I have a file called "text.bz2" which contains a number of records which i want to process. I have a script which successfully processes all the data in a standard text file and outputs the results to a different "results.txt" file, but the command I'm currently running outputs all the results of the bz2 file to the command prompt (like cat does), creates the results.txt file - but it is empty.
This is the cammand I'm running:
bzip2 -dc text.bz2 | awk ... '
'
> results.txt
The format of the data in the decompressed bz2 file is:
field1=xxx;field2=xxx;field3=111222222;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222222;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222333;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222444;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222555;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222555;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222777;field4=xxx;field5=xxx
field1=xxx;field2=xxx;field3=111222888;field4=xxx;field5=xxx
and the output is exactly as expected, as below, but instead of the results being output to a text file, it's output to the command window:
111222333 111
111222444 111
111222555 111
111222777 222
111222888 111
What am i doing wrong with my bzip / redirection command?
Many thanks
Put the > file at the end of the awk command, not on the line after it:
foo | awk 'script' > file
not
foo | awk 'script'
> file
Related
I have a script that extracts a file from a bash script combined with a binary file. It does so using the following GNU sed syntax
sed -n '/__DATA__/{n;:1;n;p;b1}' /tmp/combined.file > /tmp/binary.file
The files are assembled by cat'ing an ISO file to the end of a bash script. Which is then sent over the network to an embedded device and extracted on the device, piping the ISO file to a temporary dir and executing the bash script to install it.
However, on executing this I get a
sed: unterminated {
Am I missing something here? Is this task possible with BusyBox sed?
It tried the "Second attempt" below with OSX/BSD awk and it failed, just printing up til the first NUL character. So you can't do this job portably with awk or sed.
Here's what should work everywhere given that the POSIX standard says
the input file to tail can be any type
so the input to tail doesn't have to be a POSIX text file (no NULs) and we're exiting from awk before the first NUL is encountered in the input so they should both be happy:
$ tail -n +"$(awk '/^__DATA__$/{print NR+2; exit}' binary.bin)" binary.bin | cat -ev
ER^H^#^#^#M-^PM-^P^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#3��M-^Nռ^#|��f1�f1�fSfQ^FWM-^N�M-^N�R�^#|�^#^F�^#^A��K^F^#^#R�A��U1�0���^Sr^VM-^A�U�u^PM-^C�^At^Kf�^F�^F�B�^U�^B1�ZQ�^H�^S[^O��#PM-^C�?Q��SRP�^#|�^D^#f��^G�D^#^OM-^BM-^#^#f#M-^#�^B��fM-^A>#|��xpu ��{�D|^#^#�M-^C^#isolinux.bin missing or corrupt.^M$
f`f1�f^C^F�{f^S^V�{fRfP^FSj^Aj^PM-^I�f�6�{��^FM-^H�M-^H�M-^R�6�{M-^H�^H�A�^A^BM-^J^V�{�^SM-^Md^Pfa��^^^#Operating system load error.^M$
^��^NM-^J>b^D�^G�^P<$
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Second attempt:
Now that I have a better idea what you're trying to do (process a file consisting of POSIX text lines up to a point and then can contain NUL characters afterwards), try this:
$ cat -ev file
echo "I: Installation finished!"$
exit 0$
$
__DATA__$
$
foo^#bar^#etc
$ cat tst.awk
/^__DATA__$/ { n=NR + 1 }
n && (NR == n) { RS="\0"; ORS="" }
n && (NR > n) { print (c++ ? RS : "") $0 }
$ awk -f tst.awk file | cat -ev
foo^#bar^#etc
The above doesn't try to store any input lines containing NUL in memory, instead it reads \n-terminated text lines until it reaches the line after the one containing __DATA__ and then switches to reading NUL-terminated records into memory and printing NULs between them on output.
It's still undefined behavior per POSIX (see my comments below) but in theory it should work since it just relies on being able to set one variable (RS) to NUL rather than trying to store input strings that contain NULs. Also, setting RS to NUL has been a (flawed) workaround for awk scripts for years to be able to read a whole file into memory at once so being able to set RS to NUL should work in any modern awk.
Using the new sample you provided with the missing blank line after the __DATA__ line added:
$ cat -ev file
#!/bin/bash$
$
echo "I: Awesome Things happened here"$
exit 0$
$
__DATA__$
$
ER^H^#^#^#M-^PM-^P^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#3M-mM-zM-^NM-UM-<^#|M-{M-|f1M-[f1M-IfSfQ^FWM-^NM-]M-^NM-ERM->^#|M-?^#^FM-9^#^AM-sM-%M-jK^F^#^#RM-4AM-;M-*U1M-I0M-vM-yM-M^Sr^VM-^AM-{UM-*u^PM-^CM-a^At^KfM-G^FM-s^FM-4BM-k^UM-k^B1M-IZQM-4^HM-M^S[^OM-6M-F#PM-^CM-a?QM-wM-aSRPM-;^#|M-9^D^#fM-!M-0^GM-hD^#^OM-^BM-^#^#f#M-^#M-G^BM-bM-rfM-^A>#|M-{M-#xpu M-zM-<M-l{M-jD|^#^#M-hM-^C^#isolinux.bin missing or corrupt.^M$
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.
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ER^H^#^#^#M-^PM-^P^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#^#3M-mM-zM-^NM-UM-<^#|M-{M-|f1M-[f1M-IfSfQ^FWM-^NM-]M-^NM-ERM->^#|M-?^#^FM-9^#^AM-sM-%M-jK^F^#^#RM-4AM-;M-*U1M-I0M-vM-yM-M^Sr^VM-^AM-{UM-*u^PM-^CM-a^At^KfM-G^FM-s^FM-4BM-k^UM-k^B1M-IZQM-4^HM-M^S[^OM-6M-F#PM-^CM-a?QM-wM-aSRPM-;^#|M-9^D^#fM-!M-0^GM-hD^#^OM-^BM-^#^#f#M-^#M-G^BM-bM-rfM-^A>#|M-{M-#xpu M-zM-<M-l{M-jD|^#^#M-hM-^C^#isolinux.bin missing or corrupt.^M$
f`f1M-Rf^C^FM-x{f^S^VM-|{fRfP^FSj^Aj^PM-^IM-ffM-w6M-h{M-#M-d^FM-^HM-aM-^HM-EM-^RM-v6M-n{M-^HM-F^HM-aAM-8^A^BM-^J^VM-r{M-M^SM-^Md^PfaM-CM-h^^^#Operating system load error.^M$
^M-,M-4^NM-^J>b^DM-3^GM-M^P<$
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Original answer:
Assuming this question is related to your previous question, this will work using any awk in any shell on every UNIX box:
$ awk '/^__DATA__$/{n=NR+1} n && NR>n' file
3<ED>M-^PM-^PM-^PM-^PM-^
When it finds __DATA__ it sets a variable n to the line number to start printing after and then when n is set prints every line for which the line number is greater than n.
The above was run against this input file from your previous question:
$ cat -ev file
echo "I: Installation finished!"$
exit 0$
$
__DATA__$
$
3<ED>M-^PM-^PM-^PM-^PM-^$
I am attempting to convert the files with the titles {out1.hmm, out2.hmm, ... , outn.hmm} to unique identifiers based on the third line of the file {PF12574.hmm, PF09847.hmm, PF0024.hmm} The script works on a single file however the variable does not get overwritten and only one file remains after running the command below:
for f in *.hmm;
do output="$(sed -n '3p' < $f |
awk -F ' ' '{print $2}' |
cut -f1 -d '.' | cat)" |
mv $f "${output}".hmm; done;
The first line calls all the outn.hmms as an input. The second line sets a variable to return the desired unique identifier. SED, AWK, and CUT are used to get the unique identifier. The variable supposed to rename the current file by the unique identifier, however the variable remains locked and overwrites the previous file.
out1.hmm out2.hmm out3.hmm becomes PF12574.hmm
How can I overwrite the variable to get the following file structure:
out1.hmm out2.hmm out3.hmm becomes PF12574.hmm PF09847.hmm PF0024.hmm
You're piping the empty output of the assignment statement (to the variable named "output") into the mv command. That variable is not set yet, so what I think will happen is that you will - one after the other - rename all the files that match *.hmm to the file named ".hmm".
Try ls -a to see if that's what actually happened.
The sed, awk, cut, and (unneeded) cat are a bit much. awk can do all you need. Then do the mv as a separate command:
for f in *.hmm
do
output=$(awk 'NR == 3 {print $2}' "$f")
mv "$f" "${output%.*}.hmm"
done
Note that the above does not do any checking to verify that output is assigned to a reasonable value: one that is non-empty, that is a proper "identifier", etc.
I have seen several variations of this question, but none of the answers are helping for my particular scenario.
I am trying to load some files, adding a column for filename. This works fine only if I put the filename as the first column. If I put the filename column at the end (where I want it) it creates a new line between $0 and the rest of the print that I am unable to stop.
for f in "${FILE_LIST[#]}"
do
awk '{ print FILENAME,"\t",$0 } ' ${DEST_DIR_FILES}/$f > tmp ## this one works
awk '{ print $0,"\t",FILENAME } ' ${DEST_DIR_FILES}/$f > tmp ## this one does not work
mv tmp ${DEST_DIR_FILES}/$f
done > output
Example data:
-- I'm starting with this:
A B C
aaaa bbbb cccc
1111 2222 3333
-- I want this (new column with filename):
A B C FILENAME
aaaa bbbb cccc FILENAME
1111 2222 3333 FILENAME
-- I'm getting this (\t and filename on new line):
A B C
FILENAME
aaaa bbbb cccc
FILENAME
1111 2222 3333
FILENAME
Bonus question
I'm using a variable to pass the filename, but it is putting the whole path. What is the best way to only print the filename (without path) ~OR~ strip out the file path using a variable that holds the path?
It's almost certainly a line endings issues as your awk script a syntactically correct. I suspect your files in "${FILE_LIST[#]}" came from a Windows box and have \r\n line endings. To confirm the line endings for a given file you can run the file command on each file i.e. file filename:
# create a test file
$ echo test > foo
# use unix2dos to convert to Windows style line endings
$ unix2dos foo
unix2dos: converting file foo to DOS format ...
# Use file to confirm line endings
$ file foo
foo: ASCII text, with CRLF line terminators
# Convert back to Unix style line endings
$ dos2unix foo
dos2unix: converting file foo to Unix format ...
$ file foo
foo: ASCII text
To convert your files to Unix style line endings \n run the following command:
$ for "f" in "${FILE_LIST[#]}"; do; dos2unix "$f"; done
Explanation:
When the FILENAME is the first string on the line the carriage returns \r effectively does nothing as we are already at the start of the line. When we try to print FILENAME after any other characters we see the effects that we are brought to the start of the next line, the TAB is printed then the FILENAME.
Side note:
Awk has the variable OFS for setting the output field separator so:
$ awk '{print $0,"\t",FILENAME}' file
Can be rewritten as:
$ awk '{print $0,FILENAME}' OFS='\t' file
Bonus Answer
The best way I.M.O to strip the path of file is to use the utility basename:
$ basename /tmp/foo
foo
Using command substitution:
$ awk '{print FILENAME}' $(basename /tmp/foo)
foo
I have 100 files and want to search a specific word in the first column of each file and print the content of all columns from this word to a new file
I tried this code but doesn't work well it prints only the content of one file not all:
ls -t *.txt > Filelist.tmp
cat Filelist.tmp | while read line do; grep "searchword" | awk '{print $0}' > outputfile.txt; done
This is what you want:
$ awk '$1~/searchword/' *.txt >> output
This compares the first field against searchword and appends the line to output if it matches. The default field separator with awk is whitespace.
The main problem with your attempt is you are overwriting > the file evertime, you want to be using append >>.
How to get the first few lines from a gziped file ?
I tried zcat, but its throwing an error
zcat CONN.20111109.0057.gz|head
CONN.20111109.0057.gz.Z: A file or directory in the path name does not exist.
zcat(1) can be supplied by either compress(1) or by gzip(1). On your system, it appears to be compress(1) -- it is looking for a file with a .Z extension.
Switch to gzip -cd in place of zcat and your command should work fine:
gzip -cd CONN.20111109.0057.gz | head
Explanation
-c --stdout --to-stdout
Write output on standard output; keep original files unchanged. If there are several input files, the output consists of a sequence of independently compressed members. To obtain better compression, concatenate all input files before compressing
them.
-d --decompress --uncompress
Decompress.
On some systems (e.g., Mac), you need to use gzcat.
On a mac you need to use the < with zcat:
zcat < CONN.20111109.0057.gz|head
If a continuous range of lines needs be, one option might be:
gunzip -c file.gz | sed -n '5,10p;11q' > subFile
where the lines between 5th and 10th lines (both inclusive) of file.gz are extracted into a new subFile. For sed options, refer to the manual.
If every, say, 5th line is required:
gunzip -c file.gz | sed -n '1~5p;6q' > subFile
which extracts the 1st line and jumps over 4 lines and picks the 5th line and so on.
If you want to use zcat, this will show the first 10 rows
zcat your_filename.gz | head
Let's say you want the 16 first row
zcat your_filename.gz | head -n 16
This awk snippet will let you show not only the first few lines - but a range you can specify. It will also add line numbers which i needed for debugging an error message pointing to a certain line way down in a gzipped file.
gunzip -c file.gz | awk -v from=10 -v to=20 'NR>=from { print NR,$0; if (NR>=to) exit 1}'
Here is the awk snippet used in the one liner above. In awk NR is a built-in variable (Number of records found so far) which usually is equivalent to a line number. the from and to variable are picked up from the command line via the -v options.
NR>=from {
print NR,$0;
if (NR>=to)
exit 1
}