Bash script to list files periodically - linux

I have a huge set of files, 64,000, and I want to create a Bash script that lists the name of files using
ls -1 > file.txt
for every 4,000 files and store the resulted file.txt in a separate folder. So, every 4000 files have their names listed in a text files that is stored in a folder. The result is
folder01 contains file.txt that lists files #0-#4000
folder02 contains file.txt that lists files #4001-#8000
folder03 contains file.txt that lists files #8001-#12000
.
.
.
folder16 contains file.txt that lists files #60000-#64000
Thank you very much in advance

You can try
ls -1 | awk '
{
if (! ((NR-1)%4000)) {
if (j) close(fnn)
fn=sprintf("folder%02d",++j)
system("mkdir "fn)
fnn=fn"/file.txt"
}
print >> fnn
}'
Explanation:
NR is the current record number in awk, that is: the current line number.
NR starts at 1, on the first line, so we subtract 1 such that the if statement is true for the first line
system calls an operating system function from within awk
print in itself prints the current line to standard output, we can redirect (and append) the output to the file using >>
All uninitialized variables in awk will have a zero value, so we do not need to say j=0 in the beginning of the program

This will get you pretty close;
ls -1 | split -l 4000 -d - folder
Run the result of ls through split, breaking every 4000 lines (-l 4000), using numeric suffixes (-d), from standard input (-) and start the naming of the files with folder.
Results in folder00, folder01, ...

Here an exact solution using awk:
ls -1 | awk '
(NR-1) % 4000 == 0 {
dir = sprintf("folder%02d", ++nr)
system("mkdir -p " dir);
}
{ print >> dir "/file.txt"} '

There are already some good answers above, but I would also suggest you take a look at the watch command. This will re-run a command every n seconds, so you can, well, watch the output.

Related

Renaming Sequentially Named Files with Date Embedded

The Situation:
I have hundreds of zip files with an arbitrary date/time mixed into its name (4-6-2021 12-34-09 AM.zip). I need to get all of these files in order such that (0.zip, 1.zip 2.zip etc) with in a Linux cli system.
What I've tried:
I've tried ls -tr | while read i; do n=$((n+1)); mv -- "$i" "$(printf '%03d' "$n").zip"; done which almost does what I want but still seems to be out of order (I think its taking the order of when the file was created rather than the filename (which is what I need)).
If I can get this done, my next step would be to rename the file (yes a single file) in each zip to the name of the zip file. I'm not sure how I'd go about this either.
tl;dr
I have these files named with a weird date system. I need the date to be in order and renamed sequentially like 0.zip 1.zip 2.zip etc. It's 3:00 AM and I don't know why I'm up still trying to solve this and I have no idea how I'll rename the files in the zips to that sequential number (read above for more detail on this).
Thanks in advance!
GNU awk is an option here, redirecting the result of the file listing back into awk:
awk '{
fil=$0; # Set a variable fil to the line
gsub("-"," ",$1); # Replace "-" for " " in the first space delimited field
split($1,map," "); # Split the first field into the array map, using " " as the delimiter
if (length(map[1])==1) {
map[1]="0"map[1] # If the length of the day is 1, pad out with "0"
};
if (length(map[2])==1) {
map[2]="0"map[2] # Do the same for month
}
$1=map[1]" "map[2]" "map[3]; # Rebuilt first field based on array values
gsub("-"," ",$2); # Change "-" for " " in time
map1[mktime($1" "$2)]=fil # Get epoch format of date/time using mktime function and use this as an index for array map1 with the original line (fil) as the value
}
END {
PROCINFO["sorted_in"]="#ind_num_asc"; # At the end of processing, set the array sorting to index number ascending
cnt=0; # Initialise a cnt variable
for (i in map1) {
print "mv \""map1[i]"\" \""cnt".zip\""; # Loop through map1 array printing values and using these values along with cnt to generate and print move command
cnt++
}
}' <(for fil in *AM.zip;do echo $fil;done)
Once you are happy with the way the print command are printed, pipe the result into bash and so:
awk '{ fil=$0;gsub("-"," ",$1);split($1,map," ");if (length(map[1])==1) { map[1]="0"map[1] };if (length(map[2])==1) { map[2]="0"map[2] }$1=map[1]" "map[2]" "map[3];gsub("-"," ",$2);map1[mktime($1" "$2)]=fil} END { PROCINFO["sorted_in"]="#ind_num_asc";cnt=0;for (i in map1) { print "mv \""map1[i]"\" \""cnt".zip\"";cnt++ } }' <(for fil in *AM.zip;do echo $fil;done) | bash

Using awk to delete multiple lines using argument passed on via function

My input.csv file is semicolon separated, with the first line being a header for attributes. The first column contains customer numbers. The function is being called through a script that I activate from the terminal.
I want to delete all lines containing the customer numbers that are entered as arguments for the script. EDIT: And then export the file as a different file, while keeping the original intact.
bash deleteCustomers.sh 1 3 5
Currently only the last argument is filtered from the csv file. I understand that this is happening because the output file gets overwritten each time the loop runs, restoring all previously deleted arguments.
How can I match all the lines to be deleted, and then delete them (or print everything BUT those lines), and then output it to one file containing ALL edits?
delete_customers () {
echo "These customers will be deleted: "$#""
for i in "$#";
do
awk -F ";" -v customerNR=$i -v input="$inputFile" '($1 != customerNR) NR > 1 { print }' "input.csv" > output.csv
done
}
delete_customers "$#"
Here's some sample input (first piece of code is the first line in the csv file). In the output CSV file I want the same formatting, with the lines for some customers completely deleted.
Klantnummer;Nationaliteit;Geslacht;Title;Voornaam;MiddleInitial;Achternaam;Adres;Stad;Provincie;Provincie-voluit;Postcode;Land;Land-voluit;email;gebruikersnaam;wachtwoord;Collectief ;label;ingangsdatum;pakket;aanvullende verzekering;status;saldo;geboortedatum
1;Dutch;female;Ms.;Josanne;S;van der Rijst;Bliek 189;Hellevoetsluis;ZH;Zuid-Holland;3225 XC;NL;Netherlands;JosannevanderRijst#dayrep.com;Sourawaspen;Lae0phaxee;Klant;CZ;11-7-2010;best;tand1;verleden;-137;30-12-1995
2;Dutch;female;Mrs.;Inci;K;du Bois;Castorweg 173;Hengelo;OV;Overijssel;7557 KL;NL;Netherlands;InciduBois#gustr.com;Hisfireeness;jee0zeiChoh;Klant;CZ;30-8-2015;goed ;geen;verleden;188;1-8-1960
3;Dutch;female;Mrs.;Lusanne;G;Hijlkema;Plutostraat 198;Den Haag;ZH;Zuid-Holland;2516 AL;NL;Netherlands;LusanneHijlkema#dayrep.com;Digum1969;eiTeThun6th;Klant;Achmea;12-2-2010;best;mix;huidig;-335;9-3-1973
4;Dutch;female;Dr.;Husna;M;Hoegee;Tiendweg 89;Ameide;ZH;Zuid-Holland;4233 VW;NL;Netherlands;HusnaHoegee#fleckens.hu;Hatimon;goe5OhS4t;Klant;VGZ;9-8-2015;goed ;gezin;huidig;144;12-8-1962
5;Dutch;male;Mr.;Sieds;D;Verspeek;Willem Albert Scholtenstraat 38;Groningen;GR;Groningen;9711 XA;NL;Netherlands;SiedsVerspeek#armyspy.com;Thade1947;Taexiet9zo;Intern;CZ;17-2-2004;beter;geen;verleden;-49;12-10-1961
6;Dutch;female;Ms.;Nazmiye;R;van Spronsen;Noorderbreedte 180;Amsterdam;NH;Noord-Holland;1034 PK;NL;Netherlands;NazmiyevanSpronsen#jourrapide.com;Whinsed;Oz9ailei;Intern;VGZ;17-6-2003;beter;mix;huidig;178;8-3-1974
7;Dutch;female;Ms.;Livia;X;Breukers;Everlaan 182;Veenendaal;UT;Utrecht;3903
Try this in loop..
awk -v variable=$var '$1 != variable' input.csv
awk - to make decision based on columns
-v - to use a variable into a awk command
variable - store the value for awk to process
$var - to search for a specific string in run-time
!= - to check if not exist
input.csv - your input file
It's awk's behavior, when you use -v it can will work with variable on run-time and provide an output that doesn't contain the value you passed. This way, you get all the values that are not matching to your variable. Hope this is helpful. :)
Thanks
This bash script should work:
!/bin/bash
FILTER="!/(^"$(echo "$#" | sed -e "s/ /\|^/g")")/ {print}"
awk "$FILTER" input.csv > output.csv
The idea is to build an awk relevant FILTER and then use it.
Assuming the call parameters are: 1 2 3, the filter will be: !/(^1|^2|^3)/ {print}
!: to invert matching
^: Beginning of the line
The input data are in the input.csv file and output result will be in the output.csv file.

How to make while read faster (how to use grep instead)

I have a file named "compare" and a file named "final_contigs_c10K.fa"
I want to eleminate lines AND THE NEXT LINE from "final_contigs_c10K.fa" containing specific strings in "compare".
compare looks like this :
k119_1
k119_3
...
and the number of lines of compare is 26364.
final_contigs_c10K.fa looks like :
>k119_1
AAAACCCCC
>k119_2
CCCCC
>k119_3
AAAAAAAA
...
I want to make make final_contigs_c10K.fa into a format :
>k119_1
AAAACCCCC
>k119_3
AAAAAAAA
...
I tried this code, but this code takes too much time, though it seems to be working fine. I think it takes too much time because the number of lines in compare is 26364, which is too much compared to my other files that I had tested the code on.
while read line; do sed -i -e "/$line/ { N; d; }" final_contigs_c10K.fa; done < compare
Is there a way to make this command faster?
Using awk
$ awk 'NR==FNR{a[">" $1];next}$1 in a{p=3} --p>0' compare final_contigs_c10K.fa
>k119_1
AAAACCCCC
>k119_3
AAAAAAAA
This will produce the output to stdout ie. won't make any changes to original files.
Explained:
$ awk '
NR==FNR { # process the first file
a[">" $1] # hash to a, adding > while at it
next # process the next record
} # process th second file after this point
$1 in a { p=3 } # if current record was in compare file set p
--p>0 # print current file match and the next record
' compare final_contigs_c10K.fa # mind the file order

How to display line numbers when comparing files with linux "comm" tool

I would like to diff two very large files (multi-GB), using linux command line tools, and see the line numbers of the differences. The order of the data matters.
I am running on a Linux machine and the standard diff tool gives me the "memory exhausted" error. -H had no effect.
In my application, I only need to stream the diff results. That is, I just want to visually look at the first few differences, I don't need to inspect the entire file. If there are differences, a quick glance will tell me what is wrong.
'comm' seems well suited to this, but it does not display line numbers of the differences.
In general, my multi-GB files only have a few hundred lines that are different, the rest of the file is the same.
Is there a way to get comm to dump the line number? Or a way to make diff run without loading the entire file into memory? (like cutting the input files into 1k blocks, without actually creating a million 1k-files in my filesystem and cluttering everything up)?
I won't use comm, but as you said WHAT you need, in addition to HOW you thought you should do it, I'll focus on the "WHAT you need" instead :
An interesting way would be to use paste and awk : paste can show 2 files "side by side" using a separator. If you use \n as separator, it display the 2 files with line 1 of each , followed by line 2 of each etc.
So the script you could use could be simply (once you know that there are the same number of lines in each files) :
paste -d '\n' /tmp/file1 /tmp/file2 | awk '
NR%2 { linefirstfile=$0 ; }
!(NR%2) { if ( $0 != linefirstfile )
{ print "line",NR/2,": "; print linefirstfile ; print $0 ; } }'
(Interrestingly, this solution will allow be easily extended to do a diff of N files in a single read, whatever the sizes of the N files are ... just adding a check that all have the same amount of lines before doing the comparison steps (otherwise "paste" will in the end show only lines from the bigger files))
Here is a (short) example, to show how it works:
$ cat > /tmp/file1
A
C %FORGOT% fmsdflmdflskdf dfldksdlfkdlfkdlkf
E
$ cat > /tmp/file2
A
C sdflmsdflmsdfsklmdfksdmfksd fmsdflmdflskdf dfldksdlfkdlfkdlkf
E
$ paste -d '\n' /tmp/file1 /tmp/file2
A
A
C %FORGOT% fmsdflmdflskdf dfldksdlfkdlfkdlkf
C sdflmsdflmsdfsklmdfksdmfksd fmsdflmdflskdf dfldksdlfkdlfkdlkf
E
E
$ paste -d '\n' /tmp/file1 /tmp/file2 | awk '
NR%2 { linefirstfile=$0 ; }
!(NR%2) { if ( $0 != linefirstfile )
{ print "line",NR/2,": "; print linefirstfile ; print $0 ; } }'
line 2 :
C %FORGOT% fmsdflmdflskdf dfldksdlfkdlfkdlkf
C sdflmsdflmsdfsklmdfksdmfksd fmsdflmdflskdf dfldksdlfkdlfkdlkf
If it happens that the files don't have the same amount of lines, then you can add first a check of the number of line, comparing $(wc -l /tmp/file1) and $(wc -l /tmp/file2) , and only do the past...|awk if they have the same amount of line, to ensure the "paste" works correctly by always having one line of each! (But of course, in that case, there will be one (fast!) entire read of each file...)
You can easily adjust it to display exactly as you need it to. And you could quit after the Nth difference (either automatically, with a counter in the awk loop, or by pressing CTRL-C when you saw enough)
Which versions of diff have you tried? GNU diff has a "--speed-large-files" which may help.
The comm tool assumes the lines are sorted.

How to remove the lines which appear on file B from another file A?

I have a large file A (consisting of emails), one line for each mail. I also have another file B that contains another set of mails.
Which command would I use to remove all the addresses that appear in file B from the file A.
So, if file A contained:
A
B
C
and file B contained:
B
D
E
Then file A should be left with:
A
C
Now I know this is a question that might have been asked more often, but I only found one command online that gave me an error with a bad delimiter.
Any help would be much appreciated! Somebody will surely come up with a clever one-liner, but I'm not the shell expert.
If the files are sorted (they are in your example):
comm -23 file1 file2
-23 suppresses the lines that are in both files, or only in file 2. If the files are not sorted, pipe them through sort first...
See the man page here
grep -Fvxf <lines-to-remove> <all-lines>
works on non-sorted files (unlike comm)
maintains the order
is POSIX
Example:
cat <<EOF > A
b
1
a
0
01
b
1
EOF
cat <<EOF > B
0
1
EOF
grep -Fvxf B A
Output:
b
a
01
b
Explanation:
-F: use literal strings instead of the default BRE
-x: only consider matches that match the entire line
-v: print non-matching
-f file: take patterns from the given file
This method is slower on pre-sorted files than other methods, since it is more general. If speed matters as well, see: Fast way of finding lines in one file that are not in another?
Here's a quick bash automation for in-line operation:
remove-lines() (
remove_lines="$1"
all_lines="$2"
tmp_file="$(mktemp)"
grep -Fvxf "$remove_lines" "$all_lines" > "$tmp_file"
mv "$tmp_file" "$all_lines"
)
GitHub upstream.
usage:
remove-lines lines-to-remove remove-from-this-file
See also: https://unix.stackexchange.com/questions/28158/is-there-a-tool-to-get-the-lines-in-one-file-that-are-not-in-another
awk to the rescue!
This solution doesn't require sorted inputs. You have to provide fileB first.
awk 'NR==FNR{a[$0];next} !($0 in a)' fileB fileA
returns
A
C
How does it work?
NR==FNR{a[$0];next} idiom is for storing the first file in an associative array as keys for a later "contains" test.
NR==FNR is checking whether we're scanning the first file, where the global line counter (NR) equals to the current file line counter (FNR).
a[$0] adds the current line to the associative array as key, note that this behaves like a set, where there won't be any duplicate values (keys)
!($0 in a) we're now in the next file(s), in is a contains test, here it's checking whether current line is in the set we populated in the first step from the first file, ! negates the condition. What is missing here is the action, which by default is {print} and usually not written explicitly.
Note that this can now be used to remove blacklisted words.
$ awk '...' badwords allwords > goodwords
with a slight change it can clean multiple lists and create cleaned versions.
$ awk 'NR==FNR{a[$0];next} !($0 in a){print > FILENAME".clean"}' bad file1 file2 file3 ...
Another way to do the same thing (also requires sorted input):
join -v 1 fileA fileB
In Bash, if the files are not pre-sorted:
join -v 1 <(sort fileA) <(sort fileB)
You can do this unless your files are sorted
diff file-a file-b --new-line-format="" --old-line-format="%L" --unchanged-line-format="" > file-a
--new-line-format is for lines that are in file b but not in a
--old-.. is for lines that are in file a but not in b
--unchanged-.. is for lines that are in both.
%L makes it so the line is printed exactly.
man diff
for more details
This refinement of #karakfa's nice answer may be noticeably faster for very large files. As with that answer, neither file need be sorted, but speed is assured by virtue of awk's associative arrays. Only the lookup file is held in memory.
This formulation also allows for the possibility that only one particular field ($N) in the input file is to be used in the comparison.
# Print lines in the input unless the value in column $N
# appears in a lookup file, $LOOKUP;
# if $N is 0, then the entire line is used for comparison.
awk -v N=$N -v lookup="$LOOKUP" '
BEGIN { while ( getline < lookup ) { dictionary[$0]=$0 } }
!($N in dictionary) {print}'
(Another advantage of this approach is that it is easy to modify the comparison criterion, e.g. to trim leading and trailing white space.)
You can use Python:
python -c '
lines_to_remove = set()
with open("file B", "r") as f:
for line in f.readlines():
lines_to_remove.add(line.strip())
with open("file A", "r") as f:
for line in [line.strip() for line in f.readlines()]:
if line not in lines_to_remove:
print(line)
'
You can use -
diff fileA fileB | grep "^>" | cut -c3- > fileA
This will work for files that are not sorted as well.
Just to add to the Python answer to the user above, here is a faster solution:
python -c '
lines_to_remove = None
with open("partial file") as f:
lines_to_remove = {line.rstrip() for line in f.readlines()}
remaining_lines = None
with open("full file") as f:
remaining_lines = {line.rstrip() for line in f.readlines()} - lines_to_remove
with open("output file", "w") as f:
for line in remaining_lines:
f.write(line + "\n")
'
Raising the power of set subtraction.
To get the file after removing the lines which appears on another file
comm -23 <(sort bigFile.txt) <(sort smallfile.txt) > diff.txt
Here is a one liner that pipes the output of a website and removes the navigation elements using grep and lynx! you can replace lynx with cat FileA and unwanted-elements.txt with FileB.
lynx -dump -accept_all_cookies -nolist -width 1000 https://stackoverflow.com/ | grep -Fxvf unwanted-elements.txt
To remove common lines between two files you can use grep, comm or join command.
grep only works for small files. Use -v along with -f.
grep -vf file2 file1
This displays lines from file1 that do not match any line in file2.
comm is a utility command that works on lexically sorted files. It
takes two files as input and produces three text columns as output:
lines only in the first file; lines only in the second file; and lines
in both files. You can suppress printing of any column by using -1, -2
or -3 option accordingly.
comm -1 -3 file2 file1
This displays lines from file1 that do not match any line in file2.
Finally, there is join, a utility command that performs an equality
join on the specified files. Its -v option also allows to remove
common lines between two files.
join -v1 -v2 file1 file2

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