Search Results

Your desired output cannot be calculated from your input sample, as none of the "KPNA7_9" lines has a $7 greater than or equal 20.
Your first awk script prints two fields per line, so a $5 or $7 as...

How about getting your bash syntax right, first? What you post can't possibly run...

--- Post updated at 18:33 ---

OK, trying to guess what you're after, and making some assumptions, how about...

We are confused. As I understand it, all this is superfluous.
You just need to include the config in start of the script and that's it.
. $1
After this expression, your config will virtually be...

config=$1

echo "$@"
while read line; do
echo "$line"
done <"$config" >other_file

In the script, it is better to immediately indicate the path to the file.
. /path/to/config
You can also add a default value if a file is not specified at startup
. ${1:-/path/to/config}

---...

I made a mistake in the expression echo -e '. $1\necho var' >script.sh
I fixed it and you probably just copied it before that :)
It will be right echo -e '. $1\necho $var' >script.sh

--- Post...

Hi
Try to find out
mkdir TEST && cd $_
echo -e '. $1\necho $var' >script.sh
echo 'var=yes' >config
bash script.sh config
yes

Even if the file is moved between file systems, there should not be a problem as long as the file is kept open. Even though the file and it's contents ARE moved by the mv command, the OS keeps the...

Hi Ravinder,

As long as a mv operation is performed on the same file system - as is the case here - that should not pose a problem, since mv then only manipulates directory data: A file name is...

Hi and thanks
No, you can see what will happen
cat>>file.txt<<EOF
1
2
FORMAT new
3
4
EOF
cp file.txt file2.txt
ls
file.txt file2.txt
awk '/FORMAT/ {system("mv -n "FILENAME" "$2)}; {print...

Hello nez,

How are you?
I hope you are doing fine :)

For your this solution, if you ask me IMHO we could avoid using renaming of a Input_file with system while reading Input_file itself...

Note: -n (no clobber) for the mv command is non-standard extension to the POSIX standard. Alternatively, try using -i for interactive use (but some systems ignore -i when used in a non-interactive...

I'm sorry, you should add a check for the existence of the file
awk '/FORMAT/ {system("mv -n "FILENAME" "$10)}' *.vcf

Hi
Try this
new=$(awk '/FORMAT/ {print $10}' $f)
or
new=$(sed /FORMAT/!d;s/^.*\t//' $f)
if the file is large, it's useful to add "quit" command
new=$(sed /FORMAT/!d;s/^.*\t//;q' $f)

--- Post...

xargs is used to turn a stream on stdin into command line arguments / parameters. sh expects its commands on stdin. Try without xargs, like echo "..." | sh


Or, use your .py as the xargs' command...

(3,0) A parenthesis is a reserved symbol in bash, not a string.
"(3,0)" Try making it a string...

From my suggestion in post 5, I'm sure you can attempt to replace the sub-process on line 2 (the bit between $( and )) such that the output it creates uses a loop based on a counter to create the...

Oh? Changing basic data again?


Be aware that a good, decent, stable, consistent specification helps everyone dealing with your request, saving time and efforts.


And, either of the three...

Do you want something more like:printf -- "/path/to/xxx.py \\\\\n%s\n\t--ref /path/to/file \\\\\n\t--run /path/to/data\n" \ # Set up the output format with fixed strings and an...

That desired command is different from the one in post #1. What exactly and finally do you need?



Why the detour using $id in lieu of using the file names in the directory immediately?

Not sure I fully understand, and your "Tried" block seems to be gobbledigook, but how about
while IFS="" read -r LN
do [ "$LN" = "${LN##*id}" ] && echo "$LN" || for FN in *.bam
...

How far would this get you:
awk '{TMP[$4]=$5; VAL[$4]+=$7; CNT[$4]++} END {for (t in TMP) {i = t; gsub (/[:-]/, OFS, i); print i, TMP[t], VAL[t]/CNT[t]}}' OFS="\t" file
chr16 2097885 2097890 ...

Try:
awk '$2=="Total Sequences"{n=-3} ++n==0{print "$ts=" $2}' RS=\< FS=\> file

Try also
awk 'match ($0, /Total Sequences<\/td><td>[^<]*/) {print substr ($0, RSTART+24, RLENGTH-24)}' file
49531132

Hi
awk -F'Total Sequences[^0-9]*' '/Total Sequences/ {sub("[^0-9].*", "", $2); print $2}'

--- Post updated at 23:03 ---

sed -n 's/.*Total Sequences[^0-9]*\([0-9]*\).*/\1/p' file

--- Post...