for i in $(seq 1 10); do
echo 'bla bla'
echo 'xxx'
echo $i
done | select=$(zenity --list --title="title" --text="text" --column="X" --column="Y" --column="Z");
I try to create a checklist with zenity, my problem is that $select is always empty.
I try to do it in few other ways, like this one:
for i in $(seq 1 10)
do
x="bla bla"
y="xxx"
z="$i"
table="$table '$x' '$y' '$z'"
done
eval zenity --list --title="title" --text="text" --column="X" --column="Y" --column="Z" $table
In this way the $select variable isn't empty but if there are spaces in some variable (like $x for example) zenity split it to 2 (or more) columns.
I need other solution or any fix for my code(s)?
Thanks!
You can try this other approach:
#!/bin/bash
for i in $(seq 1 10)
do
echo "bla bla"
echo "xxx"
echo "$i"
done | zenity --list --title="title" --text="text" --column="X" --column="Y" --column="Z"
Each line populate the table from the first column to the last, and then again on a new row, until the input stream ends.
Related
my command looks like:
for i in *.fasta ; do
parallel -j 10 python script.py $i > $i.out
done
I want to add a test condition to this loop where it only executes the parallel python script if there are no identical lines in the .fasta file
an example .fasta file below:
>ref2
GGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGCATTTTGGAATTCCCTACAATCC
CCAAAGTCAAGGAGTAGTAGAATCTATGCGGAAAGAATTAAAGAAAATTATAGGACAGGT
AAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGC
>mut_1_2964_0
AAAAAAAAACGCCTGTTGGTGGGCGGGAATCAAGCAGGTATTTGGAATTCCCTACAATCC
CCAAAGTCAAGGAGTAGTAGAATCTATGTTGAAAGAATTAAAGAAAATTATAGGACAGGT
AAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGC
an example .fasta file that I would like excluded because lines 2 and 4 are identical.
>ref2
GGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGCATTTTGGAATTCCCTACAATCC
CCAAAGTCAAGGAGTAGTAGAATCTATGCGGAAAGAATTAAAGAAAATTATAGGACAGGT
AAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGC
>mut_1_2964_0
GGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGCATTTTGGAATTCCCTACAATCC
CCAAAGTCAAGGAGTAGTAGAATCTATGCGGAAAGAATTAAAGAAAATTATAGGACAGGT
AAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGC
The input files always have 4 lines exactly, and lines 2 and 4 are always the lines to be compared.
I've been using sort file.fasta | uniq -c to see if there are identical lines, but I don't know how to incorporate this into my bash loop.
EDIT:
command:
for i in read_00.fasta ; do lines=$(awk 'NR % 4 == 2' $i | sort | uniq -c | awk '$1 > 1'); if [ -z "$lines" ]; then echo $i >> not.identical.txt; fi;
read_00.fasta:
>ref
GGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGA
>mut_1_2964_0
GGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGA
Verify those specifc lines content with below awk and exit failure when lines were identical or exit success otherwise (instead of exit, you can do whatever you want to print/do for you);
awk 'NR==2{ prev=$0 } NR==4{ if(prev==$0) exit 1; else exit }' "./$yourFile"
or to output fileName instead when 2nd and 4th lines were differ:
awk 'NR==2{ prev=$0 } NR==4{ if(prev!=$0) print FILENAME; exit }' ./*.fasta
Using the exit-status of the first command then you can easily execute your next second command, like:
for file in ./*.fasta; do
awk 'NR==2{ prev=$0 } NR==4{ if(prev==$0) exit 1; else exit }' "$file" &&
{ parallel -j 10 python script.py "$file" > "$file.out"; }
done
I have a variable set in the following format:
var1="word1 word2 word3"
Is it possible to subset/delete one of the space-delimited word portably? What I want to archive is something like this:
when --ignore option is supplied with the following argument
$ cmd --ignore word1 # case 1
$ cmd --ignore "word1 word2" # case2
I want the var1 changes to have only the following value
"word2 word3" # case1
"word3" #case2
If there is no way to achieve above described, is there a way to improve the efficiency of the following for loop? (The $var1 is in a for loop so my alternative thought to achieve similar was having following code)
# while loop to get argument from options
# argument of `--ignore` is assigned to `$sh_ignore`
for i in $var1
do
# check $i in $sh_ignore instead of other way around
# to avoid unmatch when $sh_ignore has more than 1 word
if ! echo "$sh_ignore" | grep "$i";
then
# normal actions
else
# skipped
fi
done
-------Update-------
After looking around and reading the comment by #chepner I now temporarily using following code (and am looking for improvement):
sh_ignore=''
while :; do
case
# some other option handling
--ignore)
if [ "$2" ]; then
sh_ignore=$2
shift
else
# defined `die` as print err msg + exit 1
die 'ERROR: "--ignore" requires a non-empty option argument.'
fi
;;
# handling if no arg is supplied to --ignore
# handling -- and unknown opt
esac
shift
done
if [ -n "$sh_ignore" ]; then
for d in $sh_ignore
do
var1="$(echo "$var1" | sed -e "s,$d,,")"
done
fi
# for loop with trimmed $var1 as downstream
for i in $var1
do
# normal actions
done
One method might be:
var1=$(echo "$var1" |
tr ' ' '\n' |
grep -Fxv -e "$(echo "$sh_ignore" | tr ' ' '\n')" |
tr '\n' ' ')
Note: this will leave a trailing blank, which can be trimmed off via var1=${var1% }
In bash, it can be done like this:
#!/bin/bash
query='bengal'
string_to_search='bengal,toyger,bengal,persian,bengal'
delimiter='|'
replace_queries="${string_to_search//"$query"/"$delimiter"}"
delimiter_count="${replace_queries//[^"$delimiter"]}"
delimiter_count="${#delimiter_count}"
echo "Found $delimiter_count occurences of \"$query\""
Output:
Found 3 occurences of "bengal"
The caveat of course is that the delimiter cannot occur in 'query' or 'string_to_search'.
In POSIX sh, string replacement is not supported. Is there a way this can be done in POSIX sh using only shell builtins?
#!/bin/sh
query='bengal'
string_to_search='bengal,toyger,bengal,persian,bengal'
ct() (
n=0
IFS=,
q=$1
set $2
for t in "$#"; do
if [ "$t" = "$q" ]; then
n=$((n + 1))
fi
done
echo $n
)
n=$(ct "$query" "$string_to_search")
printf "found %d %s\n" $n $query
Though I'm not sure what the point is. If you've got a posix shell,
you also almost certainly have printf, sed, grep, and wc.
printf '%s\n' "$string_to_search" | sed -e 's/,/\n/g' | grep -Fx "$query" | wc -l
Think I got it...
#!/bin/sh
query='bengal'
string_to_search='bengal,toyger,bengal,persian,bengal'
i=0
process_string="$string_to_search"
while [ -n "$process_string" ]; do
case "$process_string" in
*"$query"*)
process_string="${process_string#*"$query"}"
i="$(( i + 1 ))"
;;
*)
break
;;
esac
done
echo "Found $i occurences of \"$query\""
I am trying to get the version numbers for content management systems being hosted on my server. I can do this fairly simply if the version number is stored on one line with something like this:
grep -r "\$wp_version = '" /home/
Which returns exactly what I want to stdout:
/home/$RANDOMDOMAIN/wp-includes/version.php:$wp_version = '3.7.1';
The issue I run into is when I start looking for version numbers that are stored on two or more lines, like Joomla! or Magento which use the following formats respectively:
Joomla!:
/** #var string Release version. */
public $RELEASE = '3.2';
/** #var string Maintenance version. */
public $DEV_LEVEL = '3';
Magento:
'major' => '1',
'minor' => '8',
'revision' => '1',
'patch' => '0',
I have gotten it to 'work', in a way, using the following (With this method if, for whatever reason, one of the strings I am looking for is missing the whole command becomes useless since xargs -l3 is expecting 2 rows above the path provided by -print):
find /home/ -type f -name version.php -exec grep " \$RELEASE " '{}' \; -exec grep " \$DEV_LEVEL " '{}' \; -print | xargs -l3 | sed 's/\<var\>\s//g;s/\<public\>\s//g' | awk -F\; '{print $3":"$1""$2}' | sed 's/ $DEV_LEVEL = /./g'
Which get's me output like this:
/home/$RANDOMDOMAIN/version.php:$RELEASE = 3.2.3
/home/$RANDOMDOMAIN/anotherfolder/version.php:$RELEASE = 1.5.0
I also have a working for loop that WILL exclude any file that does not contain both strings, but depending how much it has to sift through, can take significantly longer than the find one liner above:
for path in $(grep -rl " \$RELEASE " /home/ 2> /dev/null | xargs grep -rl " \$DEV_LEVEL ")
do
joomlaver="$path"
joomlaver+=$(grep " \$RELEASE " $path)
joomlaver+=$(echo " \$DEV_LEVEL = '$(grep " \$DEV_LEVEL " $path | cut -d\' -f2)';")
echo "$joomlaver" | sed 's/\<var\>\s//g;s/\<public\>\s//g;s/;//g' | awk -F\' '{ print $1""$2"."$4 }' | sed 's/\s\+//g'
unset joomlaver
done
Which get's me output like this:
/home/$RANDOMDOMAIN/version.php$RELEASE=3.2.3
/home/$RANDOMDOMAIN/anotherfolder/version.php$RELEASE=1.5.0
But I have to believe there is a simpler, shorter, more elegant way. Bash is preferred or if it can somehow be done with a perl one liner, that would work as well. Any and all help would be much appreciated. Thanks in advance. (Sorry for all the edits, but I am trying to figure this out myself as well!)
Here is a perl one-liner that will extract the $RELEASE and $DEV_LEVEL from the php file format you showed:
perl -ne '$v=$1 if /\$RELEASE\s*=\s*\047([0-9.]+)\047/; $devlevel=$1 if /\$DEV_LEVEL\s*=\s*\047([0-9.]+)\047/; if (defined $v && defined $devlevel) { print "$ARGV: Release=$v Devlevel=$devlevel\n"; last; }'
The -n makes perl effectivly wrap the whole thing inside a while (<>) { } loop. Each line is checked against two regexes. If both of them have matched then it will print the result and exit.
The \047 is used to match single quotes, otherwise the shell would get confused.
If it does not find a match, it does not print anything. Otherwise it prints something like this:
sample.php: Release=3.2 Devlevel=3
You would use it in combination with find and xargs to traverse down a directory structure, perhaps like this:
find . -name "*.php" | xargs perl -ne '$v=$1 if /\$RELEASE\s*=\s*\047([0-9.]+)\047/; $devlevel=$1 if /\$DEV_LEVEL\s*=\s*\047([0-9.]+)\047/; if (defined $v && defined $devlevel) { print "$ARGV: Release=$v Devlevel=$devlevel\n"; last; }'
You could make a similar version for the other file format (Magento?) you mentioned.
Basically right now I have a for loop running that runs a series of tests. Once the tests pass I input the results into a csv file:
for (( some statement ))
do
if[[ something ]]
input this value into a specific row and column
fi
done
What I can't figure out right now is how to input a specific value into a specific cell in the csv file. I know in awk you can read a cell with this command:
awk -v "row=2" -F'#' 'NR == row { print $2 }' some.csv and this will print the cell in the 2nd row and 2nd column. I need something similar to this except it can input a value into a specific cell instead of read it. Is there a function that does this?
You can use the following:
awk -v value=$value -v row=$row -v col=$col 'BEGIN{FS=OFS="#"} NR==row {$col=value}1' file
And set the bash values $value, $row and $col. Then you can redirect and move to the original:
awk ... file > new_file && mv new_file file
This && means that just if the first command (awk...) is executed successfully, then the second one will be performed.
Explanation
-v value=$value -v row=$row -v col=$col pass the bash variables to awk. Note value, row and col could be other names, I just used the same as bash to make it easier to understand.
BEGIN{FS=OFS="#"} set the Field Separator and Output Field Separator to be #. The OFS="#" is not necessary here, but can be useful in case you do some print.
NR==row {$col=value} when the number of record (number of line here) is equal to row, then set the col column with value value.
1 perform the default awk action: {print $0}.
Example
$ cat a
hello#how#are#you
i#am#fine#thanks
hoho#haha#hehe
$ row=2
$ col=3
$ value="XXX"
$ awk -v value=$value -v row=$row -v col=$col 'BEGIN{FS=OFS="#"} NR==row {$col=value}1' a
hello#how#are#you
i#am#XXX#thanks
hoho#haha#hehe
Your question has a 'perl' tag so here is a way to do it using Tie::Array::CSV which allows you to treat the CSV file as an array of arrays and use standard array operations:
use strict;
use warnings;
use Tie::Array::CSV;
my $row = 2;
my $col = 3;
my $value = 'value';
my $filename = '/path/to/file.csv';
tie my #file, 'Tie::Array::CSV', $filename, sep_char => '#';
$file[$row][$col] = $value;
untie #file;
using sed
row=2 # define the row number
col=3 # define the column number
value="value" # define the value you need change.
sed "$row s/[^#]\{1,\}/$value/$col" file.csv # use shell variable in sed to find row number first, then replace any word between #, and only replace the nominate column.
# So above sed command is converted to sed "2 s/[^#]\{1,\}/value/3" file.csv
If the above command is fine, and your sed command support the option -i, then run the command to change the content directly in file.csv
sed -i "$row s/[^#]\{1,\}/$value/$col" file.csv
Otherwise, you need export to temp file, and change the name back.
sed "$row s/[^#]\{1,\}/$value/$col" file.csv > temp.csv
mv temp.csv file.csv