---
title: "Annotation"
output: html_document
date: "2024-07-02"
---
### Libraries
```{r}
library(kableExtra)
library(tidyverse)
```


### check out uniprot blast output
```{bash}
head -2 /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx.tab
#lcl|NC_086373.1_cds_XP_063416577.1_1	sp|Q5RA75|F135A_PONAB	67.901	243	73	4	2587	3309	785	1024	1.01e-86	313
#lcl|NC_086373.1_cds_XP_063416577.1_1	sp|Q5RA75|F135A_PONAB	39.858	424	229	7	1	1215	1	417	2.54e-86	311
wc -l /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx.tab
#41340
```
### Test out pipe replacement
```{bash}
tr '|' '\t' < /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx.tab | head -2
```
### Replace pipes
```{bash}

tr '|' '\t'< /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx.tab > /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx_sep.tab

```

### Did the pipe separation work
```{bash}
head -2 /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx_sep.tab
```

### Check out the Uniprot table output
```{bash}
head /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/Uniprot_table

```

### Download annotation table from Uniprot
```{bash}
curl -O -H "Accept: text/plain; format=tsv" "https://rest.uniprot.org/uniprotkb/stream?compressed=true&fields=accession%2Creviewed%2Cid%2Cprotein_name%2Cgene_names%2Corganism_name%2Clength%2Cgo_p%2Cgo%2Cgo_c%2Cgo_f%2Cgo_id%2Ccc_interaction%2Cec&format=tsv&query=%28*%29+AND+%28reviewed%3Atrue%29" 
```

### Unzip annotation table
```{bash}
gzip -dc "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/stream?compressed=true&fields=accession%2Creviewed%2Cid%2Cprotein_name%2Cgene_names%2Corganism_name%2Clength%2Cgo_p%2Cgo%2Cgo_c%2Cgo_f%2Cgo_id%2Ccc_interaction%2Cec&format=tsv&query=%28*%29+AND+%28reviewed%3Atrue%29"  > "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/uniprot_proteins.tsv"

head "/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/uniprot_proteins.tsv"
```


```{r}
bltabl <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/output/Mtros-genome-uniprot_blastx_sep.tab", sep = '\t', header = FALSE)
spgo <- read.csv("/home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/uniprot_proteins.tsv", sep = '\t', header = TRUE)
str(spgo)
```