Search Results

If order is not important:

$ awk ' $0 !~ "^sample" { val[$1]=$2<0?-$2:$2; } END { for(i in val) print i":"val[i]-20"-"val[i]+120 }' inputfile
Chr28:25960066-25960206
Chr19:52245903-52246043...

By the original order
awk '/^Chr/&&!a[$1]++ {sub(/[+-]/,"");print $1":"$2-20"-"$2+120}' infile

Emergency UNIX and Linux Support !! Help Me! Forum (Request Urgent Help) (https://www.unix.com/emergency-unix-linux-support-help-me/)

README FIRST: How to Request Emergency or Urgent Help:


...

Here's an equivalent awk, just in case:
awk -F'[<>]*' '$2=="free-energy"{print $3}$2=="position"{printf "%s%s",$3,(++i%2)?" - ":RS}' infile

#!/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...

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
...

If you have ghostscript installed:


fonts=-I/usr/local/share/ghostscript/fonts
gs $fonts -dBATCH -dNOPAUSE -sDEVICE=pdfwrite -sOutputFile=file.pdf file.ps


reads file.ps and writes file.pdf;...

Before asking for a solution you should bring up-front all variables as: file(s) size, system specs, your own knowledge, etc...

awk 'BEGIN{FS=RS;RS=">"}NR==FNR{a[$1]=$0}/Chr/ && a[$1]{printf}' file1 file2

I'll opt for
awk 'BEGIN{FS=RS;RS=ORS=">"} !/miR/' file

Avoids missing ">" on 2nd line and extra ">" at end:
$ awk '{ if(NR>1&&$0!~"^miR"&&p!~"^miR")print p; p=$0}' infile

>sample1:1:1:1057:7503#0 0 0
>sample1:1:1:1057:12664#0 0 0...

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...

I'll opt for
awk 'BEGIN{FS=RS;RS=ORS=">"} !/miR/' file

Avoids missing ">" on 2nd line and extra ">" at end:
$ awk '{ if(NR>1&&$0!~"^miR"&&p!~"^miR")print p; p=$0}' infile

>sample1:1:1:1057:7503#0 0 0
>sample1:1:1:1057:12664#0 0 0...

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

That's because your problem statement is quite vague. A "read" operation does not "have" a format, which is why "read" cannot "be" in any format.

Your input data in a file or from a pipe "has" or...