---
title: "07.motifs"
format: html
editor: visual
---

## 

```{r}
library(seqinr)

# Replace 'input.fasta' with the name of your multi-sequence fasta file
input_file <- "/home/shared/8TB_HDD_02/thielkla/Karina-chinook/Olurida_v081.fa"
sequences <- read.fasta(input_file)
```



```{r}
# Replace 'output.fasta' with your desired output file name
output_file <- "/home/shared/8TB_HDD_02/thielkla/Karina-chinook/input_file"
write.fasta(sequences, names(sequences), output_file, open = "w")
```

```{bash}
#likely will not need; fix issue where gff and fa name did not match
# sed -i 's/>lcl|/>/g' ../output/10_seqs.fa
```

```{bash}
#needed downstream for IGV
/home/shared/samtools-1.12/samtools faidx \
/output/10_seqs.fa
```

```{bash}
fuzznuc -sequence ../output/10_seqs.fa -pattern CG -rformat gff -outfile ../output/CGoutput.gff
```