composition_matrix_spike script

/data/data/bowtie2-2.3.5.1-linux-x86_64/bowtie2-build /data/data/spike.fa spike
#sumest i viena folderi spike paskui ir
/data/data_fastq/reads_colapsed # export BOWTIE2_INDEXES=/data/data_fastq/reads_colapsed/spike/
/data/data_fastq/reads_colapsed # for file in *.fa; do /data/data/bowtie2-2.3.5.1-linux-x86_64/bowtie2 -f -N 0 --no-unal -x spike -U $file -S ${file%fa}sam; done
# for file in *.sam; do grep -v "@" $file | awk -F "\t|x" '{print $4, " ", $2}' | sort -k 1 | awk '{ seen[$1] += $2 } END { for (i in seen) print i, seen[i] }' | sort -k 1 > ${file}.out; done
983aaaec4dff /data/data_fastq/reads_colapsed # #for file in *.sam; do grep -v "@" $file | awk -F "\t|x" '{print $4, " ", $2}' | sort -k 1 > ${file}.out; done
# tmp yra visur po 0 dar, kad susivienodintu eiluciu sk
for file in *.out; do cat tmp >> $file; done
for file in *.out; do cat $file | awk '{ seen[$1] += $2 } END { for (i in seen) print i, seen[i] }' | sort -k 1 > ${file}.out; done
pirmas stulpelis tai tmp su nauje eilute
for file in ../????; do echo ${file:3:8} > ${file:3:8}; done
for file in *.out.out; do awk '{print $2}' $file >> ${file:0:4};done
paste -d "," tmp ???? > composition_matrix_spike.csv