NUM_SAMPLES=ls *.norm.cov.bed | wc -l | awk '{print $1}' NUM_WINDOWS=ls *.norm.cov.bed | head -n 1 | xargs awk '$1 != "X" && $1 != "Y" && $NF == 0 {x++} END {print x}'`
echo -e "$NUM_SAMPLES\t$NUM_WINDOWS" >matrix.txt
ls *.norm.cov.bed | while read FILE
do
awk '$1 != "X" && $1 != "Y" && $NF == 0 { print $4 }' $FILE
| gawk -f $CLAMMS_DIR/transpose.gawk >>matrix.txt
done`
Actually, I wonder if the "$NF==0" should be "$NF !=0"? Now the matrix is one zero matrix!
NUM_SAMPLES=ls *.norm.cov.bed | wc -l | awk '{print $1}'NUM_WINDOWS=ls *.norm.cov.bed | head -n 1 | xargs awk '$1 != "X" && $1 != "Y" && $NF == 0 {x++} END {print x}'`echo -e "$NUM_SAMPLES\t$NUM_WINDOWS" >matrix.txt
ls *.norm.cov.bed | while read FILE
do
awk '$1 != "X" && $1 != "Y" && $NF == 0 { print $4 }' $FILE
| gawk -f $CLAMMS_DIR/transpose.gawk >>matrix.txt
done`
Actually, I wonder if the "$NF==0" should be "$NF !=0"? Now the matrix is one zero matrix!