#!/bin/bash
#
#SBATCH --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=32G
#SBATCH --time=12:00:00
#SBATCH --job-name=bowtie_loop
#SBATCH --mail-type=all
#SBATCH --mail-user=kah1g14@soton.ac.uk

# Make sure to have added bowtie2 file location to PATH & created bowtie index in the working directory

## Add bowtie2 file location to path

cd /mainfs/scratch/kah1g14/bowtie2

export PATH=/mainfs/scratch/kah1g14/bowtie2/bowtie2-2.4.2-sra-linux-x86_64/:$PATH


## Align trimmed_reads in scratch directory

cd /mainfs/scratch/kah1g14/trimmed_reads

for i in trimmed_*.fastq

do (bowtie2 -x Saha_base27 --local -q $i -S /mainfs/home/kah1g14/alignment/aligned_sam/$i.sam) 2> /mainfs/home/kah1g14/alignment/bowtie_logs/${i}bowtie.log

done


## Rename .sam files in home directory

cd /mainfs/home/kah1g14/alignment/aligned_sam


for i in *.fastq.sam

do mv "$i" "${i/trimmed_/}"

done


for i in trimmed_*.fastq

do mv "$i" "${i/-1_S*_L001_/-1_}"

done


for i in trimmed_*.fastq

do mv "$i" "${i/-2_S*_L001_/-2_}"

done



for i in trimmed_*.fastq

do mv "$i" "${i/-3_S*_L001_/-3_}"

done


for i in *.fastq.sam

do mv "$i" "${i/_001.fastq/_aligned}"

done


## Rename bowtie.log files

cd /mainfs/home/kah1g14/alignment/bowtie_logs


for i in *bowtie.log

do mv "$i" "${i/trimmed_/}"

done


for i in *bowtie.log

do mv "$i" "${i/_S*_L001_/_}"

done


for i in *bowtie.log

do mv "$i" "${i/_001.fastq/_}"

done