I have a TXT files with lines of about 1 Million.
#Test.txt
zs272
zs273
zs277
zs278
zs282
zs285
zs288
zs289
zs298
zs300
zs7
zsa
zsag
zsani179yukkie
zsani182zaide
zsaqgiw
zsb86581
zsbguepqtkcn
zscazn
zscfhlsv
zscgxadrwijl
zsclions111yuen
zscwqtk
zscz
zsder
zsdfdgdgg
I wanted to delete the line which has the numbers and keeping only strings.
I tried,
grep -v '^[1-9]' Test.txt > 1_Test.txt
Couldn't get the desired result.
Expected output:
#1_Test.txt
zsa
zsag
zsbguepqtkcn
zscazn
zscfhlsv
zscgxadrwijl
zscwqtk
zscz
zsder
zsdfdgdgg
sed '/[0-9]/d' file
If you want to edit your file "in place" use sed's option -i.
awk '!/[0-9]/' file
With bash:
while read -r line; do [[ ! $line =~ [0-9] ]] && printf "%s\n" "$line"; done < file
Just remove the start of the line anchor ^.
^[1-9] regex only matches the numbers 1-9 which exists at the start.
grep -v '[1-9]' Test.txt > 1_Test.txt
to work for all digits including 0.
grep -v '[0-9]' Test.txt > 1_Test.txt
A solution in AWK!
awk '!/[0-9]+/{print}' file
Related
I have to format the width of a substring within a string using a bash script, but without using tokens or loops. A single character between two colons should be prepended by a 0 in order to match the standard width of 2 for each field.
For e.g
from:
6:0:36:35:30:30:72:6c:73:0:c:52:4c:30:31:30:31:30:30:30:31:36:39:0:1:3
to
06:00:36:35:30:30:72:6c:73:00:0c:52:4c:30:31:30:31:30:30:30:31:36:39:00:01:03
How can I do this?
sed -r 's/\<([0-9a-f])\>/0\1/g'
Search and replace with a regex. Use \< and \> to match word boundaries so [0-9a-f] only matches single digits.
$ sed -r 's/\<([0-9a-f])\>/0\1/g' <<< "6:0:36:35:30:30:72:6c:73:0:c:52:4c:30:31:30:31:30:30:30:31:36:39:0:1:3"
06:00:36:35:30:30:72:6c:73:00:0c:52:4c:30:31:30:31:30:30:30:31:36:39:00:01:03
awk -F: -v OFS=: '{for(i=1;i<=NF;i++) if(length($i)==1)gsub($i,"0&",$i)}1' file
Output:
06:00:36:35:30:30:72:6c:73:00:0c:52:4c:30:31:30:31:30:30:30:31:36:39:00:01:03
This will divide the whole line into fields separated by : , if the length of any of the field is == 1. then it will replace that field with 0field.
Bash solution:
IFS=:; for i in $string; do echo -n 0$i: | tail -c 3; done
With
str="06:00:36:35:30:30:72:6c:73:00:0c:52:4c:30:31:30:31:30:30:30:31:36:39:00:01:03"
you can add a '0' to all tokens and remove those that are unwanted:
sed -r 's/0([0-9a-f]{2})/\1/g' <<< "0${str//:/:0}"
That doesn't feel right, making errors and repairing them.
A better alternative is
echo $(IFS=:; printf "%2s:" ${str} | tr " " "0")
I want to match the numbers in the first file with the 2nd column of second file and get the matching lines in a separate output file. Kindly let me know what is wrong with the code?
I have a list of numbers in a file IDS.txt
10028615
1003
10096344
10100
10107393
10113978
10163178
118747520
I have a second File called src1src22.txt
From src:'1' To src:'22'
CHEMBL3549542 118747520
CHEMBL548732 44526300
CHEMBL1189709 11740251
CHEMBL405440 44297517
CHEMBL310280 10335685
expected newoutput.txt
CHEMBL3549542 118747520
I have written this code
while read line; do cat src1src22.txt | grep -i -w "$line" >> newoutput.txt done<IDS.txt
Your command line works - except you're missing a semicolon:
while read line; do grep -i -w "$line" src1src22.txt; done < IDS.txt >> newoutput.txt
I have found an efficient way to perform the task. Instead of a loop try this -f gives the pattern in the file next to it and searches in the next file. The chance of invalid character length which can occur with grep is reduced and looping slows the process down.
grep -iw -f IDS.txt src1src22.tx >>newoutput.txt
Try this -
awk 'NR==FNR{a[$2]=$1;next} $1 in a{print a[$1],$0}' f2 f1
CHEMBL3549542 118747520
Where f2 is src1src22.txt
I am trying to get a substring between &DEST= and the next & or a line break.
For example :
MYREQUESTISTO8764GETTHIS&DEST=SFO&ORIG=6546
In this I need to extract "SFO"
MYREQUESTISTO8764GETTHIS&DEST=SANFRANSISCO&ORIG=6546
In this I need to extract "SANFRANSISCO"
MYREQUESTISTO8764GETTHISWITH&DEST=SANJOSE
In this I need to extract "SANJOSE"
I am reading a file line by line, and I need to update the text after &DEST= and put it back in the file. The modification of the text is to mask the dest value with X character.
So, SFO should be replaced with XXX.
SANJOSE should be replaced with XXXXXXX.
Output :
MYREQUESTISTO8764GETTHIS&DEST=XXX&ORIG=6546
MYREQUESTISTO8764GETTHIS&DEST=XXXXXXXXXXXX&ORIG=6546
MYREQUESTISTO8764GETTHISWITH&DEST=XXXXXXX
Please let me know how to achieve this in script (Preferably shell or bash script).
Thanks.
$ cat file
MYREQUESTISTO8764GETTHIS&DEST=SFO&ORIG=6546
MYREQUESTISTO8764GETTHIS&DEST=PORTORICA
MYREQUESTISTO8764GETTHIS&DEST=SANFRANSISCO&ORIG=6546
MYREQUESTISTO8764GETTHISWITH&DEST=SANJOSE
$ sed -E 's/^.*&DEST=([^&]*)[&]*.*$/\1/' file
SFO
PORTORICA
SANFRANSISCO
SANJOSE
should do it
Replacing airports with an equal number of Xs
Let's consider this test file:
$ cat file
MYREQUESTISTO8764GETTHIS&DEST=SFO&ORIG=6546
MYREQUESTISTO8764GETTHIS&DEST=SANFRANSISCO&ORIG=6546
MYREQUESTISTO8764GETTHISWITH&DEST=SANJOSE
To replace the strings after &DEST= with an equal length of X and using GNU sed:
$ sed -E ':a; s/(&DEST=X*)[^X&]/\1X/; ta' file
MYREQUESTISTO8764GETTHIS&DEST=XXX&ORIG=6546
MYREQUESTISTO8764GETTHIS&DEST=XXXXXXXXXXXX&ORIG=6546
MYREQUESTISTO8764GETTHISWITH&DEST=XXXXXXX
To replace the file in-place:
sed -i -E ':a; s/(&DEST=X*)[^X&]/\1X/; ta' file
The above was tested with GNU sed. For BSD (OSX) sed, try:
sed -Ee :a -e 's/(&DEST=X*)[^X&]/\1X/' -e ta file
Or, to change in-place with BSD(OSX) sed, try:
sed -i '' -Ee :a -e 's/(&DEST=X*)[^X&]/\1X/' -e ta file
If there is some reason why it is important to use the shell to read the file line-by-line:
while IFS= read -r line
do
echo "$line" | sed -Ee :a -e 's/(&DEST=X*)[^X&]/\1X/' -e ta
done <file
How it works
Let's consider this code:
search_str="&DEST="
newfile=chart.txt
sed -E ':a; s/('"$search_str"'X*)[^X&]/\1X/; ta' "$newfile"
-E
This tells sed to use Extended Regular Expressions (ERE). This has the advantage of requiring fewer backslashes to escape things.
:a
This creates a label a.
s/('"$search_str"'X*)[^X&]/\1X/
This looks for $search_str followed by any number of X followed by any character that is not X or &. Because of the parens, everything except that last character is saved into group 1. This string is replaced by group 1, denoted \1 and an X.
ta
In sed, t is a test command. If the substitution was made (meaning that some character needed to be replaced by X), then the test evaluates to true and, in that case, ta tells sed to jump to label a.
This test-and-jump causes the substitution to be repeated as many times as necessary.
Replacing multiple tags with one sed command
$ name='DEST|ORIG'; sed -E ':a; s/(&('"$name"')=X*)[^X&]/\1X/; ta' file
MYREQUESTISTO8764GETTHIS&DEST=XXX&ORIG=XXXX
MYREQUESTISTO8764GETTHIS&DEST=XXXXXXXXXXXX&ORIG=XXXX
MYREQUESTISTO8764GETTHISWITH&DEST=XXXXXXX
Answer for original question
Using shell
$ s='MYREQUESTISTO8764GETTHIS&DEST=SFO&ORIG=6546'
$ s=${s#*&DEST=}
$ echo ${s%%&*}
SFO
How it works:
${s#*&DEST=} is prefix removal. This removes all text up to and including the first occurrence of &DEST=.
${s%%&*} is suffix removal_. It removes all text from the first & to the end of the string.
Using awk
$ echo 'MYREQUESTISTO8764GETTHIS&DEST=SFO&ORIG=6546' | awk -F'[=\n]' '$1=="DEST"{print $2}' RS='&'
SFO
How it works:
-F'[=\n]'
This tells awk to treat either an equal sign or a newline as the field separator
$1=="DEST"{print $2}
If the first field is DEST, then print the second field.
RS='&'
This sets the record separator to &.
With GNU bash:
while IFS= read -r line; do
[[ $line =~ (.*&DEST=)(.*)((&.*|$)) ]] && echo "${BASH_REMATCH[1]}fooooo${BASH_REMATCH[3]}"
done < file
Output:
MYREQUESTISTO8764GETTHIS&DEST=fooooo&ORIG=6546
MYREQUESTISTO8764GETTHIS&DEST=fooooo&ORIG=6546
MYREQUESTISTO8764GETTHISWITH&DEST=fooooo
Replace the characters between &DEST and & (or EOL) with x's:
awk -F'&DEST=' '{
printf("%s&DEST=", $1);
xlen=index($2,"&");
if ( xlen == 0) xlen=length($2)+1;
for (i=0;i<xlen;i++) printf("%s", "X");
endstr=substr($2,xlen);
printf("%s\n", endstr);
}' file
I'm trying to extract the value present between brackets in the last row of a flat file e.g. " last_line (4) ". This is the last line and I want to extract 4 and store it in a variable. I have extracted the last row using tail command but now I am unable to extract the value between the brackets.
Kindly help.
Using awk:
$ cat input
first line
2nd line
last line (4) with some data
$ awk -F'[()]' 'END{print $2}' input
4
l=$(tail -n1 filename); tmp=${l##*(}; tmp=${tmp%)*}; printf "tmp: %s\n" $tmp
Output
tmp: 4
Written in script format, you are using substring removal to trim everything up to the first ( and everything after the last ) from the last line, leaving only 4:
l=$(tail -n1 filename) ## get the last line
tmp=${l##*(} ## trim to ( from left
tmp=${tmp%)*} ## trim to ) from right
printf "tmp: %s\n" $tmp
sed:
sed -n '${s/.*(//;s/).*//;p}' file
U can use this script.
In this script i saved the last line in a tmp file and at last removed it.
the number between the brackets() is in variable WORD
#!/bin/ksh
if test "${DEBUG}" = "Y"
then
set -vx
fi
tail -1 input>>tmp
WORD=`sed -n 's/.*(//;s/).*//;p' tmp`
echo $WORD
rm tmp
I'm doing a test with these files:
comp900_c0_seq1_Glicose_1_ACTTGA_merge_R1_001.fastq
comp900_c0_seq1_Glicose_1_ACTTGA_merge_R2_001.fastq
comp900_c0_seq2_Glicose_1_ACTTGA_merge_R1_001.fastq
comp900_c0_seq2_Glicose_1_ACTTGA_merge_R2_001.fastq
comp995_c0_seq1_Glicose_1_ACTTGA_merge_R2_001.fastq
comp995_c0_seq1_Xilano_1_AGTCAA_merge_R1_001.fastq
comp995_c0_seq1_Xilano_1_AGTCAA_merge_R2_001.fastq
I want to get the files that have the same code until the first _ (underscore) and have the code R1 in different output files. The output files should be called according with the code until the first _ (underscore).
-This is my code, but I'm having trouble on making the output files.
#!/bin/bash
for i in {900..995}; do
if [[ ${i} -eq ${i} ]]; then
cat comp${i}_*_R1_001.fastq
fi
done
-I want to have two outputs:
One output will have all lines from:
comp900_c0_seq1_Glicose_1_ACTTGA_merge_R1_001.fastq
comp900_c0_seq2_Glicose_1_ACTTGA_merge_R1_001.fastq
and its name should be comp900_R1.out
The other output will have lines from:
comp995_c0_seq1_Xilano_1_AGTCAA_merge_R1_001.fastq
and its name should be comp995_R1.out
Finally, as I said, this is a small test. I want my script to work with a lot of files that have the same characteristics.
Using awk:
ls -1 *.fastq | awk -F_ '$8 == "R1" {system("cat " $0 ">>" $1 "_R1.out")}'
List all files *.fastq into awk, splitting on _. Check if 8:th part $8 is R1, then append cat >> the file into first part $1 + _R1.out, which will be comp900_R1.out or comp995_R1.out. It is assumed that no filenames contain spaces or other special characters.
Result:
File comp900_R1.out containing all lines from
comp900_c0_seq1_Glicose_1_ACTTGA_merge_R1_001.fastq
comp900_c0_seq2_Glicose_1_ACTTGA_merge_R1_001.fastq
and file comp995_R1.out containing all lines from
comp995_c0_seq1_Xilano_1_AGTCAA_merge_R1_001.fastq
My stab at a general solution:
#!/bin/bash
for f in *_R1_*; do
code=$(echo $f | cut -d _ -f 1)
cat $f >> ${code}_c0_seq1_Glicose_1_ACTTGA_merge_R1_001.fastq
done
Iterates over files with _R1_ in it, then appends its output to a file based on code.
cut pulls out the code by splitting the filename (-d _) and returning the first field (-f 1).