README.md

sequence-search

How to

Generate bowtie2 database

First download all sequences and associated occurrences from the OBIS database to data/sequences.csv and data/occurrences.csv:

create temp table sequence_hashes as
select
	dna.id,
	dna.occurrence_id,
	MD5(dna.flat->>'DNA_sequence') as hash,
	dna.flat->>'DNA_sequence' as sequence
from dna;

create temp table sequence_occurrences as
select
	sh.hash,
	round(occurrence.decimallongitude, 3) as decimalLongitude,
	round(occurrence.decimallatitude, 3) as decimalLatitude,
	occurrence.dataset_id,
	aphia.classification->>'phylum' as phylum,
	aphia.classification->>'class' as class,
	aphia.classification->>'order' as order,
	aphia.classification->>'family' as family,
	aphia.classification->>'genus' as genus,
	aphia.record->>'scientificName' as scientificName,
	count(*)
from sequence_hashes sh
left join occurrence on sh.occurrence_id = occurrence.id
left join aphia on occurrence.aphia = aphia.id 
group by
	sh.hash,
	round(occurrence.decimallongitude, 3),
	round(occurrence.decimallatitude, 3),
	occurrence.dataset_id,
	aphia.classification->>'phylum',
	aphia.classification->>'class',
	aphia.classification->>'order',
	aphia.classification->>'family',
	aphia.classification->>'genus',
	aphia.record->>'scientificName';

select * from sequence_occurrences; -- occurrences.csv

select distinct on (hash) hash, sequence -- sequences.csv
from sequence_hashes
order by hash;

Build the fasta file, occurrence sqlite database, and bowtie2 database:

./build_db.sh

Generate vsearch database

./vsearch-2.29.1-macos-aarch64/bin/vsearch --makeudb_usearch data/sequences.fasta --output data/sequences.udb

./vsearch-2.29.1-macos-aarch64/bin/vsearch --usearch_global perna.fasta --db data/sequences.udb --id 0.95 --query_cov 0.95 --maxaccepts 100 --maxrejects 100 --maxhits 10 --blast6out output.txt

Upload data

rsync -r data [email protected]:/data/sequence-search

Run the API

cd api
uvicorn main:app --reload --port 8086