I am new to programming altogether and am trying to write my first bash script.
I have a file called NUMBERS.txt that has various numbers in it, as such:
1000
1001
1001
1000
1002
1001
etc..
I would like to write a script to count the occurrence of each number, save it as a variable and print it into a new text file as such:
1001= 3
1000= 2
etc..
I am completely stuck.
Here's what I have so far:
#!/bin/bash
for Count in `grep -c '1000' /NUMBERS.txt `
do
echo 'Count = '${Count}
done
for Count in `grep -c '1001' /NUMBERS.txt `
do
echo 'Count = '${Count}
done
Sort the file then count how many times each unique line occurs:
sort NUMBERS.txt | uniq -c
Now your file is already have one number on each line, it is simpler
for i in `sort -u NUMBERS.txt ` ; do count=`grep -c "$i" NUMBERS.txt ` ; echo "$i=$count" ; done > your_result.txt
or in a different format
for i in `sort -u NUMBERS.txt `
do
count=`grep -c "$i" NUMBERS.txt `
echo "$i=$count"
done > your_result.txt
As asked by , the performance is not very good. here is a much better one
sort NUMBERS.txt | uniq -c | awk '{print $1,"=",$2}'
Basically you go through NUNMBERS.txt twice. The first pass, you get the unique numbers;
The second pass you count the occurrence of each unique number.
I'm not the best at shell script, but here is a solution that works, using bash and grep -c :
#!/bin/bash
INPUT="./numbers.txt"
OUTPUT="./result.txt"
rm -f ${OUTPUT}
# you might want to change the values
for i in {1000..2000}; do
for Count in `grep -c ${i} ${INPUT}`; do
echo "${i} = ${Count}" >> ${OUTPUT}
done
done
Related
I have 44 files (2 for each chromosome) divided in two types: .vcf and .filtered.vcf.
I would like to make a wc -l for each of them in a loop and append the output always to the same file. However, I would like to have 3 columns in this file: chr[1-22], wc -l of .vcf and wc -l of .filtered.vcf.
I've been trying to do independent wc -l for each file and paste together columnwise the 2 outputs for each of the chromosomes, but this is obviously not very efficient, because I'm generating a lot of unnecessary files. I'm trying this code for the 22 pairs of files:
wc -l file1.vcf | cut -f 1 > out1.vcf
wc -l file1.filtered.vcf | cut -f 1 > out1.filtered.vcf
paste -d "\t" out1.vcf out1.filtered.vcf
I would like to have just one output file containing three columns:
Chromosome VCFCount FilteredVCFCount
chr1 out1 out1.filtered
chr2 out2 out2.filtered
Any help will be appreciated, thank you very much in advance :)
printf "%s\n" *.filtered.vcf |
cut -d. -f1 |
sort |
xargs -n1 sh -c 'printf "%s\t%s\t%s\n" "$1" "$(wc -l <"${1}.vcf")" "$(wc -l <"${1}.filtered.vcf")"' --
Output newline separated list of files in the directory
Remove the extension with cut (probably something along xargs -i basename {} .filtered.vcf would be safer)
Sort it (for nice sorted output!) (probably something along sort -tr -k2 -n would sort numerically and would be even better).
xargs -n1 For each one file execute the script sh -c
printf "%s\t%s\t%s\n" - output with custom format string ...
"$1" - the filename and...
"(wc -l <"${1}.vcf")" - the count the lines in .vcf file and...
"$(wc -l <"${1}.filtered.vcf")" - the count of the lines in the .filtered.vcf
Example:
> touch chr{1..3}{,.filtered}.vcf
> echo > chr1.filtered.vcf ; echo > chr2.vcf ;
> printf "%s\n" *.filtered.vcf |
> cut -d. -f1 |
> sort |
> xargs -n1 sh -c 'printf "%s\t%s\t%s\n" "$1" "$(wc -l <"${1}.filtered.vcf")" "$(wc -l <"${1}.vcf")"' --
chr1 0 1
chr2 1 0
chr3 0 0
To have nice looking table with headers, use column:
> .... | column -N Chromosome,VCFCount,FilteredVCFCount -t -o ' '
Chromosome VCFCount FilteredVCFCount
chr1 0 1
chr2 1 0
chr3 0 0
Maybe try this.
for chr in chr*.vcf; do
base=${chr%.vcf}
awk -v base="$base" 'BEGIN { OFS="\t"
# Remove this to not have this pesky header line
print "Chromosome", "VCFCount", "FilteredVCFCount"
}
FNR==1 && n { p=n }
{ n=FNR }
END { print base, p, n }' "$chr" "$base.filtered.vcf"
done >counts.txt
The very simple Awk script just collects the highest line number for each file (so we basically reimplement wc -l) and prints the collected numbers in the desired format. FNR is the line number in the current input file; we simply save this, and copy the value to p to keep the saved value from the previous file in a separate variable when we switch to a new file (starting over at line number 1).
The shell parameter substitution ${variable%pattern} retrieves the value of variable with any suffix match on pattern removed. (There is also ${variable#pattern} to remove a prefix, and Bash has ## and %% to trim the longest pattern match instead of the shortest.)
If efficiency is important, you could probably refactor all of the script into a single Awk script, but this way, all the pieces are simple and hopefully understandable.
I have a directory (output) in unix (SUN). There are two types of files created with timestamp prefix to the file name. These file are created on a regular interval of 10 minutes.
e. g:
1. 20140129_170343_fail.csv (some lines are there)
2. 20140129_170343_success.csv (some lines are there)
Now I have to search for a particular string in all the files present in the output directory and if the string is found in fail and success files, I have to count the number of lines present in those files and save the output to the cnt_succ and cnt_fail variables. If the string is not found I will search again in the same directory after a sleep timer of 20 seconds.
here is my code
#!/usr/bin/ksh
for i in 1 2
do
grep -l 0140127_123933_part_hg_log_status.csv /osp/local/var/log/tool2/final_logs/* >log_t.txt; ### log_t.txt will contain all the matching file list
while read line ### reading the log_t.txt
do
echo "$line has following count"
CNT=`wc -l $line|tr -s " "|cut -d" " -f2`
CNT=`expr $CNT - 1`
echo $CNT
done <log_t.txt
if [ $CNT > 0 ]
then
exit
fi
echo "waiitng"
sleep 20
done
The problem I'm facing is, I'm not able to get the _success and _fail in file in line and and check their count
I'm not sure about ksh, but while ... do; ... done is notorious for running off with whatever variables you're using in bash. ksh might be similar.
If I've understand your question right, SunOS has grep, uniq and sort AFAIK, so a possible alternative might be...
First of all:
$ cat fail.txt
W34523TERG
ADFLKJ
W34523TERG
WER
ASDTQ34T
DBVSER6
W34523TERG
ASDTQ34T
DBVSER6
$ cat success.txt
abcde
defgh
234523452
vxczvzxc
jkl
vxczvzxc
asdf
234523452
vxczvzxc
dlkjhgl
jkl
wer
234523452
vxczvzxc
And now:
egrep "W34523TERG|ASDTQ34T" fail.txt | sort | uniq -c
2 ASDTQ34T
3 W34523TERG
egrep "234523452|vxczvzxc|jkl" success.txt | sort | uniq -c
3 234523452
2 jkl
4 vxczvzxc
Depending on the input data, you may want to see what options sort has on your system. Examining uniq's options may prove useful too (it can do more than just count duplicates).
Think you want something like this (will work in both bash and ksh)
#!/bin/ksh
while read -r file; do
lines=$(wc -l < "$file")
((sum+=$lines))
done < <(grep -Rl --include="[1|2]*_fail.csv" "somestring")
echo "$sum"
Note this will match files starting with 1 or 2 and ending in _fail.csv, not exactly clear if that's what you want or not.
e.g. Let's say I have two files, one starting with 1 (containing 4 lines) and one starting with 2 (containing 3 lines), both ending in `_fail.csv somewhere under my current working directory
> abovescript
7
Important to understand grep options here
-R, --dereference-recursive
Read all files under each directory, recursively. Follow all
symbolic links, unlike -r.
and
-l, --files-with-matches
Suppress normal output; instead print the name of each input
file from which output would normally have been printed. The
scanning will stop on the first match. (-l is specified by
POSIX.)
Finaly I'm able to find the solution. Here is the complete code:
#!/usr/bin/ksh
file_name="0140127_123933.csv"
for i in 1 2
do
grep -l $file_name /osp/local/var/log/tool2/final_logs/* >log_t.txt;
while read line
do
if [ $(echo "$line" |awk '/success/') ] ## will check the success file
then
CNT_SUCC=`wc -l $line|tr -s " "|cut -d" " -f2`
CNT_SUCC=`expr $CNT_SUCC - 1`
fi
if [ $(echo "$line" |awk '/fail/') ] ## will check the fail file
then
CNT_FAIL=`wc -l $line|tr -s " "|cut -d" " -f2`
CNT_FAIL=`expr $CNT_FAIL - 1`
fi
done <log_t.txt
if [ $CNT_SUCC > 0 ] && [ $CNT_FAIL > 0 ]
then
echo " Fail count = $CNT_FAIL"
echo " Success count = $CNT_SUCC"
exit
fi
echo "waitng for next search..."
sleep 10
done
Thanks everyone for your help.
I don't think I'm getting it right, but You can't diffrinciate the files?
maybe try:
#...
CNT=`expr $CNT - 1`
if [ $(echo $line | grep -o "fail") ]
then
#do something with fail count
else
#do something with success count
fi
Hello i'm fairly new to scripting, and struggling with trying to test/check if 4 lines in a textfile are equal to eachother, and i cannot figure this one out since comparison examples are all with two variables. i've come up with this:
#!/bin/sh
#check if mxf videofiles are older than 10 minutes and parse them into tclist.txt
find . -amin +10 |sed "s/^..//" >tclist.txt
#grep timecode and cut : from the output of mxfprobe and place that into variable TC
for z in $(cat tclist.txt); do TC=$(mxfprobe -i "$z" 2>&1 |grep timecode|sed "s/[^0-9]*//"|sed "s/://"|sed "s/://"|sed "s/://")
echo $TC >>offsetcheck.txt
done;
The output of offsetcheck.txt then looks like this:
10194013
10194013
10194014
10194014
How can i test if those 4 values are equal to eachother? (in this example two files are drifted one frame)
I've tried to place those values into an array and check them for uniqueness...
exec 10<&0
exec < offsetcheck.txt
let count=0
while read LINE; do
ARRAY[$count]=$LINE
((count++))
done
echo ${ARRAY[#]}
exec 0<&10 10<&-
if ($ARRAY !== array_unique($ARRAY))
{
echo There were duplicate values
}
... struggling with trying to test/check if 4 lines in a textfile are
equal to eachother
You could use sort and wc to determine the number of unique values in the file. The following would tell whether the file contains unique values or not:
(( $(sort -u offsetcheck.txt | wc -l) == 1 )) && echo "File contains unique values" || echo "File does not contain unique values"
If you wanted to do the same for an array, you could say:
for i in "${ARRAY[#]}"; do echo "$i" ; done | sort -u | wc -l
to get the number of unique values in the array.
If the values in the array are guaranteed not to have any space, then saying:
echo "${ARRAY[#]}" | tr ' ' '\n' | sort -u | wc -l
would suffice. (But note the if above.)
Looks to me like the whole process can be reduced to
n=$(
find . -amin +10 |
sed "s/^..//" |
xargs -I FILE mxfprobe -i "FILE" 2>&1 |
grep -h timecode |
sed 's/[^0-9]//g' |
sort -u |
wc -l
)
Then check if n == 1
Here I made a small script that take input from user searching some pattern from a file and displays required no of lines from that file where the pattern is found. Although this code is searching the pattern line wise due to standard grep practice. I mean if the pattern occurs twice on the same line, i want the output to print twice. Hope I make some sense.
#!/bin/sh
cat /dev/null>copy.txt
echo "Please enter the sentence you want to search:"
read "inputVar"
echo "Please enter the name of the file in which you want to search:"
read "inputFileName"
echo "Please enter the number of lines you want to copy:"
read "inputLineNumber"
[[-z "$inputLineNumber"]] || inputLineNumber=20
cat /dev/null > copy.txt
for N in `grep -n $inputVar $inputFileName | cut -d ":" -f1`
do
LIMIT=`expr $N + $inputLineNumber`
sed -n $N,${LIMIT}p $inputFileName >> copy.txt
echo "-----------------------" >> copy.txt
done
cat copy.txt
As I understood, the task is to count number of pattern occurrences in line. It can be done like so:
count=$((`echo "$line" | sed -e "s|$pattern|\n|g" | wc -l` - 1))
Suppose you have one file to read. Then, code will be following:
#!/bin/bash
file=$1
pattern="an."
#reading file line by line
cat -n $file | while read input
do
#storing line to $tmp
tmp=`echo $input | grep "$pattern"`
#counting occurrences count
count=$((`echo "$tmp" | sed -e "s|$pattern|\n|g" | wc -l` - 1))
#printing $tmp line $count times
for i in `seq 1 $count`
do
echo $tmp
done
done
I checked this for pattern "an." and input:
I pass here an example of many 'an' letters
an
ananas
an-an-as
Output is:
$ ./test.sh input
1 I pass here an example of many 'an' letters
1 I pass here an example of many 'an' letters
1 I pass here an example of many 'an' letters
3 ananas
4 an-an-as
4 an-an-as
Adapt this to your needs.
How about using awk?
Assume the pattern you are searching for is in variable $pattern and the file you are checking is $file
The
count=`awk 'BEGIN{n=0}{n+=split($0,a,"'$pattern'")-1}END {print n}' $file`
or for a line
count=`echo $line | awk '{n=split($0,a,"'$pattern'")-1;print n}`
I have a file (fasta) that I am using awk to extract the needed fields from (sequences with their headers). I then pipe it to a BLAST program and finally I pipe it to qsub in order to submit a job.
the file:
>sequence_1
ACTGACTGACTGACTG
>sequence_2
ACTGGTCAGTCAGTAA
>sequence_3
CCGTTGAGTAGAAGAA
and the command (which works):
awk < fasta.fasta '/^>/ { print $0 } $0 !~ /^>/' | echo "/Local/ncbi-blast-2.2.25+/bin/blastx -db blastdb.fa -outfmt 5 >> /User/blastresult.xml" | qsun -q S
what I would like to do is a add a condition that will sample the number of jobs I am running (using qstat) if it is below a certain threshold the job will be submitted.
for example:
allowed_jobs=200 #for example
awk < fasta.fasta '/^>/ { print $0 } $0 !~ /^>/' | echo "/Local/ncbi-blast-2.2.25+/bin/blastx -db blastdb.fa -outfmt 5 >> /User/blastresult.xml" | cmd=$(qstat -u User | grep -c ".") | if [ $cmd -lt $allowed_jobs ]; then qsub -q S
unfortunately (for me anyway) I have failed in all my attempts to do that.
I'd be grateful for any help
EDIT: elaborating a bit:
what I am trying to do is to extract from the fasta file this:
>sequene_x
ACTATATATATA
or basically: >HEADER\nSEQUENCE
one by one and pipe it to the blast program which can take stdin. I want to create a unique job for each sequence and this is the reason I want to pipe to qsub for each sequence.
to put it plainly the qsub submission would have looked something like this:
qsub -q S /Local/ncbi-blast-2.2.25+/bin/blastx -db blastdb.fa -query FASTA_SEQUENCE -outfmt 5 >> /User/blastresult.xml
note that the -query flag is unnecessary if stdin sequence is piped to it.
however, the main problem for me is how to incorporate the condition I mentioned above so that the sequence will be piped to qsub only if the qstat result is below a threshold. ideally if the qstat result is above the threshold it'll sleep until i goes below and then pass it forward.
thanks.
Hello I guess this is answered since long now.
I'll just provide a way to solve this, by counting the lines that should be processed (sequences) before passing it over to awk, the awk piece would go where echo time to work is.
#!/bin/bash
ct=`grep -c '^>' fasta.fasta`
if [ $ct -lt 201 ] ; then
echo time to work
else
echo too much
fi
This bit of shell reads two lines, prints them to stdout and pipes into your qsub command
while IFS= read -r header; do
IFS= read -r sequence
printf "%s\n" "$header" "$sequence" |
qsub -q S /Local/ncbi-blast-2.2.25+/bin/blastx -db blastdb.fa -outfmt 5 >> /User/blastresult.xml
done < fasta.fasta