Given common bash-tools, it is easy to split a big file (in my case a MySQL dump and thus a TSV-file) into smaller parts using the split command. Furthermore, this command supports splitting a file after n new lines (i.e. -l argument). But this command does not distinguished between escaped and unescaped newline characters and thus might break a single table row into two incomplete parts.
Example (TSV with 2 columns)
cool 2014-12-15 17:31:00
do not censor it ...^M\\n 2016-01-24 22:33:00
watch out ari, you've got compeition! hahah 2001-12-05 19:11:01
Oh God, the poor guy! xD\\nCan't wait to watch this! 2011-07-11 22:01:20
wish i could do that.\\n 2001-02-07 00:24:11
Funny! I will use this reason when I drink something in other houses 2015-06-10 12:20:00
As you can see, there are two columns (first contains the comment and the second the date), which are separated by an tab. I visualised just the escaped newlines, tabs and unescaped newlines are not printed. If you put these lines into a file and split it (e.g., split example.tsv -l 1) you will get 9 files, but there are only 6 comments (3 contain escaped newlines)! This is because escaped newlines are treated as regular newlines prefixed with a backslash. This is a huge problem for me, because splitting the file might lead to incomplete table rows in the output-files.
Is it somehow possible to ignore escaped newlines or does someone know another command which can do this?
This will break the file every 20 lines (or whatever you set n to) but not on lines that end with a backslash:
awk -v n=20 'NR==1 || (c>n && !(last~/\\$/)){c=0; close(f); f="file" ++count ".out"} {c++; print>f; last=$0}' file
How it works
-v n=20
This creates an awk variable n which we will use to decide when to split the file.
NR==1 || (c>n && !(last~/\\$/)){c=0; close(f); f="file" ++count ".out"}
Every time that we need to start a new file, we (a) set the line counter, c, to zero, (b) close the previous file, and (c) define a name for the next file.
We need to start a new file when (i) we are on the first input line, NR==1, or else when (ii) the line counter c exceeds the limit n and the last line did not end with \.
c++; print>f; last=$0
This increments the line counter, c, prints the current line to file f, and updates last to the value of the current line.
Example
Let's try this test file:
$ cat file
text1 2014-12-15 17:31:01
text2\
2014-12-15 17:31:02
text3 2014-12-15 17:31:03
text4a\
text4b\
2014-12-15 17:31:04
text5 2014-12-15 17:31:05
Now, let's run our command. To keep the example short, we set n=2:
$ awk -v n=2 'NR==1 || (c>n && !(last~/\\$/)){c=0; close(f); f="file" ++count ".out"} {c++; print>f; last=$0}' file
After the command is run, new files appear in the directory:
$ ls
file file1.out file2.out file3.out
The new files contain the old contents split every 2 lines except not split on lines ending in \:
$ cat file1.out
text1 2014-12-15 17:31:01
text2\
2014-12-15 17:31:02
$ cat file2.out
text3 2014-12-15 17:31:03
text4a\
text4b\
2014-12-15 17:31:04
$ cat file3.out
text5 2014-12-15 17:31:05
Related
I have been tinkering with this for a while but can't quite figure it out. A sample line within the file looks like this:
"...~236 characters of data...Y YYY. Y...many more characters of data"
How would I use sed or awk to replace spaces with a B character only between positions 236 and 246? In that example string it starts at character 29 and ends at character 39 within the string. I would want to preserve all the text preceding and following the target chunk of data within the line.
For clarification based on the comments, it should be applied to all lines in the file and expected output would be:
"...~236 characters of data...YBBYYY.BBY...many more characters of data"
With GNU awk:
$ awk -v FIELDWIDTHS='29 10 *' -v OFS= '{gsub(/ /, "B", $2)} 1' ip.txt
...~236 characters of data...YBBYYY.BBY...many more characters of data
FIELDWIDTHS='29 10 *' means 29 characters for first field, next 10 characters for second field and the rest for third field. OFS is set to empty, otherwise you'll get space added between the fields.
With perl:
$ perl -pe 's/^.{29}\K.{10}/$&=~tr| |B|r/e' ip.txt
...~236 characters of data...YBBYYY.BBY...many more characters of data
^.{29}\K match and ignore first 29 characters
.{10} match 10 characters
e flag to allow Perl code instead of string in replacement section
$&=~tr| |B|r convert space to B for the matched portion
Use this Perl one-liner with substr and tr. Note that this uses the fact that you can assign to substr, which changes the original string:
perl -lpe 'BEGIN { $from = 29; $to = 39; } (substr $_, ( $from - 1 ), ( $to - $from + 1 ) ) =~ tr/ /B/;' in_file > out_file
To change the file in-place, use:
perl -i.bak -lpe 'BEGIN { $from = 29; $to = 39; } (substr $_, ( $from - 1 ), ( $to - $from + 1 ) ) =~ tr/ /B/;' in_file
The Perl one-liner uses these command line flags:
-e : Tells Perl to look for code in-line, instead of in a file.
-p : Loop over the input one line at a time, assigning it to $_ by default. Add print $_ after each loop iteration.
-l : Strip the input line separator ("\n" on *NIX by default) before executing the code in-line, and append it when printing.
-i.bak : Edit input files in-place (overwrite the input file). Before overwriting, save a backup copy of the original file by appending to its name the extension .bak.
I would use GNU AWK following way, for simplicity sake say we have file.txt content
S o m e s t r i n g
and want to change spaces from 5 (inclusive) to 10 (inclusive) position then
awk 'BEGIN{FPAT=".";OFS=""}{for(i=5;i<=10;i+=1)$i=($i==" "?"B":$i);print}' file.txt
output is
S o mBeBsBt r i n g
Explanation: I set field pattern (FPAT) to any single character and output field seperator (OFS) to empty string, thus every field is populated by single characters and I do not get superfluous space when print-ing. I use for loop to access desired fields and for every one I check if it is space, if it is I assign B here otherwise I assign original value, finally I print whole changed line.
Using GNU awk:
awk -v strt=29 -v end=39 '{ ram=substr($0,strt,(end-strt));gsub(" ","B",ram);print substr($0,1,(strt-1)) ram substr($0,(end)) }' file
Explanation:
awk -v strt=29 -v end=39 '{ # Pass the start and end character positions as strt and end respectively
ram=substr($0,strt,(end-strt)); # Extract the 29th to the 39th characters of the line and read into variable ram
gsub(" ","B",ram); # Replace spaces with B in ram
print substr($0,1,(strt-1)) ram substr($0,(end)) # Rebuild the line incorporating raw and printing the result
}'file
This is certainly a suitable task for perl, and saddens me that my perl has become so rusty that this is the best I can come up with at the moment:
perl -e 'local $/=\1;while(<>) { s/ /B/ if $. >= 236 && $. <= 246; print }' input;
Another awk but using FS="":
$ awk 'BEGIN{FS=OFS=""}{for(i=29;i<=39;i++)sub(/ /,"B",$i)}1' file
Output:
"...~236 characters of data...YBBYYY.BBY...many more characters of data"
Explained:
$ awk ' # yes awk yes
BEGIN {
FS=OFS="" # set empty field delimiters
}
{
for(i=29;i<=39;i++) # between desired indexes
sub(/ /,"B",$i) # replace space with B
# if($i==" ") # couldve taken this route, too
# $i="B"
}1' file # implicit output
With sed :
sed '
H
s/\(.\{236\}\)\(.\{11\}\).*/\2/
s/ /B/g
H
g
s/\n//g
s/\(.\{236\}\)\(.\{11\}\)\(.*\)\(.\{11\}\)/\1\4\3/
x
s/.*//
x' infile
When you have an input string without \r, you can use:
sed -r 's/(.{236})(.{10})(.*)/\1\r\2\r\3/;:a;s/(\r.*) (.*\r)/\1B\2/;ta;s/\r//g' input
Explanation:
First put \r around the area that you want to change.
Next introduce a label to jump back to.
Next replace a space between 2 markers.
Repeat until all spaces are replaced.
Remove the markers.
In your case, where the length doesn't change, you can do without the markers.
Replace a space after 236..245 characters and try again when it succeeds.
sed -r ':a; s/^(.{236})([^ ]{0,9}) /\1\2B/;ta' input
This might work for you (GNU sed):
sed -E 's/./&\n/245;s//\n&/236/;h;y/ /B/;H;g;s/\n.*\n(.*)\n.*\n(.*)\n.*/\2\1/' file
Divide the problem into 2 lines, one with spaces and one with B's where there were spaces.
Then using pattern matching make a composite line from the two lines.
N.B. The newline can be used as a delimiter as it is guaranteed not to be in seds pattern space.
I have two files. One file contains a pattern that I want to match in a second file. I want to use that pattern to print between that pattern (included) up to a specified character (not included) and then concatenate into a single output file.
For instance,
File_1:
a
c
d
and File_2:
>a
MEEL
>b
MLPK
>c
MEHL
>d
MLWL
>e
MTNH
I have been using variations of this loop:
while read $id;
do
sed -n "/>$id/,/>/{//!p;}" File_2;
done < File_1
hoping to obtain something like the following output:
>a
MEEL
>c
MEHL
>d
MLWL
But have had no such luck. I have played around with grep/fgrep awk and sed and between the three cannot seem to get the right (or any output). Would someone kindly point me in the right direction?
Try:
$ awk -F'>' 'FNR==NR{a[$1]; next} NF==2{f=$2 in a} f' file1 file2
>a
MEEL
>c
MEHL
>d
MLWL
How it works
-F'>'
This sets the field separator to >.
FNR==NR{a[$1]; next}
While reading in the first file, this creates a key in array a for every line in file file.
NF==2{f=$2 in a}
For every line in file 2 that has two fields, this sets variable f to true if the second field is a key in a or false if it is not.
f
If f is true, print the line.
A plain (GNU) sed solution. Files are read only once. It is assumed that characters in File_1 needn't to be quoted in sed expression.
pat=$(sed ':a; $!{N;ba;}; y/\n/|/' File_1)
sed -E -n ":a; /^>($pat)/{:b; p; n; /^>/ba; bb}" File_2
Explanation:
The first call to sed generates a regular expression to be used in the second call to sed and stores it in the variable pat. The aim is to avoid reading repeatedly the entire File_2 for each line of File_1. It just "slurps" the File_1 and replaces new-line characters with | characters. So the sample File_1 becomes a string with the value a|c|d. The regular expression a|c|d matches if at least one of the alternatives (a, b, c for this example) matches (this is a GNU sed extension).
The second sed expression, ":a; /^>($pat)/{:b; p; n; /^>/ba; bb}", could be converted to pseudo code like this:
begin:
read next line (from File_2) or quit on end-of-file
label_a:
if line begins with `>` followed by one of the alternatives in `pat` then
label_b:
print the line
read next line (from File_2) or quit on end-of-file
if line begins with `>` goto label_a else goto label_b
else goto begin
Let me try to explain why your approach does not work well:
You need to say while read id instead of while read $id.
The sed command />$id/,/>/{//!p;} will exclude the lines which start
with >.
Then you might want to say something like:
while read id; do
sed -n "/^>$id/{N;p}" File_2
done < File_1
Output:
>a
MEEL
>c
MEHL
>d
MLWL
But the code above is inefficient because it reads File_2 as many times as the count of the id's in File_1.
Please try the elegant solution by John1024 instead.
If ed is available, and since the shell is involve.
#!/usr/bin/env bash
mapfile -t to_match < file1.txt
ed -s file2.txt <<-EOF
g/\(^>[${to_match[*]}]\)/;/^>/-1p
q
EOF
It will only run ed once and not every line that has the pattern, that matches from file1. Like say if you have a to z from file1,ed will not run 26 times.
Requires bash4+ because of mapfile.
How it works
mapfile -t to_match < file1.txt
Saves the entry/value from file1 in an array named to_match
ed -s file2.txt point ed to file2 with the -s flag which means don't print info about the file, same info you get with wc file
<<-EOF A here document, shell syntax.
g/\(^>[${to_match[*]}]\)/;/^>/-1p
g means search the whole file aka global.
( ) capture group, it needs escaping because ed only supports BRE, basic regular expression.
^> If line starts with a > the ^ is an anchor which means the start.
[ ] is a bracket expression match whatever is inside of it, in this case the value of the array "${to_match[*]}"
; Include the next address/pattern
/^>/ Match a leading >
-1 go back one line after the pattern match.
p print whatever was matched by the pattern.
q quit ed
Im new to bash and trying to extract a list of patterns from file:
File1.txt
ABC
BDF
GHJ
base.csv (tried comma separated and tab delimited)
line 1,,,,"hfhf,ferf,ju,ABC"
line 2 ,,,,,"ewy,trggt,gtg,ABC,RFR"
line 3 .."himk,n,hn.ujj., BDF"
etc
Suggested output is smth like
ABC
line 1..
line 2..(whole lines)
BDF
line 3..
and so on for each pattern from file 1
the code i tried was:
#!/bin/bash
for i in *.txt -# cycle through all files containing pattern lists
do
for q in "$i"; # # cycle through list
do
echo $q >>output.${i};
grep -f "${q}" base.csv >>output.${i};
echo "\n";
done
done
But output is only filename and then some list of strings without pattern names, e.g.
File1.txt
line 1...
line 2...
line 3..
so i don`t know to what pattern belongs each string and have to check and assign manually. Can you please point out my errors? Thanks!
grep can process multiple files in one go, and then has the attractive added bonus of indicating which file it found a match in.
grep -f File1.txt base.csv >output.txt
It's not clear what you hope for the inner loop to do; it will just loop over a single token at a time, so it's not really a loop at all.
If you want the output to be grouped per pattern, here's a for loop which looks for one pattern at a time:
while read -r pat; do
echo "$pat"
grep "$pat" *.txt
done <File1.txt >output.txt
But the most efficient way to tackle this is to write a simple Awk script which processes all the input files at once, and groups the matches before printing them.
An additional concern is anchoring. grep "ABC" will find a match in 123DEABCXYZ; is this something you want to avoid? You can improve the regex, or, again, turn to Awk which gives you more control over where exactly to look for a match in a structured line.
awk '# Read patterns into memory
NR==FNR { a[++i] = $1; next }
# Loop across patterns
{ for(j=1; j<=i; ++j)
if($0 ~ a[j]) {
print FILENAME ":" FNR ":" $0 >>output.a[j]
next }
}' File1.txt base.csv
You're not actually reading the files, you're just handling the filenames. Try this:
#!/bin/bash
for i in *.txt # cycle through all files containing pattern lists
do
while read -r q # read file line by line
do
echo "$q" >>"output.${i}"
grep -f "${q}" base.csv >>"output.${i}"
echo "\n"
done < "${i}"
done
Here is one that separates (with split, comma-separatd with quotes and spaces stripped off) words from file2 to an array (word[]) and stores the record names (line 1 etc.) to it comma-separated:
awk '
NR==FNR {
n=split($0,tmp,/[" ]*(,|$)[" ]*/) # split words
for(i=2;i<=n;i++) # after first
if(tmp[i]!="") # non-empties
word[tmp[i]]=word[tmp[i]] (word[tmp[i]]==""?"":",") tmp[1] # hash rownames
record[tmp[1]]=$0 # store records
next
}
($1 in word) { # word found
n=split(word[$1],tmp,",") # get record names
print $1 ":" # output word
for(i=1;i<=n;i++) # and records
print record[tmp[i]]
}' file2 file1
Output:
ABC:
line 1,,,,"hfhf,ferf,ju,ABC"
line 2 ,,,,,"ewy,trggt,gtg,ABC,RFR"
BDF:
line 3 .."himk,n,hn.ujj., BDF"
Thank you for your kind help, my friends.
Tried both variants above but kept getting various errors ( "do" expected) or misbehavior ( gets names of pattern blocks, eg ABC, BDF, but no lines.
Gave up for a while and then eventually tried another way
While base goal were to cycle through pattern list files, search for patterns in huge file and write out specific columns from lines found - i simply wrote
for *i in *txt # cycle throughfiles w/ patterns
do
grep -F -f "$i" bigfile.csv >> ${i}.out1 #greps all patterns from current file
cut -f 2,3,4,7 ${i}.out1>> ${i}.out2 # cuts columns of interest and writes them out to another file
done
I'm aware that this code should be improved using some fancy pipeline features, but it works perfectly as is, hope it`ll help somebody in similar situation. You can easily add some echoes to write out pattern list names as i initially requested
Suppose I have a file that resembles the following format:
\\ Random other lines \\
...
27861NA+ NA+89122 13.480 11.554 10.082
27862NA+ NA+89123 2.166 5.896 10.108
27863NA+ NA+89124 8.289 6.843 3.090
27864NA+ NA+89125 12.972 5.936 4.498
27865CL- CL-89126 13.914 2.125 12.915
27866CL- CL-89127 12.050 13.907 3.559
...
\\ Random other lines \\
I am trying to find a way of replacing the last 24 characters of each line with a string that I have prepared, for the first 3 instances of lines in the file that contain the string "NA+".
For example, my output would ideally look like:
\\ Random other lines \\
...
27861NA+ NA+89122 my first string hello
27862NA+ NA+89123 my second string foo
27863NA+ NA+89124 my final string bar $$
27864NA+ NA+89125 12.972 5.936 4.498
27865CL- CL-89126 13.914 2.125 12.915
27866CL- CL-89127 12.050 13.907 3.559
...
\\ Random other lines \\
So far, I have found a sed command that will remove the last 24 characters from every line in the file:
sed 's/.\{24\}$//' myfile.txt
And also an awk command that will return the kth line that contains the desired substring:
awk '/NA+/{i++}i==1' myfile.txt
Does anyone have an idea about how I could replace the last 24 characters in the 1st, 2nd, and 3rd lines of my file that each contain a certain substring?
With single awk:
awk -v str="my string" '!f && /NA\+/{ f=1; n=NR+3 }n && n>NR{ $4=$5=""; $3=str }1' myfile.txt
string="my first string hello"
awk -v string="$string" '{ if ( $0 ~ "NA" ) {cnt++} if (cnt < 4 ) { print substr($0,1,length($0)-23)string } else { print }}' NA
Using awk, set a string and pass it awk with -v. Search for strings containing NA and the increment the variable cnt. When cnt is less that 4, print the everything but the last 23 characters adding the string passed to the end. Otherwise print the line.
This might work for you (GNU sed):
sed '/NA+/{x;s/\n/&/3;x;ta;H;s/.\{24\}$/some string/;b;:a;n;ba}' file
This uses the hold space (HS) to keep a count of the number of lines the script has seen of the required string (NA+). Once it has seen n (in this case n=3) such lines it just prints the remainder of the file.
I'm trying to delete two lines either side of a pattern match from a file full of transactions. Ie. find the match then delete two lines before it, then delete two lines after it and then delete the match. The write this back to the original file.
So the input data is
D28/10/2011
T-3.48
PINITIAL BALANCE
M
^
and my pattern is
sed -i '/PINITIAL BALANCE/,+2d' test.txt
However this is only deleting two lines after the pattern match and then deleting the pattern match. I can't work out any logical way to delete all 5 lines of data from the original file using sed.
an awk one-liner may do the job:
awk '/PINITIAL BALANCE/{for(x=NR-2;x<=NR+2;x++)d[x];}{a[NR]=$0}END{for(i=1;i<=NR;i++)if(!(i in d))print a[i]}' file
test:
kent$ cat file
######
foo
D28/10/2011
T-3.48
PINITIAL BALANCE
M
x
bar
######
this line will be kept
here
comes
PINITIAL BALANCE
again
blah
this line will be kept too
########
kent$ awk '/PINITIAL BALANCE/{for(x=NR-2;x<=NR+2;x++)d[x];}{a[NR]=$0}END{for(i=1;i<=NR;i++)if(!(i in d))print a[i]}' file
######
foo
bar
######
this line will be kept
this line will be kept too
########
add some explanation
awk '/PINITIAL BALANCE/{for(x=NR-2;x<=NR+2;x++)d[x];} #if match found, add the line and +- 2 lines' line number in an array "d"
{a[NR]=$0} # save all lines in an array with line number as index
END{for(i=1;i<=NR;i++)if(!(i in d))print a[i]}' #finally print only those index not in array "d"
file # your input file
sed will do it:
sed '/\n/!N;/\n.*\n/!N;/\n.*\n.*PINITIAL BALANCE/{$d;N;N;d};P;D'
It works this way:
if sed has only one string in pattern space it joins another one
if there are only two it joins the third one
if it does natch to pattern LINE + LINE + LINE with BALANCE it joins two following strings, deletes them and goes at the beginning
if not, it prints the first string from pattern and deletes it and goes at the beginning without swiping the pattern space
To prevent the appearance of pattern on the first string you should modify the script:
sed '1{/PINITIAL BALANCE/{N;N;d}};/\n/!N;/\n.*\n/!N;/\n.*\n.*PINITIAL BALANCE/{$d;N;N;d};P;D'
However, it fails in case you have another PINITIAL BALANCE in string which are going to be deleted. However, other solutions fails too =)
For such a task, I would probably reach for a more advanced tool like Perl:
perl -ne 'push #x, $_;
if (#x > 4) {
if ($x[2] =~ /PINITIAL BALANCE/) { undef #x }
else { print shift #x }
}
END { print #x }' input-file > output-file
This will remove 5 lines from the input file. These lines will be the 2 lines before the match, the matched line, and the two lines afterwards. You can change the total number of lines being removed modifying #x > 4 (this removes 5 lines) and the line being matched modifying $x[2] (this makes the match on the third line to be removed and so removes the two lines before the match).
A more simple and easy to understand solution might be:
awk '/PINITIAL BALANCE/ {print NR-2 "," NR+2 "d"}' input_filename \
| sed -f - input_filename > output_filename
awk is used to make a sed-script that deletes the lines in question and the result is written on the output_filename.
This uses two processes which might be less efficient than the other answers.
This might work for you (GNU sed):
sed ':a;$q;N;s/\n/&/2;Ta;/\nPINITIAL BALANCE$/!{P;D};$q;N;$q;N;d' file
save this code into a file grep.sed
H
s:.*::
x
s:^\n::
:r
/PINITIAL BALANCE/ {
N
N
d
}
/.*\n.*\n/ {
P
D
}
x
d
and run a command like this:
`sed -i -f grep.sed FILE`
You can use it so either:
sed -i 'H;s:.*::;x;s:^\n::;:r;/PINITIAL BALANCE/{N;N;d;};/.*\n.*\n/{P;D;};x;d' FILE