Egrep and Awk to output columns of a line , with a specific value for the first column
I am to tasked to write a shell program which when ran as such
./tool.sh -f file -id id OR ./tool.sh -id id -f file
must output the name surname and birthdate (3 columns of the file ) for that specific id.
So far my code is structured as such :
elif [ "$#" -eq 4 ];
then
while [ "$1" != "" ];
do
case $1 in
-f)
cat < "$2" | egrep '"$4"' | awk ' {print $3 "\t" $2 "\t" $5}'
shift 4
;;
-id)
cat < "$4" | egrep '"$2"' | awk ' {print $3 "\t" $2 "\t" $5}'
shift 4
esac
done
(Ignoring the opening elif cause there are more subtasks for later)
My output is nothing. The program just runs.
I've tested the cat < people.dat | egrep '125' | awk ' {print $3 "\t" $2 "\t" $5}'
and it runs just fine.
I also had an instance where i had an output from the program while it was run like so
cat < "$2" | egrep '["$4"]' | awk ' {print $3 "\t" $2 "\t" $5}'
but it wasnt only that specific ID.
`egrep "$4"` was correct instead of `egrep '["$4"]'` in
`cat < "$2" | egrep '["$4"]' | awk ' {print $3 "\t" $2 "\t" $5}'`
Double quotes allow variables, single quotes don't. No commands need
certain types of quotes, they are purely a shell feature that are not
passed to the command. mentioned by(#that other guy)
Related
I have used the following a guide with these commands:
echo "accession\taccession.version\ttaxid\tgi" > reference_proteomes.taxid_map
zcat */*/*.idmapping.gz | grep "NCBI_TaxID" | awk '{print $1 "\t" $1 "\t" $3 "\t" 0}' >> reference_proteomes.taxid_map
I used echo "accession\taccession.version\ttaxid\tgi" > reference_proteomes.taxid_map & zcat *.idmapping.gz | grep "NCBI_TaxID" | awk '{print $1 "\t" $1 "\t" $3 "\t" 0}' >> reference_proteomes.taxid_map
but I received the messaged that the argument list is too long:/usr/bin/zcat: Argument list too long
so I have tried xargs in this: find /Volumes/My\ Passport\ for\ Mac/uniprot | xargs zcat *.idmapping.gz | grep "NCBI_TaxID" | awk '{print $1 "\t" $1 "\t" $3 "\t" 0}' >> reference_proteomes.taxid_map
but still received the long list argument message -bash: /usr/bin/xargs: Argument list too long, any suggestion?
This is a part of my shell script.
for line in `cat $1`
do
startNum=`echo $line | awk -F "," '{print $1}'`
endNum=`echo $line | awk -F "," '{print $2}'`
operator=`echo $line | awk -F "," '{print $3}'`
termPrefix=`echo $line | awk -F "," '{print $4}'`
if [[ "$endNum" == 81* ]] || [[ "$endNum" == 33* ]] || [[ "$endNum" == 55* ]]
then
areaCode="${endNum:0:2}"
series="${endNum:2:4}"
startCLI="${startNum:6:4}"
endCLI="${endNum:6:4}"
else
areaCode="${endNum:0:3}"
series="${endNum:3:3}"
startCLI="${startNum:6:4}"
endCLI="${endNum:6:4}"
fi
echo "Add,${areaCode},${series},${startCLI},${endCLI},${termPrefix},"
#>> ${File}
done
input is csv contains below many rows :
5557017101,5557017101,102,1694
5515585614,5515585614,102,084
Output od shell script :
,dd,55,5701,7101,7101,1694
,dd,55,1558,5614,5614,0848
Not sure why comma is coming in startign of output, instead as per shell script it should come in the end.
please help
Here is a suggested awk command that should replace all of your shell+awk code. This awk also takes care of trailing \r:
awk -v RS=$'\r' 'BEGIN{FS=OFS=","} NF>3{
startNum=$1; endNum=$2; termPrefix=$4;
if (endNum ~ /^(81|33|55)/) {
areaCode=substr(endNum,1,2); series=substr(endNum,3,4)
}
else {
areaCode=substr(endNum,1,3); series=substr(endNum,4,3)
}
startCLI=substr(startNum,7,4); endCLI=substr(endNum,7,4);
print "Add", areaCode, series, startCLI, endCLI, termPrefix
}' file
Add,55,5701,7101,7101,1694
Add,55,1558,8561,5614,084
I am storing date inside a variable and using that in the sed as below.
DateTime=`date "+%m/%d/%Y"`
Plc_hldr1=`head -$i place_holder.txt | tail -1 | awk -F ' ' '{ print $1 }'`
Plc_hldr2=`head -$i place_holder.txt | tail -1 | awk -F ' ' '{ print $2 }'`
sed "s/$Plc_hldr1/$DateTime/;s/$Plc_hldr2/$Total/" html_format.htm >> /u/raskar/test/html_final.htm
While running the sed command I am getting the below error.
sed: 0602-404 Function s/%%DDMS1RT%%/01/02/2014/;s/%%DDMS1C%%/1235/ cannot be parsed.
I suppose this is happening as the date contains the following output which includes slashes '/'
01/02/2014
I tried with different quotes around the date. How do I make it run?
Change the separator to something else that won't appear in your patterns, for example:
sed "s?$Plc_hldr1?$DateTime?;s?$Plc_hldr2?$Total?"
Not the direct quertion but replace
Plc_hldr1=`head -$i place_holder.txt | tail -1 | awk -F ' ' '{ print $1 }'`
Plc_hldr2=`head -$i place_holder.txt | tail -1 | awk -F ' ' '{ print $2 }'`
by
Plc_hldr1=`sed -n "$i {s/ .*//p;q}"`
Plc_hldr2=`sed -n "$i {s/[^ ]\{1,\} \{1,\}\([^ ]\{1,\}\) .*/\1/p;q}"`
and with aix/ksh
sed -n "$i {s/\([^ ]\{1,\} \{1,\}[^ ]\{1,\}\) .*/\1/p;q}" | read Plc_hldr1 Plc_hldr2
I'm using the following awk command:
my_command | awk -F "[[:space:]]{2,}+" 'NR>1 {print $2}' | egrep "^[[:alnum:]]"
which successfully returns my data like this:
fileName1
file Name 1
file Nameone
f i l e Name 1
So as you can see some file names have spaces. This is fine as I'm just trying to echo the file name (nothing special). The problem is calling that specific row within a loop. I'm trying to do it this way:
i=1
for num in $rows
do
fileName=$(my_command | awk -F "[[:space:]]{2,}+" 'NR==$i {print $2}' | egrep "^[[:alnum:]])"
echo "$num $fileName"
$((i++))
done
But my output is always null
I've also tried using awk -v record=$i and then printing $record but I get the below results.
f i l e Name 1
EDIT
Sorry for the confusion: rows is a variable that list ids like this 11 12 13
and each one of those ids ties to a file name. My command without doing any parsing looks like this:
id File Info OS
11 File Name1 OS1
12 Fi leNa me2 OS2
13 FileName 3 OS3
I can only use the id field to run a the command that I need, but I want to use the File Info field to notify the user of the actual File that the command is being executed against.
I think your $i does not expand as expected. You should quote your arguments this way:
fileName=$(my_command | awk -F "[[:space:]]{2,}+" "NR==$i {print \$2}" | egrep "^[[:alnum:]]")
And you forgot the other ).
EDIT
As an update to your requirement you could just pass the rows to a single awk command instead of a repeatitive one inside a loop:
#!/bin/bash
ROWS=(11 12)
function my_command {
# This function just emulates my_command and should be removed later.
echo " id File Info OS
11 File Name1 OS1
12 Fi leNa me2 OS2
13 FileName 3 OS3"
}
awk -- '
BEGIN {
input = ARGV[1]
while (getline line < input) {
sub(/^ +/, "", line)
split(line, a, / +/)
for (i = 2; i < ARGC; ++i) {
if (a[1] == ARGV[i]) {
printf "%s %s\n", a[1], a[2]
break
}
}
}
exit
}
' <(my_command) "${ROWS[#]}"
That awk command could be condensed to one line as:
awk -- 'BEGIN { input = ARGV[1]; while (getline line < input) { sub(/^ +/, "", line); split(line, a, / +/); for (i = 2; i < ARGC; ++i) { if (a[1] == ARGV[i]) {; printf "%s %s\n", a[1], a[2]; break; }; }; }; exit; }' <(my_command) "${ROWS[#]}"
Or better yet just use Bash instead as a whole:
#!/bin/bash
ROWS=(11 12)
while IFS=$' ' read -r LINE; do
IFS='|' read -ra FIELDS <<< "${LINE// +( )/|}"
for R in "${ROWS[#]}"; do
if [[ ${FIELDS[0]} == "$R" ]]; then
echo "${R} ${FIELDS[1]}"
break
fi
done
done < <(my_command)
It should give an output like:
11 File Name1
12 Fi leNa me2
Shell variables aren't expanded inside single-quoted strings. Use the -v option to set an awk variable to the shell variable:
fileName=$(my_command | awk -v i=$i -F "[[:space:]]{2,}+" 'NR==i {print $2}' | egrep "^[[:alnum:]])"
This method avoids having to escape all the $ characters in the awk script, as required in konsolebox's answer.
As you already heard, you need to populate an awk variable from your shell variable to be able to use the desired value within the awk script so thi:
awk -F "[[:space:]]{2,}+" 'NR==$i {print $2}' | egrep "^[[:alnum:]]"
should be this:
awk -v i="$i" -F "[[:space:]]{2,}+" 'NR==i {print $2}' | egrep "^[[:alnum:]]"
Also, though, you don't need awk AND grep since awk can do anything grep van do so you can change this part of your script:
awk -v i="$i" -F "[[:space:]]{2,}+" 'NR==i {print $2}' | egrep "^[[:alnum:]]"
to this:
awk -v i="$i" -F "[[:space:]]{2,}+" '(NR==i) && ($2~/^[[:alnum:]]/){print $2}'
and you don't need a + after a numeric range so you can change {2,}+ to just {2,}:
awk -v i="$i" -F "[[:space:]]{2,}" '(NR==i) && ($2~/^[[:alnum:]]/){print $2}'
Most importantly, though, instead of invoking awk once for every invocation of my_command, you can just invoke it once for all of them, i.e. instead of this (assuming this does what you want):
i=1
for num in rows
do
fileName=$(my_command | awk -v i="$i" -F "[[:space:]]{2,}" '(NR==i) && ($2~/^[[:alnum:]]/){print $2}')
echo "$num $fileName"
$((i++))
done
you can do something more like this:
for num in rows
do
my_command
done |
awk -F '[[:space:]]{2,}' '$2~/^[[:alnum:]]/{print NR, $2}'
I say "something like" because you don't tell us what "my_command", "rows" or "num" are so I can't be precise but hopefully you see the pattern. If you give us more info we can provide a better answer.
It's pretty inefficient to rerun my_command (and awk) every time through the loop just to extract one line from its output. Especially when all you're doing is printing out part of each line in order. (I'm assuming that my_command really is exactly the same command and produces the same output every time through your loop.)
If that's the case, this one-liner should do the trick:
paste -d' ' <(printf '%s\n' $rows) <(my_command |
awk -F '[[:space:]]{2,}+' '($2 ~ /^[::alnum::]/) {print $2}')
My goal is to find out the length of the second field and if the length is more than five characters, then I need to show the entire record using shell scripts/command.
echo "From the csv file"
cat latency.csv |
while read line
do
latency=`echo $line | cut -d"," -f2 | tr -d " "`
length=$(echo ${#latency})
if [ $length -gt 5 ]
then
echo $line
fi
done
There is nothing wrong with my code, but being UNIX/Linux, I thought there should be a simpler way of doing such things.
Is there one such simpler method?
awk -F, 'length($2)>5' file
this should work
updated
awk -F, '{a=$0;gsub(/ /,"",$2);if(length($2)>5)print a}' file
awk -F, '{
t = $2
gsub(/ /, x, t)
if (length(t) > 5)
print
}' latency.csv
Or:
perl -F, -ane'
print if
$F[1] =~ tr/ //dc > 5
' latency.csv