notification.
Are you aware of any API that can be used to get the .gp files?

Best,
Francisco

[ChongLC]

Dear Developer,

I knew that they have the E-utilies function. You may want to refer to their documentation (https://www.ncbi.nlm.nih.gov/books/NBK25501/).

If I do not understand wrongly, you may download using the E-Utilities perl script by having a slight change.
my $db = "protein";
my $query = "txid10239[Organism]";
my $report = "genpept";

Past three years, I downloaded using the batch Entrez function. However, I noticed there are some empty batches. Just for your information in case you are not aware of it.

As I also missed the notification sometimes, perhaps we can have further conversation through email ([email protected]) if you don't mind.

Best regards,
CHONG

[ChongLC]

Dear Prof. Francisco,

It looks great while trying with a small dataset download (txid: 12637).
The command used:
python3 NCBI_downloader.py -q "txid12637[Organism:exp]" -d "protein" -nv -o denv.txt -f gb

Do close the issue if required. Thank you.

Best regards,
CHONG

[StuntsPT]

Dear @ChongLC,
Great to hear it seems to be working. I will keep the issue open until I turn this makeshift version into a real integrated part of the program.

Best,
Francisco