2019-10-24_depresiju duomenys sutvarkyti_2

for file in *ds.*; do cd $file; rm DEIM*; cd ..; done
#288 lieka
for file in *ds.*; do cd $file; gunzip DEP*.gz; cd ..; done
#rmdir tuscias dar
for file in *ds.*; do mkdir ${file:0:4}; done
for file in *ds.*; do mv $file/*.fastq ${file:0:4}; done
for file in ????; do cd $file && cat *.fastq > ${file}.fastq && cd ..; done
for file in ????; do echo -n "${file}, " && grep "@" $file/${file}.fastq | wc -l; done > number_of_reads.csv
#dabar cutadapt (process_reads.sh 134)
for file in ????; do cd $file && cutadapt -a AACTGTAGGCACCATCAAT -g GTTCAGAGTTCTACAGTCCGACGATC -m 18 -q 20 --discard-untrimmed ${file}.fastq > ${file%.fastq}_clipped.fastq && cd ..; done
for file in ????; do cd $file && fastq2fasta.pl ${file}_clipped.fastq > ${file}_reads.fa && collapse_reads_md.pl ${file}_reads.fa seq > ${file}_reads_colapsed.fa && cd ..; done
for file in ????; do mv ${file}/${file}_reads_colapsed.fa reads_colapsed/; done
java -jar -Xms8g -Xmx200g /tools/seqbuster/miraligner/miraligner-3.2/miraligner.jar -sub 1 -trim 3 -add 3 -s hsa -i reads_colapsed/ -db /data/databases_2019-10-23/ -o "aligner_output" -freq
#paskui $3 ir $4 ir stulpelyje failo pavadinima