---
title: "01-0040029-geneID"
output: html_document
date: "2024-10-03"
---

![GO0040029](http://gannet.fish.washington.edu/seashell/snaps/Monosnap_QuickGOTerm_GO0040029_2024-10-03_16-29-35.png)

# Apul

```{bash}
curl -o ../output/01-geneID/Apul-genes.fasta https://gannet.fish.washington.edu/seashell/bu-github/deep-dive-expression/D-Apul/output/07-Apul-Hisat/genes.fasta

```


```{bash}
# Set the variable for the GO term
GO_TERM="0040029"

fasta="../output/01-geneID/Apul-genes.fasta"

sp="Apul"


# Use the variable in the curl command
curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A${GO_TERM}%29%29+AND+%28reviewed%3Atrue%29" -o "../output/01-geneID/SwissProt-GO:${GO_TERM}.fa"



head ../output/01-geneID/SwissProt-GO:${GO_TERM}.fa
grep -c ">" ../output/01-geneID/SwissProt-GO:${GO_TERM}.fa



/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in ../output/01-geneID/SwissProt-GO:${GO_TERM}.fa \
-dbtype prot \
-out ../output/01-geneID/SwissProt-GO:${GO_TERM}


/home/shared/ncbi-blast-2.15.0+/bin/blastx \
-query $fasta \
-db ../output/01-geneID/SwissProt-GO:${GO_TERM} \
-out ../output/01-geneID/${sp}_blastx-GO:${GO_TERM}_out.tab \
-evalue 1E-05 \
-num_threads 48 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
2>/dev/null

head ../output/01-geneID/${sp}_blastx-GO:${GO_TERM}_out.tab
wc -l ../output/01-geneID/${sp}_blastx-GO:${GO_TERM}_out.tab
```