I have some files of this form: 2014.144.09.27.56.0195.IU.SDV.00.BHZ.M.SAC and I want to extract the SDV, 00 ,BHZ variables, in order to find a file, of this form ./POLEZEROFILES/SAC_PZs_IU_SDV_BHZ_00_2014.112.19.50.00.0000_2599.365.23.59.59.99999, using these variables. I am using this forloop, that for every ".SAC" file, it finds the corresponding "SAC_PZs_" file, with the same variables in the filename.
#!/bin/sh
ALIST=(*SAC)
for ((i=0;i<${#ALIST[#]};i++));do
A="${ALIST[i]}"
staname=`ls "$A" | awk -F"[_.]" '{print $8}'`
staXX=`ls "$A" | awk -F"[_.]" '{print $9}'`
stacomp=`ls "$A" | awk -F"[_.]" '{print $10}'`
B=`find ./POLEZEROFILES -name "SAC*_${staname}_*${stacomp}_*${staXX}*" -print`
echo "${A}" "${B}"
done
This code works for some filenames, but in some cases it outputs 2 filenames, ignoring the 00 variable.For example,
for this $A:
2014.144.09.27.33.0195.IU.RSSD.00.BHZ.M.SAC
it outputs 2 $B:
./POLEZEROFILES/SAC_PZs_IU_RSSD_BHZ_10_2011.209.05.56.00.0000_2599.365.23.59.59.99999
./POLEZEROFILES/SAC_PZs_IU_RSSD_BHZ_00_2011.208.18.13.59.0000_2599.365.23.59.59.99999
The second output is the right one.
Can anyone figure out the problem?
Not related to your problem but a general comment. You don't need ls in those awk lines. echo will work just fine (as will awk ... <<<"$A").
Your problem is that your pattern matches too loosely.
Your second to last * consumes up to the 00.0000.... bit in your first filename and then matches. You need to anchor your desired patterns better. So if you know that stacomp and staXX will be next to each other drop the * between them. If you don't know that then at least put a _ after staXX to anchor the following character.
There's also no need for the array and manual for loop here.
Just for A in *SAC; do will work for your loop.
Related
I have a task where I'm given an input of the format:
4
A CS 22 M
B ECE 23 M
C CS 23 F
D CS 22 F
as the user input from the command line. From this, we have to perform tasks like determine the number of male and female students, determine which department has the most students, etc. I have done this using awk with the input as a file. Is there any way to do this with a user input instead of a file?
Example of a command I used for a file (where the content in the file is in the same format):
numberofmales=$(awk -F ' ' '{print $4}' file.txt | grep M | wc -l) #list number of males
Not Reproducible
It works fine for me, so your problem can't be reproduced with either GNU or BSD awk under Bash 5.0.18(1). With your posted code and file sample:
$ numberofmales=$(awk -F ' ' '{print $4}' file.txt | grep M | wc -l)
$ echo $numberofmales
2
Check to make sure you don't have problems in your input file, or elsewhere in your code.
Also, note that if you call awk without a file argument or input from a pipe, it tries to collect data from standard input. It may not actually be hanging; it's probably just waiting on end-of-file, which you can trigger with CTRL+D.
Recommended Improvements
Even if your code works, it can be improved. Consider the following, which skips the unnecessary field-separator definition and performs all the actions of your pipeline within awk.
males=$(
awk 'tolower($4)=="m" {count++}; END {print count}' file.txt
)
echo "$males"
Fewer moving parts are often easier to debug, and can often be more performant on large datasets. However, your mileage may vary.
User Input
If you want to use user input rather than a file, you can use standard input to collect your data, and then pass it as a quoted argument to a function. For example:
count_males () {
awk 'tolower($4)=="m" {count++}; END {print count}' <<< "$*"
}
echo "Enter data (CTRL-D when done):"
data=$(cat -)
# If at command prompt, wait until EOF above before
# pasting this line. Won't matter in scripts.
males=$(count_males "$data")
The result is now stored in males, and you can echo "$males" or make use of the variable in whatever other way you like.
Bash indeed does not care whether a file handle is connected to standard input or to a file, and neither does Awk.
However, if you want to pass the same input to multiple Awk instances, it really does make sense to store it in a temporary file.
A better overall solution is to write a better Awk script so you only need to read the input once.
awk 'NF > 1 { ++a[$4] } END { for (g in a) print g, a[g] }'
Demo: https://ideone.com/0ML7Xk
The NF > 1 condition is to skip the silly first line. Probably don't put that information there in the first place and let Awk figure out how many lines there are; it's probably better at counting than you are anyway.
I have large files of HTTP access logs and I'm trying to generate hourly counts for a specific query string. Obviously, the correct solution is to dump everything into splunk or graylog or something, but I can't set all that up at the moment for this one-time deal.
The quick-and-dirty is:
for hour in 0{0..9} {10..23}
do
grep $QUERY $FILE | egrep -c "^\S* $hour:"
# or, alternately
# egrep -c "^\S* $hour:.*$QUERY" $FILE
# not sure which one's better
done
But these files average 15-20M lines, and I really don't want to parse through each file 24 times. It would be far more efficient to parse the file and count each instance of $hour in one go. Is there any way to accomplish this?
You can ask grep to output the matching part of each line with -o and then use uniq -c to count the results:
grep "$QUERY" "$FILE" | grep -o "^\S* [0-2][0-9]:" | sed 's/^\S* //' | uniq -c
The sed command is there to keep only the two digit hour and the colon, which you can also remove with another sed expression if you want.
Caveats: this solution works with GNU grep and GNU sed, and will produce no output, rather than "0", for hours with no log entries. Kudos to #EdMorton for pointing these issues out in the comments, and other issues that were fixed in the answer above.
Assuming the timestamp appears with a space before the 2-digit hour, then a colon after
gawk -v patt="$QUERY" '
$0 ~ patt && match($0, / ([0-9][0-9]):/, m) {
print > (m[1] "." FILENAME)
}
' "$FILE"
This will create 24 files.
Requires GNU awk for the 3-arg form of match()
This is probably what you really need, using GNU awk for the 3rd arg to match() and making assumptions about what your input might look like, what your QUERY variable might contain, and what the output should look like:
awk -v query="$QUERY" '
match($0, " ([0-9][0-9]):.*"query, a) { cnt[a[1]+0]++ }
END {
for (hr=0; hr<=23; hr++) {
printf "%02d = %d\n", hr, cnt[hr]
}
}
' "$FILE"
Don't really use all upper case for non-exported shell variables btw - see Correct Bash and shell script variable capitalization.
I have some output files (5000 files) of .log which are the results of QM computations. Inside each file there are two special lines indicate the number of electrons and orbitals, like this below as an example (with exact spaces as in output files):
Number of electrons = 9
Number of orbitals = 13
I thought about a script (bash or Fortran), as a solution to this problem, which grep these two lines (at same time) and get the corresponding integer values (9 and 13, for instance), compare them and finds the difference between two values, and finally, list them in a new text file with the corresponding filenames.
I would really appreciate any help given.
Am posting an attempt in GNU Awk, and have tested it in that only.
#!/bin/bash
for file in *.log
do
awk -F'=[[:blank:]]*' '/Number of/{printf "%s%s",$2,(NR%2?" ":RS)}' "$file" | awk 'function abs(v) {return v < 0 ? -v : v} {print abs($1-$2)}' >> output_"$file"
done
The reason I split the AWK logic to two was to reduce the complexity in doing it in single huge command. The first part is for extracting the numbers from your log file in a columnar format and second for getting their absolute value.
I will break-down the AWK logic:-
-F'=[[:blank:]]*' is a mult0 character delimiter logic including = and one or more instances of [[:blank:]] whitespace characters.
'/Number of/{printf "%s%s",$2,(NR%2?" ":RS)}' searches for lines starting with Number of and prints it in a columnar fashion, i.e. as 9 13 from your sample file.
The second part is self-explanatory. I have written a function to get the absolute value from the two returned values and print it.
Each output is saved in a file named output_, for you to process it further.
Run the script from your command line as bash script.sh, where script.sh is the name containing the above lines.
Update:-
In case if you are interested in negative values too i.e. without the absolute function, change the awk statement to
awk -F'=[[:blank:]]*' '/Number of/{printf "%s%s",$2,(NR%2?" ":RS)}' "$file" | awk '{print ($1-$2)}' >> output_"$file"
Bad way to do it (but it will work)-
while read file
do
first=$(awk -F= '/^Number/ {print $2}' "$file" | head -1)
second=$(awk -F= '/^Number/ {print $2}' "$file" | tail -1)
if [ "$first" -gt "$second" ]
then
echo $(("$first" - "$second"))
else
echo $(("$second" - "$first"))
fi > "$file"_answer ;
done < list_of_files
This method picks up the values (in the awk one liner and compares them.
It then subtracts them to give you one value which it saves in the file called "$file"_answer. i.e. the initial file name with '_answer' as a suffix to the name.
You may need to tweak this code to fit your purposes exactly.
I have made a script to practice my Bash, only to realize that this script does not take tabulation into account, which is a problem since it is designed to find and replace a pattern in a Python script (which obviously needs tabulation to work).
Here is my code. Is there a simple way to get around this problem ?
pressure=1
nline=$(cat /myfile.py | wc -l) # find the line length of the file
echo $nline
for ((c=0;c<=${nline};c++))
do
res=$( tail -n $(($(($nline+1))-$c)) myfile.py | head -n 1 | awk 'gsub("="," ",$1){print $1}' | awk '{print$1}')
#echo $res
if [ $res == 'pressure_run' ]
then
echo "pressure_run='${pressure}'" >> myfile_mod.py
else
echo $( tail -n $(($nline-$c)) myfile.py | head -n 1) >> myfile_mod.py
fi
done
Basically, it finds the line that has pressure_run=something and replaces it by pressure_run=$pressure. The rest of the file should be untouched. But in this case, all tabulation is deleted.
If you want to just do the replacement as quickly as possible, sed is the way to go as pointed out in shellter's comment:
sed "s/\(pressure_run=\).*/\1$pressure/" myfile.py
For Bash training, as you say, you may want to loop manually over your file. A few remarks for your current version:
Is /myfile.py really in the root directory? Later, you don't refer to it at that location.
cat ... | wc -l is a useless use of cat and better written as wc -l < myfile.py.
Your for loop is executed one more time than you have lines.
To get the next line, you do "show me all lines, but counting from the back, don't show me c lines, and then show me the first line of these". There must be a simpler way, right?
To get what's the left-hand side of an assignment, you say "in the first space-separated field, replace = with a space , then show my the first space separated field of the result". There must be a simpler way, right? This is, by the way, where you strip out the leading tabs (your first awk command does it).
To print the unchanged line, you do the same complicated thing as before.
A band-aid solution
A minimal change that would get you the result you want would be to modify the awk command: instead of
awk 'gsub("="," ",$1){print $1}' | awk '{print$1}'
you could use
awk -F '=' '{ print $1 }'
"Fields are separated by =; give me the first one". This preserves leading tabs.
The replacements have to be adjusted a little bit as well; you now want to match something that ends in pressure_run:
if [[ $res == *pressure_run ]]
I've used the more flexible [[ ]] instead of [ ] and added a * to pressure_run (which must not be quoted): "if $res ends in pressure_run, then..."
The replacement has to use $res, which has the proper amount of tabs:
echo "$res='${pressure}'" >> myfile_mod.py
Instead of appending each line each loop (and opening the file each time), you could just redirect output of your whole loop with done > myfile_mod.py.
This prints literally ${pressure} as in your version, because it's single quoted. If you want to replace that by the value of $pressure, you have to remove the single quotes (and the braces aren't needed here, but don't hurt):
echo "$res=$pressure" >> myfile_mod.py
This fixes your example, but it should be pointed out that enumerating lines and then getting one at a time with tail | head is a really bad idea. You traverse the file for every single line twice, it's very error prone and hard to read. (Thanks to tripleee for suggesting to mention this more clearly.)
A proper solution
This all being said, there are preferred ways of doing what you did. You essentially loop over a file, and if a line matches pressure_run=, you want to replace what's on the right-hand side with $pressure (or the value of that variable). Here is how I would do it:
#!/bin/bash
pressure=1
# Regular expression to match lines we want to change
re='^[[:space:]]*pressure_run='
# Read lines from myfile.py
while IFS= read -r line; do
# If the line matches the regular expression
if [[ $line =~ $re ]]; then
# Print what we matched (with whitespace!), then the value of $pressure
line="${BASH_REMATCH[0]}"$pressure
fi
# Print the (potentially modified) line
echo "$line"
# Read from myfile.py, write to myfile_mod.py
done < myfile.py > myfile_mod.py
For a test file that looks like
blah
test
pressure_run=no_tab
blah
something
pressure_run=one_tab
pressure_run=two_tabs
the result is
blah
test
pressure_run=1
blah
something
pressure_run=1
pressure_run=1
Recommended reading
How to read a file line-by-line (explains the IFS= and -r business, which is quite essential to preserve whitespace)
BashGuide
I have a directory with files that I want to process one by one and for which each output looks like this:
==== S=721 I=47 D=654 N=2964 WER=47.976% (1422)
Then I want to calculate the average percentage (column 6) by piping the output to AWK. I would prefer to do this all in one script and wrote the following code:
for f in $dir; do
echo -ne "$f "
process $f
done | awk '{print $7}' | awk -F "=" '{sum+=$2}END{print sum/NR}'
When I run this several times, I often get different results although in my view nothing really changes. The result is almost always incorrect though.
However, if I only put the for loop in the script and pipe to AWK on the command line, the result is always the same and correct.
What is the difference and how can I change my script to achieve the correct result?
Guessing a little about what you're trying to do, and without more details it's hard to say what exactly is going wrong.
for f in $dir; do
unset TEMPVAR
echo -ne "$f "
TEMPVAR=$(process $f | awk '{print $7}')
ARRAY+=($TEMPVAR)
done
I would append all your values to an array inside your for loop. Now all your percentages are in $ARRAY. It should be easy to calculate the average value, using whatever tool you like.
This will also help you troubleshoot. If you get too few elements in the array ${#ARRAY[#]} then you will know where your loop is terminating early.
# To get the percentage of all files
Percs=$(sed -r 's/.*WER=([[:digit:].]*).*/\1/' *)
# The divisor
Lines=$(wc -l <<< "$Percs")
# To change new lines into spaces
P=$(echo $Percs)
# Execute one time without the bc. It's easier to understand
echo "scale=3; (${P// /+})/$Lines" | bc