---
title: "003_cod-transcriptome"
author: "Kathleen Durkin"
date: "2023-10-18"
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Code outline copied and modified from Roberts Lab blast tutorial file (./001-blast.Rmd)



## Download stand-alone blast (optional)
see ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/
```{bash}
cd
cd ~/RobertsLab_OnboardingTasks/Applications
curl -O https://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.14.1+-x64-win64.tar.gz
tar -xf ncbi-blast-2.14.1+-x64-win64.tar.gz
```


## Set blast directory

```{bash}
bldir="~/RobertsLab_OnboardingTasks/Applications/ncbi-blast-2.14.1+/bin/"
#run blastx help to test 
${bldir}blastx.exe -h
```

## Create blast database (protein)

Check release at https://www.uniprot.org/downloads. For example the release used here is **r2021_04**

```{bash}
cd ../big-stuff
curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
mv uniprot_sprot.fasta.gz uniprot_sprot_r2021_04.fasta.gz
gunzip -k uniprot_sprot_r2021_04.fasta.gz
cd -
```


```{bash}
#will need to re assign bldir
bldir=/Applications/bioinfo/ncbi-blast-2.12.0+/bin/

${bldir}makeblastdb \
-in ../big-stuff/uniprot_sprot_r2021_04.fasta \
-dbtype prot \
-out ../big-stuff/uniprot_sprot_r2021_04
```


```{bash}

#will need to re assign bldir
bldir=/Applications/bioinfo/ncbi-blast-2.12.0+/bin/


${bldir}blastx \
-query ../data/tutorial/Ab_4denovo_CLC6_a.fa \
-db ../big-stuff/uniprot_sprot_r2021_04 \
-out ../analyses/tutorial/Ab_4-uniprot_blastx.tab \
-evalue 1E-20 \
-num_threads 8 \
-max_target_seqs 1 \
-outfmt 6
```

```{bash}
head -3 ../analyses/tutorial/Ab_4-uniprot_blastx.tab
```