---
title: "Blast"
output: html_document
date: "2023-03-30"
---

# BLAST
This assignment is for FISH 546.
-----------------
Below is the session info for this markdown file created in jupyter Rstudio server.
```{r, echo=TRUE}
sessionInfo()
```

# Download Stand-alone BLAST
downloaded software:
```{bash}
cd ~/applications
curl -O https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.13.0+-x64-linux.tar.gz
```



the bash command "tar" will unzip the file
&&& this will not work as you have to navigate to dir first....

```{bash}
cd ~/applications # sr added
tar -xf ncbi-blast-2.13.0+-x64-linux.tar.gz
```


```{bash}
~/applications/ncbi-blast-2.13.0+/bin/blastx -h
```

# Make a BLAST database

```{bash}
cd ../data
curl -O https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_sprot.fasta.gz
mv uniprot_sprot.fasta.gz uniprot_sprot_r2023_01.fasta.gz
gunzip -k uniprot_sprot_r2023_01.fasta.gz
ls ../data
```


```{bash}
~/applications/ncbi-blast-2.13.0+/bin/makeblastdb \
-in ../data/uniprot_sprot_r2023_01.fasta \
-dbtype prot \
-out ../blastdb/uniprot_sprot_r2023_01
```
### Get query sequence

```{bash}
curl https://eagle.fish.washington.edu/cnidarian/Ab_4denovo_CLC6_a.fa \
-k \
> ../data/Ab_4denovo_CLC6_a.fa
```

```{bash}
head ../data/Ab_4denovo_CLC6_a.fa
echo "How many sequences are there?"
grep -c ">" ../data/Ab_4denovo_CLC6_a.fa
```
# Running BLAST
```{bash}
~/applications/ncbi-blast-2.13.0+/bin/blastx \
-query ../data/Ab_4denovo_CLC6_a.fa \
-db ../blastdb/uniprot_sprot_r2023_01 \
-out ../output/Ab_4-uniprot_blastx.tab \
-evalue 1E-20 \
-num_threads 20 \
-max_target_seqs 1 \
-outfmt 6
```

```{bash}
head -2 ../output/Ab_4-uniprot_blastx.tab
wc -l ../output/Ab_4-uniprot_blastx.tab
```



# Joining blast table with annotation table
```{bash}
head -2 ../output/Ab_4-uniprot_blastx.tab
wc -l ../output/Ab_4-uniprot_blastx.tab
```

```{bash}
tr '|' '\t' < ../output/Ab_4-uniprot_blastx.tab | head -2
```
```{bash}
tr '|' '\t' < ../output/Ab_4-uniprot_blastx.tab \
> ../output/Ab_4-uniprot_blastx_sep.tab
```


```{r}
install.packages("curl")
```

```{r}
library("curl")
```




```{r}
# requirements
library(tidyverse)
#creating my blast table as an object
bltabl <- read.csv("../output/Ab_4-uniprot_blastx_sep.tab", sep = '\t', header = FALSE)
#reading in annotation table and saving as object
library(httr)
url <- "https://gannet.fish.washington.edu/seashell/snaps/uniprot_table_r2023_01.tab"
response <- GET(url, config(ssl_verifypeer = FALSE))
spgo <- read.csv(text = rawToChar(response$content), sep = "\t", header = TRUE)


```

```{r}
left_join(bltabl, spgo,  by = c("V3" = "Entry")) %>%
  select(V1, V3, V13, Protein.names, Organism, Gene.Ontology..biological.process., Gene.Ontology.IDs) %>% mutate(V1 = str_replace_all(V1, 
            pattern = "solid0078_20110412_FRAG_BC_WHITE_WHITE_F3_QV_SE_trimmed", replacement = "Ab")) %>%
  write_delim("../output/blast_annot_go.tab", delim = '\t')

```