I am working with the set of txt file containing multi column information present in one line. Within my bash script I use the following AWK expression to take the filename from each of the txt filles as well as the number from the 5th column and save it in 2 column format in results.CSV file (piped to SED, which remove path of the file and its extension from the final CSV file):
awk '-F, *' '{if(FNR==2) printf("%s| %s \n", FILENAME,$5) }' ${tmp}/*.txt | sed 's|\/Users/gleb/Desktop/scripts/clusterizator/tmp/||; s|\.txt||' >> ${home}/"${experiment}".csv
obtaining something (for 5 txt filles) like this as CSV:
lig177_cl_5.2| -0.1400
lig331_cl_3.5| -8.0000
lig394_cl_1.9| -4.3600
lig420_cl_3.8| -5.5200
lig550_cl_2.0| -4.3200
How it would be possible to modify my AWK expression in order to exclude "_cl_x.x" from the name of each txt file as well as add the name of the CSV as the comment to the first line of the resulted CSV file:
# results.CSV
lig177| -0.1400
lig331| -8.0000
lig394| -4.3600
lig420| -5.5200
lig550| -4.3200
based on the rest of the pipe, I think you want to do something like this and get rid of sed invocations.
awk -F', *' 'FNR==2 {f=FILENAME;
sub(/.*\//,"",f);
sub(/_.*/ ,"",f);
printf("%s| %s\n", f, $5) }' "${tmp}"/*.txt >> "${home}/${experiment}.csv"
this will convert
/Users/gleb/Desktop/scripts/clusterizator/tmp/lig177_cl_5.2.txt
to
lig177
The pattern replacement is generic
/path/to/the/file/filename_otherstringshere...
will extract only filename. From the last / char to the first _ char. This is based the greedy matching of regex patterns.
For the output filename, it's easier to do it before awk call, since it's a one line only.
$ echo "${experiment}.csv" > "${home}/${experiment}.csv"
$ awk ... >> "${home}/${experiment}.csv"
Related
I have scenario where we want to replace multiple double quotes to single quotes between the data, but as the input data is separated with "comma" delimiter and all column data is enclosed with double quotes "" got an issue and the same explained below:
The sample data looks like this:
"int","","123","abd"""sf123","top"
So, the output would be:
"int","","123","abd"sf123","top"
tried below approach to get the resolution, but only first occurrence is working, not sure what is the issue??
sed -ie 's/,"",/,"NULL",/g;s/""/"/g;s/,"NULL",/,"",/g' inputfile.txt
replacing all ---> from ,"", to ,"NULL",
replacing all multiple occurrences of ---> from """ or "" or """" to " (single occurrence)
replacing 1 step changes back to original ---> from ,"NULL", to ,"",
But, only first occurrence is getting changed and remaining looks same as below:
If input is :
"int","","","123","abd"""sf123","top"
the output is coming as:
"int","","NULL","123","abd"sf123","top"
But, the output should be:
"int","","","123","abd"sf123","top"
You may try this perl with a lookahead:
perl -pe 's/("")+(?=")//g' file
"int","","123","abd"sf123","top"
"int","","","123","abd"sf123","top"
"123"abcs"
Where input is:
cat file
"int","","123","abd"""sf123","top"
"int","","","123","abd"""sf123","top"
"123"""""abcs"
Breakup:
("")+: Match 1+ pairs of double quotes
(?="): If those pairs are followed by a single "
Using sed
$ sed -E 's/(,"",)?"+(",)?/\1"\2/g' input_file
"int","","123","abd"sf123","top"
"int","","NULL","123","abd"sf123","top"
"int","","","123","abd"sf123","top"
In awk with your shown samples please try following awk code. Written and tested in GNU awk, should work in any version of awk.
awk '
BEGIN{ FS=OFS="," }
{
for(i=1;i<=NF;i++){
if($i!~/^""$/){
gsub(/"+/,"\"",$i)
}
}
}
1
' Input_file
Explanation: Simple explanation would be, setting field separator and output field separator as , for all the lines of Input_file. Then traversing through each field of line, if a field is NOT NULL then Globally replacing all 1 or more occurrences of " with single occurrence of ". Then printing the line.
With sed you could repeat 1 or more times sets of "" using a group followed by matching a single "
Then in the replacement use a single "
sed -E 's/("")+"/"/g' file
For this content
$ cat file
"int","","123","abd"""sf123","top"
"int","","","123","abd"""sf123","top"
"123"""""abcs"
The output is
"int","","123","abd"sf123","top"
"int","","","123","abd"sf123","top"
"123"abcs"
sed s'#"""#"#' file
That works. I will demonstrate another method though, which you may also find useful in other situations.
#!/bin/sh -x
cat > ed1 <<EOF
3s/"""/"/
wq
EOF
cp file stack
cat stack | tr ',' '\n' > f2
ed -s f2 < ed1
cat f2 | tr '\n' ',' > stack
rm -v ./f2
rm -v ./ed1
The point of this is that if you have a big csv record all on one line, and you want to edit a specific field, then if you know the field number, you can convert all the commas to carriage returns, and use the field number as a line number to either substitute, append after it, or insert before it with Ed; and then re-convert back to csv.
I have a file named file.txt
$cat file.txt
1./abc/cde/go/ftg133333.jpg
2./abc/cde/go/ftg24555.jpg
3./abc/cde/go/ftg133333.gif
4./abt/cte/come/ftg24555.jpg
5./abc/cde/go/ftg133333.jpg
6./abc/cde/go/ftg24555.pdf
MY GOAL: To get only one line from lines who's first, second and third PATH are the same and have the same file EXTENSION.
Note each PATH is separated by forward slash "/". Eg in the first line of the list, the first PATH is abc, second PATH is cde and third PATH is go.
File EXTENSION is .jpg, .gif,.pdf... always at the end of the line.
HERE IS WHAT I TRIED
sort -u -t '/' -k1 -k2 -k3
My thoughts
Using / as a delimiter gives me 4 fields in each line. Sorting them with "-u" will remove all but 1 line with unique First, Second and 3rd field/PATH. But obviously, I didn't take into account the EXTENSION(jpg,pdf,gif) in this case.
MY QUESTION
I need a way to grep only 1 of the lines if the first, second and third field are same and have the same EXTENSION using "/" as delimiter to divide it into fields. I want to output it to a another file, say file2.txt.
In the file2.txt, how do I add a word say "KALI" before the extension in each line, so it will look something like /abc/cde/go/ftg13333KALI.jpg using line 1 as an example in file.txt above.
Desired Output
/abc/cde/go/ftg133333KALI.jpg
/abt/cte/come/ftg24555KALI.jpg
/abc/cde/go/ftg133333KALI.gif
/abc/cde/go/ftg24555KALI.pdf
COMMENT
Line 1,2 & 5 have the same 1st,2nd and 3rd field, with same file extension
".jpg" so only line 1 should be in the output.
Line 3 is in the output even though it has same 1st,2nd and 3rd field with
1,2 and 5, because the extension is different ".gif".
Line 4 has different 1st, 2nd and 3rd field, hence it in output.
Line 6 is in the output even though it has same 1st,2nd and 3rd field with
1,2 and 5, because the extension is different ".pdf".
$ awk '{ # using awk
n=split($0,a,/\//) # split by / to get all path components
m=split(a[n],b,".") # split last by . to get the extension
}
m>1 && !seen[a[2],a[3],a[4],b[m]]++ { # if ext exists and is unique with 3 1st dirs
for(i=2;i<=n;i++) # loop component parts and print
printf "/%s%s",a[i],(i==n?ORS:"")
}' file
Output:
/abc/cde/go/ftg133333.jpg
/abc/cde/go/ftg133333.gif
/abt/cte/come/ftg24555.jpg
/abc/cde/go/ftg24555.pdf
I split by / separately from .s in case there are .s in dir names.
Missed the KALI part:
$ awk '{
n=split($0,a,/\//)
m=split(a[n],b,".")
}
m>1&&!seen[a[2],a[3],a[4],b[m]]++ {
for(i=2;i<n;i++)
printf "/%s",a[i]
for(i=1;i<=m;i++)
printf "%s%s",(i==1?"/":(i==m?"KALI.":".")),b[i]
print ""
}' file
Output:
/abc/cde/go/ftg133333KALI.jpg
/abc/cde/go/ftg133333KALI.gif
/abt/cte/come/ftg24555KALI.jpg
/abc/cde/go/ftg24555KALI.pdf
Using awk:
$ awk -F/ '{ split($5, ext, "\\.")
if (!(($2,$3,$4,ext[2]) in files)) files[$2,$3,$4,ext[2]]=$0
}
END { for (f in files) {
sub("\\.", "KALI.", files[f])
print files[f]
}}' input.txt
/abt/cte/come/ftg24555KALI.jpg
/abc/cde/go/ftg133333KALI.gif
/abc/cde/go/ftg24555KALI.pdf
/abc/cde/go/ftg133333KALI.jpg
another awk
$ awk -F'[./]' '!a[$2,$3,$4,$NF]++' file
/abc/cde/go/ftg133333.jpg
/abc/cde/go/ftg133333.gif
/abt/cte/come/ftg24555.jpg
/abc/cde/go/ftg24555.pdf
assumes . doesn't exist in directory names (not necessarily true in general).
XYZNA0000778800Z
16123000012300321000000008000000000000000
16124000012300322000000007000000000000000
17234000012300323000000005000000000000000
17345000012300324000000004000000000000000
17456000012300325000000003000000000000000
9
XYZNA0000778900Z
16123000012300321000000008000000000000000
16124000012300322000000007000000000000000
17234000012300323000000005000000000000000
17345000012300324000000004000000000000000
17456000012300325000000003000000000000000
9
I have above file format from which I want to find a matching record. For example, match a number(7789) on line starting with XYZ and once matched look for a matching number (7345) in lines below starting with 1 until it reaches to line starting with 9. retrieve the entire line record. How can I accomplish this using shell script, awk, sed or any combination.
Expected Output:
XYZNA0000778900Z
17345000012300324000000004000000000000000
With sed one can do:
$ sed -n '/^XYZ.*7789/,/^9$/{/^1.*7345/p}' file
17345000012300324000000004000000000000000
Breakdown:
sed -n ' ' # -n disabled automatic printing
/^XYZ.*7789/, # Match line starting with XYZ, and
# containing 7789
/^1.*7345/p # Print line starting with 1 and
# containing 7345, which is coming
# after the previous match
/^9$/ { } # Match line that is 9
range { stuff } will execute stuff when it's inside range, in this case the range is starting at /^XYZ.*7789/ and ending with /^9$/.
.* will match anything but newlines zero or more times.
If you want to print the whole block matching the conditions, one can use:
$ sed -n '/^XYZ.*7789/{:s;N;/\n9$/!bs;/\n1.*7345/p}' file
XYZNA0000778900Z
16123000012300321000000008000000000000000
16124000012300322000000007000000000000000
17234000012300323000000005000000000000000
17345000012300324000000004000000000000000
17456000012300325000000003000000000000000
9
This works by reading lines between ^XYZ.*7779 and ^9$ into the pattern
space. And then printing the whole thing if ^1.*7345 can be matches:
sed -n ' ' # -n disables printing
/^XYZ.*7789/{ } # Match line starting
# with XYZ that also contains 7789
:s; # Define label s
N; # Append next line to pattern space
/\n9$/!bs; # Goto s unless \n9$ matches
/\n1.*7345/p # Print whole pattern space
# if \n1.*7345 matches
I'd use awk:
awk -v rid=7789 -v fid=7345 -v RS='\n9\n' -F '\n' 'index($1, rid) { for(i = 2; i < $NF; ++i) { if(index($i, fid)) { print $i; next } } }' filename
This works as follows:
-v RS='\n9\n' is the meat of the whole thing. Awk separates its input into records (by default lines). This sets the record separator to \n9\n, which means that records are separated by lines with a single 9 on them. These records are further separated into fields, and
-F '\n' tells awk that fields in a record are separated by newlines, so that each line in a record becomes a field.
-v rid=7789 -v fid=7345 sets two awk variables rid and fid (meant by me as record identifier and field identifier, respectively. The names are arbitrary.) to your search strings. You could encode these in the awk script directly, but this way makes it easier and safer to replace the values with those of a shell variables (which I expect you'll want to do).
Then the code:
index($1, rid) { # In records whose first field contains rid
for(i = 2; i < $NF; ++i) { # Walk through the fields from the second
if(index($i, fid)) { # When you find one that contains fid
print $i # Print it,
next # and continue with the next record.
} # Remove the "next" line if you want all matching
} # fields.
}
Note that multi-character record separators are not strictly required by POSIX awk, and I'm not certain if BSD awk accepts it. Both GNU awk and mawk do, though.
EDIT: Misread question the first time around.
an extendable awk script can be
$ awk '/^9$/{s=0} s&&/7345/; /^XYZ/&&/7789/{s=1} ' file
set flag s when line starts with XYZ and contains 7789; reset when line is just 9, and print when flag is set and contains pattern 7345.
This might work for you (GNU sed):
sed -n '/^XYZ/h;//!H;/^9/!b;x;/^XYZ[^\n]*7789/!b;/7345/p' file
Use the option -n for the grep-like nature of sed. Gather up records beginning with XYZ and ending in 9. Reject any records which do not have 7789 in the header. Print any remaining records that contain 7345.
If the 7345 will always follow the header,this could be shortened to:
sed -n '/^XYZ/h;//!H;/^9/!b;x;/^XYZ[^\n]*7789.*7345/p' file
If all records are well-formed (begin XYZ and end in 9) then use:
sed -n '/^XYZ/h;//!H;/^9/!b;x;/^[^\n]*7789.*7345/p' file
I've read a couple of other questions about this, but none of them seem to be working. I'm currently trying to split something like file A.txt using the delimiter "STOPHERE".
This is the code:
#!/bin/bash
awk 'BEGIN{
RS = "STOPHERE"
file = 0}
{
file++
print $0 > ("sepf" file)
}' A.txt
File A:
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa lwdjnuqqfqaaaaaaaaaa qlknfqek fkgnl efekfnwegelflfne
ldnwefne f STOPHEREsdfnkjnf nnnnnnnnnnnnnnnnnnnnnnnasd fefffffffffffffflllo
aldn3orn STOPHERE
fknjke bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbowqff STOPHERE i
asfjfenf STOPHERE
Into these:
sepf1:
aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa lwdjnuqqfqaaaaaaaaaa qlknfqek fkgnl efekfnwegelflfne
ldnwefne f
sepf2:
sdfnkjnf nnnnnnnnnnnnnnnnnnnnnnnasd fefffffffffffffflllo
aldn3orn
sepf3:
#line starts here
fknjke bbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbbowqff
sepf4:
i
asfjfenf
So basically, the formatting has to stay exactly the same between the STOPHERE.
But for some reason, this is the kind of output I'm getting in some of the files:
Eg: sepf2
TOPHEREsdfnkjnf nnnnnnnnnnnnnnnnnnnnnnnasd fefffffffffffffflllo
aldn3orn
Any ideas as to why the "TOPHERE" remains??
GNU awk allows RS to be a regex. So you can provide multiple characters as a record separator. Your code can also be simplified as AWK provides a default value of 0.
So this will generate separate files for each record.
awk -v RS="STOPHERE" '{print $0 > ("sepf" ++file)}'
I have a data file which looks like the following:
0.00000-130250.92921 28880.20200-159131.13121 301.58706
0.05000-130250.73120 28156.69202-158407.42322 294.03167
0.10000-130250.79137 28237.16138-158487.95275 294.87198
0.15000-130250.81209 28168.63042-158419.44250 294.15634
0.20000-130250.82418 28149.57611-158400.40029 293.95736
0.25000-130250.88438 28069.57135-158320.45573 293.12189
0.30000-130251.06059 28071.30576-158322.36635 293.14000
0.35000-130250.96639 28084.46351-158335.42990 293.27741
as you can see some of the columns which start with "-" sign are
joined to the previous one, for instance: 0.35000-130250.96639
this should be 0.35000 and -130250.96639. I can separate the
columns with VIM but I wanted to know if it is possible to do that
with AWK.
Thanks.
You can use sed: replace each - with a space and -:
sed -e 's/-/ -/g' input > output
The /g means globally, i.e. it replaces all occurrences on each line, not just the first one.
Using just awk
awk '{ gsub("-"," -") ; print }'