Related
I have a multifasta file that looks like this:
( all sequences are >100bp, more than one line, and same lenght )
>Lineage1_samplenameA
CGCTTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAA
>Lineage2_samplenameB
AAATTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAG
>Lineage3_samplenameC
CGCTTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAA
>Lineage3_samplenameD
CGCTTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAA
I need to remove the duplicates BUT keep at least on sequence per lineage. So in this simple example (Notice samplenameA,C and D are identical) above I would want to remove only samplenameD or samplenameC but not both of them. In the end I want to get the same header information as in the original file.
Example output:
>Lineage1_samplenameA
CGCTTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAA
>Lineage2_samplenameB
AAATTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAG
>Lineage3_samplenameC
CGCTTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAA
I found out a way that works to remove just the duplicates. Thanks to Pierre Lindenbaum.
sed -e '/^>/s/$/#/' -e 's/^>/#/'
file.fasta |\
tr -d '\n' | tr "#" "\n" | tr "#"
"\t" |\
sort -u -t ' ' -f -k 2,2 |\
sed -e 's/^/>/' -e 's/\t/\n/'
Running this on my example above would result in:
>Lineage1_samplenameA
CGCTTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAA
>Lineage2_samplenameB
AAATTCAACGGAATGGATCTACGTTACAGCCTGCATAAAGAAAACGGAGTTGCCGAGGACGAAAGCGACTTTAGGTTCTGTCCGTTGTCTTTGGCGGAAG
—> so losing the lineage 3 sequence
Now I’m just looking for a quick solution to remove duplicates but keep at least one sequence per lineage based on the fasta header.
I’m new to scripting... any ideas in bash/python/R are welcome.
Thanks!!!
In this case I can see two relatively good alternatives. A) look into existing tools (such as the Biopython library, or FASTX toolkit. I think both of them have good commands to do most of the work here, so it may be worthwhile to learn them. Or, B) write your own. In this case you may want to try (I'll stick to python):
loop over the file, line-by-line, and add the lineage/sequence data to a dictionary. I suggest using the sequence as a key. This way, you can easily know if you already encountered this key.
myfasta = {}
if myfasta[sequence]:
myfasta[sequence].append(lineage_id)
else:
myfasta[sequence] = [lineage_id]
This way your key (sequence) will hold the list of lineage_ids that have the same sequence. Note that the annoying bits of this solution will be to loop over the file, separate lineage-id from sequence, account for sequences that may extend to multiple lines, etc.
After that, you can loop over the dictionary, and write the sequences to file by using only the first lineage_id from the list within the dictionary.
I would like to update a large number of C++ source files with an extra include directive before any existing #includes. For this sort of task, I normally use a small bash script with sed to re-write the file.
How do I get sed to replace just the first occurrence of a string in a file rather than replacing every occurrence?
If I use
sed s/#include/#include "newfile.h"\n#include/
it replaces all #includes.
Alternative suggestions to achieve the same thing are also welcome.
A sed script that will only replace the first occurrence of "Apple" by "Banana"
Example
Input: Output:
Apple Banana
Apple Apple
Orange Orange
Apple Apple
This is the simple script: Editor's note: works with GNU sed only.
sed '0,/Apple/{s/Apple/Banana/}' input_filename
The first two parameters 0 and /Apple/ are the range specifier. The s/Apple/Banana/ is what is executed within that range. So in this case "within the range of the beginning (0) up to the first instance of Apple, replace Apple with Banana. Only the first Apple will be replaced.
Background: In traditional sed the range specifier is also "begin here" and "end here" (inclusive). However the lowest "begin" is the first line (line 1), and if the "end here" is a regex, then it is only attempted to match against on the next line after "begin", so the earliest possible end is line 2. So since range is inclusive, smallest possible range is "2 lines" and smallest starting range is both lines 1 and 2 (i.e. if there's an occurrence on line 1, occurrences on line 2 will also be changed, not desired in this case). GNU sed adds its own extension of allowing specifying start as the "pseudo" line 0 so that the end of the range can be line 1, allowing it a range of "only the first line" if the regex matches the first line.
Or a simplified version (an empty RE like // means to re-use the one specified before it, so this is equivalent):
sed '0,/Apple/{s//Banana/}' input_filename
And the curly braces are optional for the s command, so this is also equivalent:
sed '0,/Apple/s//Banana/' input_filename
All of these work on GNU sed only.
You can also install GNU sed on OS X using homebrew brew install gnu-sed.
# sed script to change "foo" to "bar" only on the first occurrence
1{x;s/^/first/;x;}
1,/foo/{x;/first/s///;x;s/foo/bar/;}
#---end of script---
or, if you prefer: Editor's note: works with GNU sed only.
sed '0,/foo/s//bar/' file
Source
An overview of the many helpful existing answers, complemented with explanations:
The examples here use a simplified use case: replace the word 'foo' with 'bar' in the first matching line only.
Due to use of ANSI C-quoted strings ($'...') to provide the sample input lines, bash, ksh, or zsh is assumed as the shell.
GNU sed only:
Ben Hoffstein's anwswer shows us that GNU provides an extension to the POSIX specification for sed that allows the following 2-address form: 0,/re/ (re represents an arbitrary regular expression here).
0,/re/ allows the regex to match on the very first line also. In other words: such an address will create a range from the 1st line up to and including the line that matches re - whether re occurs on the 1st line or on any subsequent line.
Contrast this with the POSIX-compliant form 1,/re/, which creates a range that matches from the 1st line up to and including the line that matches re on subsequent lines; in other words: this will not detect the first occurrence of an re match if it happens to occur on the 1st line and also prevents the use of shorthand // for reuse of the most recently used regex (see next point).1
If you combine a 0,/re/ address with an s/.../.../ (substitution) call that uses the same regular expression, your command will effectively only perform the substitution on the first line that matches re.
sed provides a convenient shortcut for reusing the most recently applied regular expression: an empty delimiter pair, //.
$ sed '0,/foo/ s//bar/' <<<$'1st foo\nUnrelated\n2nd foo\n3rd foo'
1st bar # only 1st match of 'foo' replaced
Unrelated
2nd foo
3rd foo
A POSIX-features-only sed such as BSD (macOS) sed (will also work with GNU sed):
Since 0,/re/ cannot be used and the form 1,/re/ will not detect re if it happens to occur on the very first line (see above), special handling for the 1st line is required.
MikhailVS's answer mentions the technique, put into a concrete example here:
$ sed -e '1 s/foo/bar/; t' -e '1,// s//bar/' <<<$'1st foo\nUnrelated\n2nd foo\n3rd foo'
1st bar # only 1st match of 'foo' replaced
Unrelated
2nd foo
3rd foo
Note:
The empty regex // shortcut is employed twice here: once for the endpoint of the range, and once in the s call; in both cases, regex foo is implicitly reused, allowing us not to have to duplicate it, which makes both for shorter and more maintainable code.
POSIX sed needs actual newlines after certain functions, such as after the name of a label or even its omission, as is the case with t here; strategically splitting the script into multiple -e options is an alternative to using an actual newlines: end each -e script chunk where a newline would normally need to go.
1 s/foo/bar/ replaces foo on the 1st line only, if found there.
If so, t branches to the end of the script (skips remaining commands on the line). (The t function branches to a label only if the most recent s call performed an actual substitution; in the absence of a label, as is the case here, the end of the script is branched to).
When that happens, range address 1,//, which normally finds the first occurrence starting from line 2, will not match, and the range will not be processed, because the address is evaluated when the current line is already 2.
Conversely, if there's no match on the 1st line, 1,// will be entered, and will find the true first match.
The net effect is the same as with GNU sed's 0,/re/: only the first occurrence is replaced, whether it occurs on the 1st line or any other.
NON-range approaches
potong's answer demonstrates loop techniques that bypass the need for a range; since he uses GNU sed syntax, here are the POSIX-compliant equivalents:
Loop technique 1: On first match, perform the substitution, then enter a loop that simply prints the remaining lines as-is:
$ sed -e '/foo/ {s//bar/; ' -e ':a' -e '$!{n;ba' -e '};}' <<<$'1st foo\nUnrelated\n2nd foo\n3rd foo'
1st bar
Unrelated
2nd foo
3rd foo
Loop technique 2, for smallish files only: read the entire input into memory, then perform a single substitution on it.
$ sed -e ':a' -e '$!{N;ba' -e '}; s/foo/bar/' <<<$'1st foo\nUnrelated\n2nd foo\n3rd foo'
1st bar
Unrelated
2nd foo
3rd foo
1 1.61803 provides examples of what happens with 1,/re/, with and without a subsequent s//:
sed '1,/foo/ s/foo/bar/' <<<$'1foo\n2foo' yields $'1bar\n2bar'; i.e., both lines were updated, because line number 1 matches the 1st line, and regex /foo/ - the end of the range - is then only looked for starting on the next line. Therefore, both lines are selected in this case, and the s/foo/bar/ substitution is performed on both of them.
sed '1,/foo/ s//bar/' <<<$'1foo\n2foo\n3foo' fails: with sed: first RE may not be empty (BSD/macOS) and sed: -e expression #1, char 0: no previous regular expression (GNU), because, at the time the 1st line is being processed (due to line number 1 starting the range), no regex has been applied yet, so // doesn't refer to anything.
With the exception of GNU sed's special 0,/re/ syntax, any range that starts with a line number effectively precludes use of //.
sed '0,/pattern/s/pattern/replacement/' filename
this worked for me.
example
sed '0,/<Menu>/s/<Menu>/<Menu><Menu>Sub menu<\/Menu>/' try.txt > abc.txt
Editor's note: both work with GNU sed only.
You could use awk to do something similar..
awk '/#include/ && !done { print "#include \"newfile.h\""; done=1;}; 1;' file.c
Explanation:
/#include/ && !done
Runs the action statement between {} when the line matches "#include" and we haven't already processed it.
{print "#include \"newfile.h\""; done=1;}
This prints #include "newfile.h", we need to escape the quotes. Then we set the done variable to 1, so we don't add more includes.
1;
This means "print out the line" - an empty action defaults to print $0, which prints out the whole line. A one liner and easier to understand than sed IMO :-)
Quite a comprehensive collection of answers on linuxtopia sed FAQ. It also highlights that some answers people provided won't work with non-GNU version of sed, eg
sed '0,/RE/s//to_that/' file
in non-GNU version will have to be
sed -e '1s/RE/to_that/;t' -e '1,/RE/s//to_that/'
However, this version won't work with gnu sed.
Here's a version that works with both:
-e '/RE/{s//to_that/;:a' -e '$!N;$!ba' -e '}'
ex:
sed -e '/Apple/{s//Banana/;:a' -e '$!N;$!ba' -e '}' filename
With GNU sed's -z option you could process the whole file as if it was only one line. That way a s/…/…/ would only replace the first match in the whole file. Remember: s/…/…/ only replaces the first match in each line, but with the -z option sed treats the whole file as a single line.
sed -z 's/#include/#include "newfile.h"\n#include'
In the general case you have to rewrite your sed expression since the pattern space now holds the whole file instead of just one line. Some examples:
s/text.*// can be rewritten as s/text[^\n]*//. [^\n] matches everything except the newline character. [^\n]* will match all symbols after text until a newline is reached.
s/^text// can be rewritten as s/(^|\n)text//.
s/text$// can be rewritten as s/text(\n|$)//.
#!/bin/sed -f
1,/^#include/ {
/^#include/i\
#include "newfile.h"
}
How this script works: For lines between 1 and the first #include (after line 1), if the line starts with #include, then prepend the specified line.
However, if the first #include is in line 1, then both line 1 and the next subsequent #include will have the line prepended. If you are using GNU sed, it has an extension where 0,/^#include/ (instead of 1,) will do the right thing.
Just add the number of occurrence at the end:
sed s/#include/#include "newfile.h"\n#include/1
A possible solution:
/#include/!{p;d;}
i\
#include "newfile.h"
:a
n
ba
Explanation:
read lines until we find the #include, print these lines then start new cycle
insert the new include line
enter a loop that just reads lines (by default sed will also print these lines), we won't get back to the first part of the script from here
I know this is an old post but I had a solution that I used to use:
grep -E -m 1 -n 'old' file | sed 's/:.*$//' - | sed 's/$/s\/old\/new\//' - | sed -f - file
Basically use grep to print the first occurrence and stop there. Additionally print line number ie 5:line. Pipe that into sed and remove the : and anything after so you are just left with a line number. Pipe that into sed which adds s/.*/replace to the end number, which results in a 1 line script which is piped into the last sed to run as a script on the file.
so if regex = #include and replace = blah and the first occurrence grep finds is on line 5 then the data piped to the last sed would be 5s/.*/blah/.
Works even if first occurrence is on the first line.
i would do this with an awk script:
BEGIN {i=0}
(i==0) && /#include/ {print "#include \"newfile.h\""; i=1}
{print $0}
END {}
then run it with awk:
awk -f awkscript headerfile.h > headerfilenew.h
might be sloppy, I'm new to this.
As an alternative suggestion you may want to look at the ed command.
man 1 ed
teststr='
#include <stdio.h>
#include <stdlib.h>
#include <inttypes.h>
'
# for in-place file editing use "ed -s file" and replace ",p" with "w"
# cf. http://wiki.bash-hackers.org/howto/edit-ed
cat <<-'EOF' | sed -e 's/^ *//' -e 's/ *$//' | ed -s <(echo "$teststr")
H
/# *include/i
#include "newfile.h"
.
,p
q
EOF
I finally got this to work in a Bash script used to insert a unique timestamp in each item in an RSS feed:
sed "1,/====RSSpermalink====/s/====RSSpermalink====/${nowms}/" \
production-feed2.xml.tmp2 > production-feed2.xml.tmp.$counter
It changes the first occurrence only.
${nowms} is the time in milliseconds set by a Perl script, $counter is a counter used for loop control within the script, \ allows the command to be continued on the next line.
The file is read in and stdout is redirected to a work file.
The way I understand it, 1,/====RSSpermalink====/ tells sed when to stop by setting a range limitation, and then s/====RSSpermalink====/${nowms}/ is the familiar sed command to replace the first string with the second.
In my case I put the command in double quotation marks becauase I am using it in a Bash script with variables.
Using FreeBSD ed and avoid ed's "no match" error in case there is no include statement in a file to be processed:
teststr='
#include <stdio.h>
#include <stdlib.h>
#include <inttypes.h>
'
# using FreeBSD ed
# to avoid ed's "no match" error, see
# *emphasized text*http://codesnippets.joyent.com/posts/show/11917
cat <<-'EOF' | sed -e 's/^ *//' -e 's/ *$//' | ed -s <(echo "$teststr")
H
,g/# *include/u\
u\
i\
#include "newfile.h"\
.
,p
q
EOF
This might work for you (GNU sed):
sed -si '/#include/{s//& "newfile.h\n&/;:a;$!{n;ba}}' file1 file2 file....
or if memory is not a problem:
sed -si ':a;$!{N;ba};s/#include/& "newfile.h\n&/' file1 file2 file...
If anyone came here to replace a character for the first occurrence in all lines (like myself), use this:
sed '/old/s/old/new/1' file
-bash-4.2$ cat file
123a456a789a
12a34a56
a12
-bash-4.2$ sed '/a/s/a/b/1' file
123b456a789a
12b34a56
b12
By changing 1 to 2 for example, you can replace all the second a's only instead.
The use case can perhaps be that your occurences are spread throughout your file, but you know your only concern is in the first 10, 20 or 100 lines.
Then simply adressing those lines fixes the issue - even if the wording of the OP regards first only.
sed '1,10s/#include/#include "newfile.h"\n#include/'
The following command removes the first occurrence of a string, within a file. It removes the empty line too. It is presented on an xml file, but it would work with any file.
Useful if you work with xml files and you want to remove a tag. In this example it removes the first occurrence of the "isTag" tag.
Command:
sed -e 0,/'<isTag>false<\/isTag>'/{s/'<isTag>false<\/isTag>'//} -e 's/ *$//' -e '/^$/d' source.txt > output.txt
Source file (source.txt)
<xml>
<testdata>
<canUseUpdate>true</canUseUpdate>
<isTag>false</isTag>
<moduleLocations>
<module>esa_jee6</module>
<isTag>false</isTag>
</moduleLocations>
<node>
<isTag>false</isTag>
</node>
</testdata>
</xml>
Result file (output.txt)
<xml>
<testdata>
<canUseUpdate>true</canUseUpdate>
<moduleLocations>
<module>esa_jee6</module>
<isTag>false</isTag>
</moduleLocations>
<node>
<isTag>false</isTag>
</node>
</testdata>
</xml>
ps: it didn't work for me on Solaris SunOS 5.10 (quite old), but it works on Linux 2.6, sed version 4.1.5
Nothing new but perhaps a little more concrete answer: sed -rn '0,/foo(bar).*/ s%%\1%p'
Example: xwininfo -name unity-launcher produces output like:
xwininfo: Window id: 0x2200003 "unity-launcher"
Absolute upper-left X: -2980
Absolute upper-left Y: -198
Relative upper-left X: 0
Relative upper-left Y: 0
Width: 2880
Height: 98
Depth: 24
Visual: 0x21
Visual Class: TrueColor
Border width: 0
Class: InputOutput
Colormap: 0x20 (installed)
Bit Gravity State: ForgetGravity
Window Gravity State: NorthWestGravity
Backing Store State: NotUseful
Save Under State: no
Map State: IsViewable
Override Redirect State: no
Corners: +-2980+-198 -2980+-198 -2980-1900 +-2980-1900
-geometry 2880x98+-2980+-198
Extracting window ID with xwininfo -name unity-launcher|sed -rn '0,/^xwininfo: Window id: (0x[0-9a-fA-F]+).*/ s%%\1%p' produces:
0x2200003
POSIXly (also valid in sed), Only one regex used, need memory only for one line (as usual):
sed '/\(#include\).*/!b;//{h;s//\1 "newfile.h"/;G};:1;n;b1'
Explained:
sed '
/\(#include\).*/!b # Only one regex used. On lines not matching
# the text `#include` **yet**,
# branch to end, cause the default print. Re-start.
//{ # On first line matching previous regex.
h # hold the line.
s//\1 "newfile.h"/ # append ` "newfile.h"` to the `#include` matched.
G # append a newline.
} # end of replacement.
:1 # Once **one** replacement got done (the first match)
n # Loop continually reading a line each time
b1 # and printing it by default.
' # end of sed script.
A possible solution here might be to tell the compiler to include the header without it being mentioned in the source files. IN GCC there are these options:
-include file
Process file as if "#include "file"" appeared as the first line of
the primary source file. However, the first directory searched for
file is the preprocessor's working directory instead of the
directory containing the main source file. If not found there, it
is searched for in the remainder of the "#include "..."" search
chain as normal.
If multiple -include options are given, the files are included in
the order they appear on the command line.
-imacros file
Exactly like -include, except that any output produced by scanning
file is thrown away. Macros it defines remain defined. This
allows you to acquire all the macros from a header without also
processing its declarations.
All files specified by -imacros are processed before all files
specified by -include.
Microsoft's compiler has the /FI (forced include) option.
This feature can be handy for some common header, like platform configuration. The Linux kernel's Makefile uses -include for this.
I needed a solution that would work both on GNU and BSD, and I also knew that the first line would never be the one I'd need to update:
sed -e "1,/pattern/s/pattern/replacement/"
Trying the // feature to not repeat the pattern did not work for me, hence needing to repeat it.
I will make a suggestion that is not exactly what the original question asks for, but for those who also want to specifically replace perhaps the second occurrence of a match, or any other specifically enumerated regular expression match. Use a python script, and a for loop, call it from a bash script if needed. Here's what it looked like for me, where I was replacing specific lines containing the string --project:
def replace_models(file_path, pixel_model, obj_model):
# find your file --project matches
pattern = re.compile(r'--project.*')
new_file = ""
with open(file_path, 'r') as f:
match = 1
for line in f:
# Remove line ending before we do replacement
line = line.strip()
# replace first --project line match with pixel
if match == 1:
result = re.sub(pattern, "--project='" + pixel_model + "'", line)
# replace second --project line match with object
elif match == 2:
result = re.sub(pattern, "--project='" + obj_model + "'", line)
else:
result = line
# Check that a substitution was actually made
if result is not line:
# Add a backslash to the replaced line
result += " \\"
print("\nReplaced ", line, " with ", result)
# Increment number of matches found
match += 1
# Add the potentially modified line to our new file
new_file = new_file + result + "\n"
# close file / save output
f.close()
fout = open(file_path, "w")
fout.write(new_file)
fout.close()
sed -e 's/pattern/REPLACEMENT/1' <INPUTFILE
I have a file which contains multiple like this:
s10123-yyy.bkp.abc01.zone,Windows File =
System,N/A,defaultBackupSet,default,272188(* )(S =
),Completed,INCR,Mixed,02/28/2015 19:00:27,02/28/2015 =
19:03:06,02/28/2015 20:32:11,02/28/2015 =
20:32:09,12.08,53.93%,0.18,98.52%,0%,0.12,1:28:23,N/A,8.203,N/A,67303,0,8=
3,"Disk_Library2, Disk_Library6,",N/A,N/A,=0A=
Which I need to make it in one line like this:
s10123-yyy.bkp.abc01.zone,Windows File System,N/A,defaultBackupSet,default,272188(* )(S ),Completed,INCR,Mixed,02/28/2015 19:00:27,02/28/2015 19:03:06,02/28/2015 20:32:11,02/28/2015 20:32:09,12.08,53.93%,0.18,98.52%,0%,0.12,1:28:23,N/A,8.203,N/A,67303,0,83,"Disk_Library2, Disk_Library6,",N/A,N/A
If I do it manually, I highlight the "=" and press "delete" button twice to connect and get the desired result.
The last 5 character ",=0A=" needs to be deleted too.
Awk, Sed, Bash, Perl or Python script would be preferred.
Appreciate you help.
Thanks!
This is most simple with awk1:
awk -v RS=',=0A=\n' -F '=\n' -v OFS= '{ $1 = $1 } 1' filename
The trick is to
use ,=0A=\n as record separator RS
=\n as field separator
have an empty output field separator OFS, so that the fields are printed directly one after the other, and
force the rebuilding of the output record with $1 = $1 before printing it.
Addendum: Obligatory crazy sed solution:
sed -n '/,=0A=$/ { s///; H; s/.*//; x; s/\n//g; p; d; }; /=$/ { s///; H; }' filename
I don't recommend that you use that; I just like writing things in sed that shouldn't be written in sed. It's fun!
1 Tested with GNU awk and mawk, which are the most common ones. Multi-character RS is not strictly required by POSIX, though, so more esoteric awks may reject this. Thanks to #TomFenech for pointing this out.
Through Perl.
perl -0777pe 's/=\n|,=[^,]*$//sg' file
In Python, Create a list and then use the extend method to add the lines to the list, versus append.
This is a Perl solution:
perl -l -0777 -pwe"s/,?=(?:0A=)?\n//g" file
-0777 disables input record separator, making the file into one single line.
-p reads input from file and prints it back to standard output.
-l (before -0) adds newline to your print statements.
The regex s/,?=(?:0A=)?\n//g finds an optional comma, followed by =, followed by optional 0A= string, and ending with newline.
I don't know if all your files are just one of these long lines. If it is multiple such lines, you should set the input record separator to =0A=\n, most likely, chomp the lines and delete =\n.
sed
sed '
:a
/,=0A=$/ {s///; s/\n//g} # "end of line", remove the chars and newlines
/ \?=$/ {s///; N; ba} # line continuation: remove the chars, append
# the next line, goto a
' file
I have many large (~30 MB a piece) tab-delimited text files with variable-width lines. I want to extract the 2nd field from the nth (here, n=4) and next-to-last line (the last line is empty). I can get them separately using awk:
awk 'NR==4{print $2}' filename.dat
and (I don't comprehend this entirely but)
awk '{y=x "\n" $2};END{print y}' filename.dat
but is there a way to get them together in one call? My broader intention is to wrap it in a Python script to harvest these values from a large number of files (many thousands) in separate directories and I want to reduce the number of system calls. Thanks a bunch -
Edit: I know I can read over the whole file with Python to extract those values, but thought awk might be more appropriate for the task (having to do with one of the two values located near the end of the large file).
awk 'NR==4{print $2};{y=x "\n" $2};END{print y}' filename.dat
You can pass the number of lines into awk:
awk -v lines=$( wc -l < filename.dat ) -v n=4 '
NR == n || NR == lines-1 {print $2}
' filename.dat
Note, in the wc command, use the < redirection to avoid the filename being printed.
Here's how to implement this in Python without reading the whole file
To get the nth line, you have no choice but to read the file up to the nth line as the lines are variable width.
To get the second to last line, guess how long the line might be (be generous) and seek to that many bytes before the end of the file.
read() from the point you have seeked to. Count the number of newline characters - You need at least two. If there are less than 2 newlines double your guess and try again
split the data you read at newlines - the line you seek will be the second to last item in the split
This is my solution in Python. Inspired by this other code:
def readfields(filename,nfromtop=3,nfrombottom=-2,fieldnum=1,blocksize=4096):
f = open(filename,'r')
out = ''
for i,line in enumerate(f):
if i==nfromtop:
out += line.split('\t')[fieldnum]+'\t'
break
f.seek(-blocksize,2)
out += str.split(f.read(blocksize),'\n')[nfrombottom].split('\t')[fieldnum]
return out
When I profiled it, the difference was 0.09 seconds quicker than a solution calling awk (awk 'NR==4{print $2};{y=x $2};END{print y}' filename.dat) with the subprocess module. Not a dealbreaker, but when the rest of the script is in Python it appears there is a payoff in going there (especially since I have a lot of these files).
In our project we need to import the csv file to postgres.
There are multiple types of files meaning the length of the file changes as some files are with fewer columns and some with all of them.
We need a fast way to import this file to postgres. I want to use COPY FROM of the postgres since the speed requirement of the processing are very high(almost 150 files per minute with 20K file size each).
Since the file columns numbers are not fixed, I need to pre-process the file before I pass it to the postgres procedure. The pre-processing is simply to add extra commas in the csv for columns, which are not there in the file.
There are two options for me to preprocess the file - use python or use Sed.
My first question is, what would be the fastest way of pre-process the file?
Second question is, If I use sed how would I insert a comma after say 4th, 5th comma fields?
e.g. if file has entries like
1,23,56,we,89,2009-12-06
and I need to edit the file with final output like:
1,23,56,we,,89,,2009-12-06
Are you aware of the fact that COPY FROM lets you specify which columns (as well as in which order they) are to be imported?
COPY tablename ( column1, column2, ... ) FROM ...
Specifying directly, at the Postgres level, which columns to import and in what order, will typically be the fastest and most efficient import method.
This having been said, there is a much simpler (and portable) way of using sed (than what has been presented in other posts) to replace an n th occurrence, e.g. replace the 4th and 5th occurrences of a comma with double commas:
echo '1,23,56,we,89,2009-12-06' | sed -e 's/,/,,/5;s/,/,,/4'
produces:
1,23,56,we,,89,,2009-12-06
Notice that I replaced the rightmost fields (#5) first.
I see that you have also tagged your question as perl-related, although you make no explicit reference to perl in the body of the question; here would be one possible implementation which gives you the flexibility of also reordering or otherwise processing fields:
echo '1,23,56,we,89,2009-12-06' |
perl -F/,/ -nae 'print "$F[0],$F[1],$F[2],$F[3],,$F[4],,$F[5]"'
also produces:
1,23,56,we,,89,,2009-12-06
Very similarly with awk, for the record:
echo '1,23,56,we,89,2009-12-06' |
awk -F, '{print $1","$2","$3","$4",,"$5",,"$6}'
I will leave Python to someone else. :)
Small note on the Perl example: I am using the -a and -F options to autosplit so I have a shorter command string; however, this leaves the newline embedded in the last field ($F[5]) which is fine as long as that field doesn't have to be reordered somewhere else. Should that situation arise, slightly more typing would be needed in order to zap the newline via chomp, then split by hand and finally print our own newline character \n (the awk example above does not have this problem):
perl -ne 'chomp;#F=split/,/;print "$F[0],$F[1],$F[2],$F[3],,$F[4],,$F[5]\n"'
EDIT (an idea inspired by Vivin):
COMMAS_TO_DOUBLE="1 4 5"
echo '1,23,56,we,89,2009-12-06' |
sed -e `for f in $COMMAS_TO_DOUBLE ; do echo "s/,/,,/$f" ; done |
sort -t/ -k4,4nr | paste -s -d ';'`
1,,23,56,we,,89,,2009-12-06
Sorry, couldn't resist it. :)
To answer your first question, sed would have less overhead, but might be painful. awk would be a little better (it's more powerful). Perl or Python have more overhead, but would be easier to work with (regarding Perl, that's maybe a little subjective ;). Personally, I'd use Perl).
As far as the second question, I think the problem might be a little more complex. For example, don't you need to examine the string to figure out what fields are actually missing? Or is it guaranteed that it will always be the 4th and 5th? If it's the first case case, it would be way easier to do this in Python or Perl rather than in sed. Otherwise:
echo "1,23,56,we,89,2009-12-06" | sed -e 's/\([^,]\+\),\([^,]\+\),\([^,]\+\),\([^,]\+\),\([^,]\+\),/\1,\2,\3,\4,,\5,,/'
or (easier on the eyes):
echo "1,23,56,we,89,2009-12-06" | sed -e 's/\(\([^,]\+,\)\{3\}\)\([^,]\+\),\([^,]\+\),/\1,\3,,\4,,/'
This will add a comma after the 5th and 4th columns assuming there are no other commas in the text.
Or you can use two seds for something that's a little less ugly (only slightly, though):
echo "1,23,56,we,89,2009-12-06" | sed -e 's/\(\([^,]*,\)\{4\}\)/\1,/' | sed -e 's/\(\([^,]*,\)\{6\}\)/\1,/'
#OP, you are processing a csv file, which have distinct fields and delimiters. Use a tool that can split on delimiters and give you fields to work with easily. sed is not one of them, although it can be done, as some of the answers suggested, but you will get sed regex that is hard to read when it gets complicated. Use tools like awk/Python/Perl where they work with fields and delimiters easily, best of all, modules that specifically tailored to processing csv is available. For your example, a simple Python approach (without the use of csv module which ideally you should try to use it)
for line in open("file"):
line=line.rstrip() #strip new lines
sline=line.split(",")
if len(sline) < 8: # you want exact 8 fields
sline.insert(4,"")
sline.insert(6,"")
line=','.join(sline)
print line
output
$ more file
1,23,56,we,89,2009-12-06
$ ./python.py
1,23,56,we,,89,,2009-12-06
sed 's/^([^,]*,){4}/&,/' <original.csv >output.csv
Will add a comma after the 4th comma separated field (by matching 4 repetitions of <anything>, and then adding a comma after that). Note that there is a catch; make sure none of these values are quoted strings with commas in them.
You could chain multiple replacements via pipes if necessary, or modify the regex to add in any needed commas at the same time (though that gets more complex; you'd need to use subgroup captures in your replacement text).
Don't know regarding speed, but here is sed expr that should do the job:
sed -i 's/\(\([^,]*,\)\{4\}\)/\1,/' file_name
Just replace 4 by desured number of columns
Depending on your requirements, consider using ETL software for this and future tasks. Tools like Pentaho and Talend offer you a great deal of flexibility and you don't have to write a single line of code.