I'm just trying to count the occurrences of a word without writing an iteration file by file. I don't mind which kind of file it is. The closest I got is:
COUNT=$(grep -r -n -i "theWordImSearchingFor" .)
echo $COUNT
I thought about splitting that by spaces, but the problem is the output does not contain just the filename and the line but also the content (and that may have tons of spaces). w.g. I got:
./doc1.txt:29: This is the content containing theWordImSearchingFor but also other stuff
./doc1.txt:43: This is another line containing theWordImSearchingFor
./dir123/doc2.txt:339: .This is another...file...theWordImSearchingFor....
Any idea on how to keep it simple? TIA
To count the number of occurrences of a specific word, you need to use the same layout of code, but simpler. There are many ways to do this, but there are two much simpler versions of the word count that you have listed here.
The much two simpler versions,
1st way
2nd way
They both should work, unless problem with package installation.
Related
I have a set of .gprobs files that I need to import into Plink. However, I keep getting the same error -- a problem in a specific line, even after I removed that line and the lines around it.
The data: I concatenated all 22 chromosome .gprobs files. To do so, I did replace the '---' at the beginning of the individual .gprobs files with the corresponding chromosome number (so now each line starts CHR SNP BP A1 A2...) . I also removed the SNPs that weren't imputed well (INFO scores below 0.7)
Code:
plink --gen data_chrALL.gprobs_chrcol_below0.7inforemoved --sample data_chr1.sample --out data_chrALL.gprobs_plink
The error message:
--data: 13404k variants converted.Error: Line 13404781 of .gen file has fewer tokens than expected.
As I said above, I removed that specific line and reran it, and got the same exact error message. I tried removing the lines above and below (in case the numbering was off by a header or something?) but again, same exact error.
Any thoughts or suggestions would be greatly appreciated!!! I'm not sure if this is the best place to post this, but I'm in desperate need of help.
Plink is trying to tell you that it expects a certain number of items on each line (3N+5 fields where N is the number of samples) and on some lines it doesn´t see them. So,
(1) First of all, I would try to compare the lines causing errors to the ones which do not to see that the number of tockens/columns is actually the same, that it is correct and that there are no extra spaces or special characters which could cause escaping or misreading of the line. Also I would check which variants are causing troubles: maybe they are multiallelic or indels or something else and Plink doesn´t know how to deal with them. Or maybe there are no minor allele homozygotes at all for that variant and it is expressed in incorrect manner.
(2) I would check the specifications for the input files, both .gen and .sample to see that they are correct. As the files originate from Impute2 there might be some subtle differences.
(3) I would also update Plink version. From the code it seems that you are using either version 1.07 or 1.09. 1.x versions cannot represent probabilities and will make hard-calls so your lose a lot of information because of that. Plink 2.0 can utilize the probabilities and also should have better support for them. You will still be able to use hard-calls if you want.
I need help understanding a weird problem with sed, bash and a while loop.
MY data looks like this:
-File 1- CSV
account,hostnames,status,ipaddress,port,user,pass
-File 2- XML - This is a sample record set for two entries under one account
<accountname="account">
<cname="fqdn or simple name goes here">
<field="hostname">ahostname or ipv4 goes here</field>
<protocol>aprotocol</protocol>
<field="port">aportnumber</field>
<field="username">ausername</field>
<field="password">apassword</field>
</cname>
<cname="fqdn or simple name goes here">
<field="hostname">ahostname or ipv4 goes here</field>
<protocol>aprotocol</protocol>
<field="port">aportnumber</field>
<field="username">ausername</field>
<field="password">apassword</field>
</cname>
</accountname>
So far, I can add records in between the respective account holder from File1 to File2. But, if I need to remove records that no longer exists it does not work efficiently since it wipes other records from different accounts, ie it does not delete between a matched accountname.
I import from File 1 into File 2 with a while loop in my bash program:
-Bash Program excerpts-
//Read File in to F//
cat File 2 | while read F
do
//extract fields from F into variables
_vmname="$(echo $F |grep 'cname'| sed 's/<cname="//g' |sed 's/.\{2\}$//g')"
_account="$(echo $F | grep 'accountname' | sed 's/accountname="//g' |sed 's/.\{2\}$//g')"
// I then compare my File1 and look for stale records that are still in File2
if grep "$_vmname" File1 ;then
continue
else
// if not matched, delete between the respective accountname
sed -i '/'"$_account"'/,/<\/accountname>/ {/'"$_vmname"'/,/<\/cname>/d}' File2
If I manually declare _vmname and _account and run
sed -i '/'"$_account"'/,/<\/accountname>/ {/'"$_vmname"'/,/<\/cname>/d}' File2
It removes the stale records from File2. When I let my bash script run, it does not.
I think I have three problems:
Reading the variables for _vmname and _account name inside a loop makes it read numerous times. Any better way to do is appreciated.
I do not think the sed statement for matching these two patterns and then delete works like I want inside a while loop.
I may have a logic problem with my thought chain.
Any pointers, and please no awk, perl, lxml or python for this one.
Thanks!
and please no awk
I appreciate that you want to keep things simple, and I suppose awk seems more complicated than what you're doing. But I'd like to point out you have so far 3 grep and 4 sed invocations per line in the file, to process another file N times, once per line. That's O(mn) using the slowest method on the planet to read the file (a while loop). And it doesn't work.
I may have a logic problem with my thought chain.
I'm afraid we must allow for that possibility!
The right advice is to tackle XML with an XML parser, because XML is not a regular language and so can't be parsed with regular expressions. And that's really what you need here, because your program processes the whole XML document. You're not just plucking out bits and depending on incidental formatting artifacts; you want to add records that aren't there and remove those that "no longer exist". Apparently there is information in the XML document you need to preserve, else you would just produce it from the CSV. A parser would spoon-feed it to you.
The second-best advice is to use awk. I suppose you might try an approach like:
Process the CSV and produce the XML to be inserted.
In awk, first read the new input XML into an array keyed by cname, Then process the XML target once. For every CNAME, consult your array; if you find a match, insert your pre-constructed XML replacement (or modify the "paragraph" accordingly).
I'm not sure what the delete criteria are, so I don't know if it can be done in the same pass with step #2. If not, extract the salient information somehow. Maybe print a list of keys from each of the two files, and use comm(1) to produce a list of to-be-deleted. Then, similar to step #2, read in that list, and process the XML file one more time. Write anything you delete to stderr so you can keep track of what went missing, from what lines.
Any pointers
Whenever you find yourself processing the same file N times for N inputs, you know you're headed for trouble. One of the two inputs is always smaller, and that one can be put in some kind of array. cat file | while read is another warning signal, telling you use awk or any of a dozen obvious utilities that understand lines of text.
You posted your question on SO two weeks ago. I suspect no one answered it because you warned them away: preemptively saying, in effect, don't tell me to use good tools. I'm only here to suggest that you'll be more comfortable after you take off that straightjacket. Better tools, in this case, are the only right answer.
I am trying to write a bash script that uses sed to modify lines in a config file not containing a specific string. To illustrate by example, I could have ...
/some/file/path1 ipAddress1/subnetMask(rw,sync,no_root_squash)
/some/file/path2 ipAddress1/subnetMask(rw,sync,no_root_squash,anonuid=-1)
/some/file/path3 ipAddress2/subnetMask(rw,sync,no_root_squash,anonuid=0)
/some/file/path4 ipAddress2/subnetMask(rw,sync,no_root_squash,anongid=-1)
/some/file/path5 ipAddress2/subnetMask(rw,sync,no_root_squash,anonuid=-1,anongid=-1)
And I want every line's parenthetical list to be changed such that it contains strings anonuid=-1 and anongid=-1 within its parentheses ...
/some/file/path1 ipAddress1/subnetMask(rw,sync,no_root_squash,anonuid=-1,anongid=-1)
/some/file/path2 ipAddress1/subnetMask(rw,sync,no_root_squash,anonuid=-1,anongid=-1)
/some/file/path3 ipAddress2/subnetMask(rw,sync,no_root_squash,anonuid=-1,anongid=-1)
/some/file/path4 ipAddress2/subnetMask(rw,sync,no_root_squash,anongid=-1,anonuid=-1)
/some/file/path5 ipAddress2/subnetMask(rw,sync,no_root_squash,anonuid=-1,anongid=-1)
As can be seen from the example, both anonuid and anongid may already exist within the parentheses, but it is possible that the original parenthetical list has one string but not the other (lines 2, 3, and 4), the list has neither (line 1), the list has both already set properly (line 5), or even one or both of them are set incorrectly (line 3). When either anonuid or anongid is set to a value other than -1, it must be changed to the proper value of -1 (line 3).
What would be the best way to edit my config file using sed such that anonuid=-1 and anongid=-1 is contained in each line's parenthetical list, separated by a comma delimiter of course?
I think this does what you want:
sed -e '/anonuid/{s/anonuid=[-0-9]*/anonuid=-1/;b gid;};s/)$/,anonuid=-1)/;:gid;/anongid/{s/anongid=[-0-9]*/anongid=-1/;b;};s/)$/,anongid=-1)/'
Basically, it has two nearly identical parts with the first dealing with anonuid and the second anongid, each with a bit of logic to decide if it needs to replace or add the appropriate values. (It doesn't bother to check if the value is already correct, that would just complicate things while not changing the results.)
You can use sed to specify the lines you are interested in:
$ sed '/anonuid=..*,anongid=..*)$/!p' $file
The above will print (p) all lines that don't match the regular expression between the two slashes. I negated the expression by using the !. This way, you're not matching lines with both anaonuid and anongid in them.
Now, you can work on the non-matching lines and editing those with the sed s command:
$ sed '/anonuid=..*,anongid=..*)$/!s/from/to/`
The manipulation might be fairly complex, and you might be passing multiple sed commands to get everything just right.
However, if the string no_root_squash appear in each line you want to change, why not take the simple way out:
$ sed 's/no_root_squash.*$/no_root_squash,anonuid=-1,anongid=-1)/' $file
This is looking for that no_root_squash string, and replacing everything from that string to the end of the line with the text you want. Are there lines you are touching that don't need to be edited? Yes, but you're not really changing those lines. You're basically substituting /no_root_squash,anonuid=-1,anongid=-1) with the same /no_root_squash,anonuid=-1,anongid=-1).
This may be faster even though it's replacing text that doesn't need replacing because there's less processing going on. Plus, it's easier to understand and support in the future.
Response
Thanks David! Yeah I was considering going that route, but I didn't want to rely 100% on every line containing no_root_squash. My current config file only ends in that string, but I'm just not 100% sure that won't potentially be different in the field. Do you think there would be a way to change that so it just overwrites from the end of the last string not containing anonuid=-1 or anongid=-1 onward?
What can you guarantee will be in each line?
You might be able to do a capture group:
sed 's/\(sync,[^,)]*\).*/\1,anonuid=-1,anongid=-1)/' $file
The \(..\) is a capture group. It basically captures that portion of the matching regular expression, and then allows you to reuse it via the \1. I'm capturing from the word sync to a group of characters not including a comma or a closing parentheses. Then, I'm appending the capture group, a comma, and your anon uid and gid.
Will that work?
Maybe I am oversimplifying:
sed 's/anonuid=[-0-9]*[^)]//g;s/anongid=[-0-9]*[^)]//g;s/[)]/anonuid=-1,anongid=-1)/g' test.txt > test3.txt
This just drops any current instance of anonuid or anongid and adds the string
"anonuid=-1,anongid=-1" into the parentheses
Ok,first post..
So I have this assignment to decrypt cryptograms by hand,but I also wanted to automate the process a little if not all at least a few parts,so i browsed around and found some sed and awk one liners to do some things I wanted done,but not all i wanted/needed.
There are some websites that sort of do what I want, but I really want to just do it in bash for some reason,just because I want to understand it better and such :)
The script would take a filename as parameter and output another file such as solution$1 when done.
if [ -e "$PWD/$1" ]; then
echo "$1 exists"
else
echo "$1 doesnt exists"
fi
Would start the script to see if the file in param exists..
Then I found this one liner
sed -e "s/./\0\n/g" $1 | while read c;do echo -n "$c" ; done
Which works fine but I would need to have the number of occurences per letter, I really don't see how to do that.
Here is what I'm trying to achieve more or less http://25yearsofprogramming.com/fun/ciphers.htm for the counting unique letter occurences and such.
I then need to put all letters in lowercase.
After this I see the script doing theses things..
-a subscript that scans a dictionary file for certain pattern and size of words
the bigger words the better.
For example: let's say the solution is the word "apparel" and the crypted word is "zxxzgvk"
is there a regex way to express the pattern that compares those two words and lists the word "apparel" in a dictionnary file because "appa" and "zxxz" are similar patterns and "zxxzgvk" is of similar length with "apparel"
Can this be part done and is it realistic to view the problem like this or is this just far fetched ?
Another subscript who takes the found letters from the previous output word and that swap
letters in the cryptogram.
The swapped letters will be in uppercase to differentiate them over time.
I'll have to figure out then how to proceed to maybe rescan the new found words to see if they're found in a dictionnary file partly or fully as well,then swap more letters or not.
Did anyone see this problem in the past and tried to solve it with the patterns in words
like i described it,or is this just too complex ?
Should I log any of the swaps ?
Maybe just scan through all the crypted words and swap as I go along then do another sweep
with having for constraint in the first sweep to not change uppercase letters(actually to use them as more precise patterns..!)
Anyone did some similar script/program in another langage? If so which one? Maybe I can relate somehow :)
Maybe we can use your insight as to how you thought out your code.
I will happily include the cryptograms I have decoded and the one I have yet to decode :)
Again, the focus of my assignment is not to do this script but just to resolve the cryptograms. But doing scripts or at least trying to see how I would do this script does help me understand a little more how to think in terms of code. Feel free to point me in the right directions!
The cryptogram itself is based on simple alphabetic substitution.
I have done a pastebin here with the code to be :) http://pastebin.com/UEQDsbPk
In pseudocode the way I see it is :
call program with an input filename in param and optionally a second filename(dictionary)
verify the input file exists and isnt empty
read the file's content and echo it on screen
transform to lowercase
scan through the text and count the amount of each letter to do a frequency analysis
ask the user what langage is the text supposed to be (english default)
use the response to specify which letter frequencies to use as a baseline
swap letters corresponding to the frequency analysis in uppercase..
print the changed document on screen
ask the user to swap letters in the crypted text
if user had given a dictionary file as the second argument
then scan the cipher for words and find the bigger words
find words with a similar pattern (some letters repeating letters) in the dictionary file
list on screen the results if any
offer to swap the letters corresponding in the cipher
print modified cipher on screen
ask again to swap letters or find more similar words
More or less it the way I see the script structured.
Do you see anything that I should add,did i miss something?
I hope this revised version is more clear for everyone!
Tl,dr to be frank. To the only question i've found - the answer is yes:) Please split it to smaller tasks and we'll be happy to assist you - if you won't find the answer to these smaller questions before.
If you can put it out in pseudocode, it would be easier. There's all kinds of text-manipulating stuff in unix. The means to employ depend on how big are your texts. I believe they are not so big, or you would have used some compiled language.
For example the easy but costly gawk way to count frequences:
awk -F "" '{for(i=1;i<=NF;i++) freq[$i]++;}END{for(i in freq) printf("%c %d\n", i, freq[i]);}'
As for transliterating, there is tr utility. You can forge and then pass to it the actual strings in each case (that stands true for Caesar-like ciphers).
grep -o . inputfile | sort | uniq -c | sort -rn
Example:
$ echo 'aAAbbbBBBB123AB' | grep -o . | sort | uniq -c | sort -rn
5 B
3 b
3 A
1 a
1 3
1 2
1 1
I have 2 files that are generated elsewhere. First one is "what to search", and second one is the replacement. Both files are huge, about 2-3mb each.
I need to write a bash script that takes an even bigger file (about 200-300mb) and replaces all occurrences of file1 contents to file2 contents.
Problem is, file1 and file2 can contain any possible characters, including regexp special symbols.
How can I solve this problem using sed?
Thanks in advance.
Maybe have a look at chgrep:
http://www.bmk-it.com/projects/chgrep/
Cheers,
gregx
Since you don't actually need regular expressions, just direct string matching, sed is overkill. What you're really looking for is a fixed-string (maybe even binary) stream editor. Unfortunately, I don't know of one... I hate to suggest possibly reinventing a wheel, but you could write something fairly quickly in C that'd do what you want. A rough draft outline:
read search-file into memory
create a buffer of the same size as search-file
read from stdin (or input-file) into buffer.
For each character, if it does not match the parallel character from search-file, shift the buffer. To find out how much to shift it by, read until you find a match to the first character of input-file, then check to see if the rest matches, repeating until you've found a partial match to input-file (or gotten to the end of the buffer). When you shift, print all the non-matching characters to stdout (or output-file)
If the buffer ever fills up, i.e. totally matches input-file, print replacement-file to stdout (or output-file). Depending on memory vs. speed, you can keep replacement-file in memory or read it from disk each time.
You could also attempt to automatically escape all regex characters from your input file. This could be done with a horribly ugly list of sed substitutions, like
sed -e 's/\\/\\\\/g' -e 's#/#\/#' -e 's/\[/\\[/g' ...
(make sure you do the \ one first!)
I don't know about sed but in Perl you could do (off the top of my head, untested):
perl -0777 -pe 'BEGIN{local $/ = undef; open FROM, "<", shift #ARGV; $from = <FROM>; open TO, "<" shift #ARGV; $to = <TO>} s/\Q$from\E/$to/sog' file1 file2 bigger-file > new-bigger-file
If you're interesting in trying Perl, I could try testing it for you tomorrow.
But it sucks the entire bigger-file into memory because it ignores line-breaks so that your search text can span multiple lines. This will meant that it uses quite a lot of memory!
This answer assumes that the search file is one long search string over multiple lines which must be matched in its entirety rather than a number of separate search strings, any of which can be matched.