---
title: "06-summer2021_blast"
output: html_document
date: "2024-02-26"
---
Rmd to perform BLAST with the _Pycnopodia helianthoides_ genome gene list against the published _Pycnopodia helianthoides_ genome. 

Genome gene list: `project-pycno-sizeclass-2022/data/augustus.hints.codingseq`

Based on this jupyter notebook by Steven Roberts: https://github.com/RobertsLab/code/blob/master/09-blast.ipynb 

```{bash}
pwd
```

```{bash}
/home/shared/ncbi-blast-2.15.0+/bin/blastx -h
```


# Create a BLAST database
I would like to make a database of UniProt/Swiss-prot. see https://www.uniprot.org/downloads 

```{bash}
cd /home/shared/8TB_HDD_02/graceac9/GitHub/paper-pycno-sswd-2021/analyses/06-BLAST
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_03.fasta.gz
gunzip -k uniprot_sprot_r2021_03.fasta.gz
cd -
```

```{bash}
pwd
```

```{python}
bldr = "/home/shared/ncbi-blast-2.15.0+/bin/"
```

```{bash}
${bldr}makeblastdb \
-in /home/shared/8TB_HDD_02/graceac9/GitHub/paper-pycno-sswd-2021/analyses/06-BLAST/uniprot_sprot_r2021_03.fasta \
-dbtype prot \
-out /home/shared/8TB_HDD_02/graceac9/GitHub/paper-pycno-sswd-2021/analyses/06-BLAST/uniprot_sprot_r2021_03
```

# Get a Query Sequence
```{bash}
pwd
```

`rsync` the data/augustus.hints.codingseq to the raven code directory. 

In command line, `ssh` into Raven, and into this working directory. Then use code below to `rsync` data to this directory.

Code:    
`rsync --archive --progress --verbose graceac9@raven.fish.washington.edu:/home/shared/8TB_HDD_02/graceac9/GitHub/project-pycno-sizeclass-2022/data/augustus.hints.codingseq /home/shared/8TB_HDD_02/graceac9/GitHub/paper-pycno-sswd-2021/code/`


```{python}
#how many sequences? lets count ">" as we know each contig has 1
!grep -c ">" augustus.hints.codingseq
```
26581 sequences 

# Run BLAST

```{bash}
pwd
```


Set paths to programs:
```{python}
blast_dir="/home/shared/ncbi-blast-2.15.0+/bin"
blastx="${blast_dir}/blastx"
```

Set paths to files:
```{python}
genome_fasta="/home/shared/8TB_HDD_02/graceac9/GitHub/paper-pycno-sswd-2021/code/augustus.hints.codingseq"
sp_db=""
```

```{bash}
pwd
```

code from: https://sr320.github.io/tumbling-oysters/posts/sr320-04-mytgo/index.html 

```{bash}
/home/shared/ncbi-blast-2.15.0+/bin/blastx \
-query augustus.hints.codingseq \
-db ../analyses/06-BLAST/uniprot_sprot_r2021_03 \
-out ../analyses/06-BLAST/summer2021-uniprot_blastx.tab \
-evalue 1E-20 \
-num_threads 40 \
-max_target_seqs 1 \
-outfmt 6
```

```{bash}
head -2 ../analyses/06-BLAST/summer2021-uniprot_blastx.tab
```

Note:    
In excel, I separated the columns that were "|" deliminated and made them "tab" delimited. 


# Annotate the blast output with uniprot-SP-GO
```{bash}
pwd
```

Move the `/analyses/06-BLAST/summer2021-uniprot_blastx.tab` to the code directory

the uniprot-SP-GO.sorted and GO-GOslim.sorted exist in my crab repositories, so I'll copy them over into this code directory

Check that everything is in the working directory:
```{bash}
ls
```

Yep!