---
title: "08-comparative-BLASTs"
author: "Zach Bengtsson"
date: "2023-12-29"
output: html_document
---

```{r setup, include=FALSE}
library(knitr)
library(tidyverse)
library(kableExtra)
library(DT)
library(Biostrings)
library(tm)
knitr::opts_chunk$set(
  echo = TRUE,         # Display code chunks
  eval = FALSE,         # Evaluate code chunks
  warning = FALSE,     # Hide warnings
  message = FALSE,     # Hide messages
  fig.width = 6,       # Set plot width in inches
  fig.height = 4,      # Set plot height in inches
  fig.align = "center", # Align plots to the center
  comment = ""         # Prevents appending '##' to beginning of lines in code output
)
```

# Download FASTAS

# Data Download
Grab 3 FASTAs (currently messing around with my old ones while I wait for the new ones to finish)

```{r, engine='bash'}
cd ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs

#Apul
curl -O https://raw.githubusercontent.com/urol-e5/deep-dive/main/D-Apul/output/05.33-lncRNA-discovery/Apul_lncRNA.fasta
#Peve
curl -O https://raw.githubusercontent.com/urol-e5/deep-dive/main/E-Peve/output/Peve_lncRNA.fasta
#Pmea
curl -O https://raw.githubusercontent.com/urol-e5/deep-dive/main/F-Pmea/output/02-lncRNA-discovery/Pmea_lncRNA.fasta

head ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/*fasta
```

# Merge FASTAs
```{bash}
cd ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs

cat Apul_lncRNA.fasta Peve_lncRNA.fasta Pmea_lncRNA.fasta > merged_lncRNAs.fasta

head merged_lncRNAs.fasta
```

# BLASTs

Make database for each species
Apul
```{r, engine='bash'}
/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/Apul_lncRNA.fasta \
-dbtype nucl \
-out ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/blasts/Apul-db/Apul_lncRNA
```

Peve
```{r, engine='bash'}
/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/Peve_lncRNA.fasta \
-dbtype nucl \
-out ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/blasts/Peve-db/Peve_lncRNA
```

Pmea
```{r, engine='bash'}
/home/shared/ncbi-blast-2.11.0+/bin/makeblastdb \
-in ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/Pmea_lncRNA.fasta \
-dbtype nucl \
-out ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/blasts/Pmea-db/Pmea_lncRNA
```

A pul to all
```{r, engine='bash'}
cd /home/shared/8TB_HDD_02/zbengt

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/merged_lncRNAs.fasta \
-db ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/blasts/Apul-db/Apul_lncRNA \
-out ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Apul.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Apul.tab
```

Peve to all
```{r, engine='bash'}
cd /home/shared/8TB_HDD_02/zbengt

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/merged_lncRNAs.fasta \
-db ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/blasts/Peve-db/Peve_lncRNA \
-out ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Peve.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Peve.tab
```

Pmea to all
```{r, engine='bash'}
cd /home/shared/8TB_HDD_02/zbengt

/home/shared/ncbi-blast-2.11.0+/bin/blastn \
-task blastn \
-query ~/github/deep-dive/DEF-cross-species/data/08-comparative-BLASTs/merged_lncRNAs.fasta \
-db ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/blasts/Pmea-db/Pmea_lncRNA \
-out ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Pmea.tab \
-evalue 1E-40 \
-num_threads 40 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Apul.tab
```

# Join BLAST tables
```{r}
apul <- read.table("~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Apul.tab", sep="\t", header=FALSE)
peve <- read.table("~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Peve.tab", sep="\t", header=FALSE)
pmea <- read.table("~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/Pmea.tab", sep="\t", header=FALSE)
```

```{r}
combined_blast <- rbind(apul, peve, pmea)
```

```{r}
write.table(combined_blast, "~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/combined_blast.tab", sep="\t", row.names=FALSE, quote=FALSE)
```



Hits...
```{r, engine='bash'}
wc -l ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/combined_blast.tab
head ~/github/deep-dive/DEF-cross-species/output/08-comparative-BLASTs/combined_blast.tab
```