Search Results

The OP's post is contradictory, because on the first line it says it should be followed by a number, but if ChrX is valid too then indeed it should be /^Chr[0-9X]/

awk -F- '/^Chr[0-9]/&&!A[$0]++{print $1":"$2-10 FS $2+10}' file

grep ^Chr. input | while read a ; do echo "${a%-*}:$((${a#*-}-10))-$((${a#*-}+10))" ; done

awk -F"-" '/^Chr[0-9[X]/{print $1":"$2-10"-"$2+10}' file

Please, use code tags to make the code more readable.
Howto:

Select the text corresponding to code
Click on the 'code' button in the editor's...

Try this Posix version, which should be insensitive to leading spaces:
INFILE=infile # Put the name of your file here
while read line
do
case $line in
"Initial dG"*)
printf...

What's the output of this:
#!/bin/bash
while IFS=':=' read A B C
do
echo "A='$A' B='$B' C='$C'"
done <$INFILE

---------- Post updated at 23:06 ---------- Previous update was at 21:52...

This means the output of program $INFILE is presented as a file. Using backticks instead means the output of program $INFILE is presented as a variable.

Correct would be:
done < "$INFILE"


...

You can make a sort of cheap xml parser of sed:

sed -n '
s/.*<free-energy>\([^<]*\)<.*/\1/p
t
/<base-id>/{
:loop
N
/<\/base-id-3p>/!b loop
...

#!/bin/bash
while IFS='<>' read Null Tag Val Null
do
case $Tag in
free-energy)
echo $Val
Pos=0 ;;
position)
((Pos++))
((Pos%2)) && echo -n...

How about this awk script (process.awk):

BEGIN {
FS=">";RS=">";ORS="";
}
$NF { d++
system("mkdir dir"d);
print ">"$0 > ("dir"d"/input");
system("cd dir"d"; mfold seq=input");
}
...

This want to be a solution for your problem
awk -F\> '/>/{++d;system("mkdir "d)}NF{print > (d"/"$NF)}' file
however if you expect something else please post the required output base on original...

Little issue, but simple code.

awk 'BEGIN{RS=ORS=">";FS="\n"} NF==2' infile

sample1:1:1:1057:7503#0 0 0
>sample1:1:1:1057:12664#0 0 0
>sample1:1:1:1059:6357#0 0 0
>sample1:1:1:1059:10418#0 0...

try like this
samtools faidx Bos_taurusUMD3.fa "$line"

My input file (data1) is like this
Chr8:4000-4500
Chr10:4000-4600

I written a shell program like this.
while read LINE;
do echo "$LINE";
samtools faidx Bos_taurusUMD3.fa "$line";
done <...