sequence_similarity_clustering.Rmd

---
title: "sequence_similarity_clustering"
output: html_document
---

# df: "/Users/rebeccachristensen/Desktop/Cremer_Lab_2022/main/workflow/out/sequenceSimilarity/select_ref_blast.out"
# imported as: ref_blast_percid
# long to wide formatting
```{r}
# ref_blast_percid_wide <- reshape(ref_blast_percid[1:3], idvar = "query_id", timevar = "subject_id", direction = "wide", v.names = "perc_id")

ref_blast_percid_wide <- spread(ref_blast_percid[1:3], query_id, perc_id)
View(ref_blast_percid_wide)

# ref_blast_percpos_wide <- spread(ref_blast_percid[c(1,2,4)], query_id, perc_pos)
# View(ref_blast_percpos_wide)

write.csv(ref_blast_percid_wide, "select_ref_blast_wide_nuc.csv")

```

# subsetting df by percid threshold
```{r}
THRESHOLD = 90

select_ref_blast_threshold <- subset(ref_blast_percid, perc_id > THRESHOLD & subject_id != query_id)

write.xlsx(select_ref_blast_threshold, "select_ref_blast_96_threshold_nuc.xlsx")
```