cd /media/bioinfoteam/SCRATCH_850GB/temp_metatranscriptomic/sequences


# change for a simpler name: keep the first part of the file name
for filename in $(ls *'.fastq.gz')

do
echo $filename

fileID=`expr match "$filename" '\([0-9]*C_L1_R[1-2]*\)'`

new_filename=$fileID'.fastq.gz'
echo $new_filename

mv $filename $new_filename
done


# unzip files
for filename in $(ls *'.fastq.gz')

do

gzip -d $filename

done


# transform fastq to fasta
for filename in $(ls *'.fastq')

do

basename="${filename%.*}"

fastaname=$basename'.fasta'

echo $fastaname

sed -n '1~4s/^@/>/p;2~4p' $filename > $fastaname

done

## tranform fastq to fasta on specific samples
for i in {58..60}

do
filename1=${i}C_L1_R1.fastq
filename2=${i}C_L1_R2.fastq 

fastaname1=${i}C_L1_R1.fasta
fastaname2=${i}C_L1_R2.fasta

echo $fastaname1 $fastaname2

sed -n '1~4s/^@/>/p;2~4p' $filename1 > $fastaname1
sed -n '1~4s/^@/>/p;2~4p' $filename2 > $fastaname2

done