I'm trying to isolate lines that contain the following: '[Homosapiens]' from a file.
My file looks something like this:
br
blabla
>blabldi[Homosapiens]
>skadlfjkl[Musmusculus]
I only want to isolate the third line.
I have tried the following:
grep -F '\*[Homosapiens]' mytext.txt
and
fgrep '\*[Homosapiens]' mytext.txt
but both are not working.
Can anyone solve this problem?
What about the following:
fgrep "[Homosapiens]" mytext.txt
Or:
grep "\[Homosapiens\]" mytext.txt
Two remarks:
grep (or whatever of its family members fgrep, egrep, ...) search for an entry inside a line of text, so there is no need to try to fit the whole line inside your grep expression.
The square brackets have a special meaning (grep [a-e] means a search for all letters from 'a' to 'e'). Using a backslash in front of a square bracket disables that feature and gives you the opportunity to look for a square bracket.
Related
I have a text file using markup language (similar to wikipedia articles)
cat test.txt
This is a sample text having: colon in the text. and there is more [[in single or double: brackets]]. I need to select the first word only.
and second line with no [brackets] colon in it.
I need to select the word "having:" only because that is part of regular text. I tried
grep -v '[*:*]' test.txt
This will correctly avoid the tags, but does not select the expected word.
The square brackets specify a character class, so your regular expression looks for any occurrence of one of the characters * or : (or *, but we said that already, didn't we?)
grep has the option -o to only print the matching text, so something lie
grep -ow '[^[:space:]]*:[^[:space:]]*' file.txt
would extract any text with a colon in it, surrounded by zero or more non-whitespace characters on each side. The -w option adds the condition that the match needs to be between word boundaries.
However, if you want to restrict in which context you want to match the text, you will probably need to switch to a more capable tool than plain grep. For example, you could use sed to preprocess each line to remove any bracketed text, and then look for matches in the remaining text.
sed -e 's/\[.*]//g' -e 's/ [^: ]*$/ /' -e 's/[^: ]* //g' -e 's/ /\n/' file.txt
(This assumes that your sed recognizes \n in the replacement string as a literal newline. There are simple workarounds available if it doesn't, but let's not go there if it's not necessary.)
In brief, we first replace any text between square brackets. (This needs to be improved if your input could contain multiple sequences of square brackets on a line with normal text between them. Your example only shows nested square brackets, but my approach is probably too simple for either case.) Then, we remove any words which don't contain a colon, with a special provision for the last word on the line, and some subsequent cleanup. Finally, we replace any remaining spaces with newlines, and (implicitly) print whatever is left. (This still ends up printing one newline too many, but that is easy to fix up later.)
Alternatively, we could use sed to remove any bracketed expressions, then use grep on the remaining tokens.
sed -e :a -e 's/\[[^][]*\]//' -e ta file.txt |
grep -ow '[^[:space:]]*:[^[:space:]]*'
The :a creates a label a and ta says to jump back to that label and try again if the regex matched. This one also demonstrates how to handle nested and repeated brackets. (I suppose it could be refactored into the previous attempt, so we could avoid the pipe to grep. But outlining different solution models is also useful here, I suppose.)
If you wanted to ensure that there is at least one non-colon character adjacent to the colon, you could do something like
... file.txt |
grep -owE '[^:[:space:]]+:[^[:space:]]*|[^[:space:]]*:[^: [:space:]]+'
where the -E option selects a slightly more modern regex dialect which allows us to use | between alternatives and + for one or more repetitions. (Basic grep in 1969 did not have these features at all; much later, the POSIX standard grafted them on with a slightly wacky syntax which requires you to backslash them to remove the literal meaning and select the metacharacter behavior... but let's not go there.)
Notice also how [^:[:space:]] matches a single character which is not a colon or a whitespace character, where [:space:] is the (slightly arcane) special POSIX named character class which matches any whitespace character (regular space, horizontal tab, vertical tab, possibly Unicode whitespace characters, depending on locale).
Awk easily lets you iterate over the tokens on a line. The requirement to ignore matches within square brackets complicates matters somewhat; you could keep a separate variable to keep track of whether you are inside brackets or not.
awk '{ for(i=1; i<=NF; ++i) {
if($i ~ /\]/) { brackets=0; next }
if($i ~ /\[/) brackets=1;
if(brackets) next;
if($i ~ /:/) print $i }' file.txt
This again hard-codes some perhaps incorrect assumptions about how the brackets can be placed. It will behave unexpectedly if a single token contains a closing square bracket followed by an opening one, and has an oversimplified treatment of nested brackets (the first closing bracket after a series of opening brackets will effectively assume we are no longer inside brackets).
A combined solution using sed and awk:
sed 's/ /\n/g' test.txt | gawk 'i==0 && $0~/:$/{ print $0 }/\[/{ i++} /\]/ {i--}'
sed will change all spaces to a newline
awk (or gawk) will output all lines matching $0~/:$/, as long as i equals zero
The last part of the awk stuff keeps a count of the opening and closing brackets.
Another solution using sed and grep:
sed -r -e 's/\[.*\]+//g' -e 's/ /\n/g' test.txt | grep ':$'
's/\[.*\]+//g' will filter the stuff between brackets
's/ /\n/g' will replace a space with a newline
grep will only find lines ending with :
A third on using only awk:
gawk '{ for (t=1;t<=NF;t++){
if(i==0 && $t~/:$/) print $t;
i=i+gsub(/\[/,"",$t)-gsub(/\]/,"",$t) }}' test.txt
gsub returns the number of replacements.
The variable i is used to count the level of brackets. On every [ it is incremented by 1, and on every ] it is decremented by one. This is done because gsub(/\[/,"",$t) returns the number of replaced characters. When having a token like [[][ the count is increased by (3-1=) 2. When a token has brackets AND a semicolon my code will fail, because the token will match, if it ends with a :, before the count of the brackets.
How can I use the BBedit grep option to replace LaTeX commands like
\textcolor{blue}{Some text}
by the contents of the second set of braces, so
Some text
?
The BBEdit Grep Tutorial gives a lot of information and good examples on using the grep option in BBEdit. What you are trying to achieve is actually a variation of one of the examples. The solution is to enter the following:
Find: \\textcolor\{blue\}\{([^\}]*)\}
Replace: \1
The relevant part is the "Find" section. The first part: \\textcolor\{blue\}\{ basically searches for the content \textcolor{blue}{. You need the \s to escape special characters.
Next, we have the cryptic sequence ([^\}]*): The (...) saves everything inside the parentheses into the variable \1, which you can use in the "Replace" section to insert the content. The [^\}]* consists of ^\} which means match all characters which are not ^ a closing brace \}. With [...]* we say, match any number of "not brace" characters. Overall, this expression makes the grep match all characters which are not closing braces, and saves them into \1.
Finally, the expression ends with a \}, i.e. a closing brace, which is the end of what we want to find.
The "Replace" only contains \1, which is everything inside the parentheses (...) in the "Find" field.
There is a possibility to search using grep in TextWrangler
I want to find and replace the following word: bauvol, but not bauvolumen.
I tried typing ^bauvol$ into the search field but that didn't do the trick, it didn't find anything, although the word is clearly there.
I think it's because, in grep, the ^and $signify start and end of line, not a word?!
You want to use \b as word boundaries, as #gromi08 said:
\bbauvol\b
If you want to copy any portion of this word (so you can replace it, modify it, change the case, etc.) it is usually best to wrap it in ( and ) braces so you can reference them in the Replace box:
Find:
(\bbauvol\b)
Replace:
<some_tag>\1</some_tag>
Did you have anything specific you were trying to do with the result once you found it (cut it, duplicate it, etc.)?
Use the -w option of grep (see grep man-page.
This option searches for the expression as a word.
Therefore the command will be:
cat file.txt | grep -w bauvol
And yes, ^ and $ are for start and end of line.
I am trying to grep the output of a command that outputs unknown text and a directory per line. Below is an example of what I mean:
.MHuj.5.. /var/log/messages
The text and directory may be different from time to time or system to system. All I want to do though is be able to grep the directory out and send it to a variable.
I have looked around but cannot figure out how to grep to the end of a word. I know I can start the search phrase looking for a "/", but I don't know how to tell grep to stop at the end of the word, or if it will consider the next "/" a new word or not. The directories listed could change, so I can't assume the same amount of directories will be listed each time. In some cases, there will be multiple lines listed and each will have a directory list in it's output. Thanks for any help you can provide!
If your directory paths does not have spaces then you can do:
$ echo '.MHuj.5.. /var/log/messages' | awk '{print $NF}'
/var/log/messages
It's not clear from a single example whether we can generalize that e.g. the first occurrence of a slash marks the beginning of the data you want to extract. If that holds, try
grep -o '/.*' file
To fetch everything after the last space, try
grep -o '[^ ]*$' file
For more advanced pattern matching and extraction, maybe look at sed, or Awk or Perl or Python.
Your line can be described as:
^\S+\s+(\S+)$
That's assuming whitespace is your delimiter between the random text and the directory. It simply separates the whitespace from the non-whitespace and captures the second part.
Or you might want to look into the word boundary character class: \b.
I know you said to use grep, but I can't help to mention that this is trivially done using awk:
awk '{ print $NF }' input.txt
This is assuming that a whitespace is the delimiter and that the path does not contain any whitespaces.
I have a file where I want to grep for lines that start with either -rwx or drwx AND end in any number.
I've got this, but it isnt quite right. Any ideas?
grep [^.rwx]*[0-9] usrLog.txt
The tricky part is a regex that includes a dash as one of the valid characters in a character class. The dash has to come immediately after the start for a (normal) character class and immediately after the caret for a negated character class. If you need a close square bracket too, then you need the close square bracket followed by the dash. Mercifully, you only need dash, hence the notation chosen.
grep '^[-d]rwx.*[0-9]$' "$#"
See: Regular Expressions and grep for POSIX-standard details.
It looks like you were on the right track... The ^ character matches beginning-of-line, and $ matches end-of-line. Jonathan's pattern will work for you... just wanted to give you the explanation behind it
It should be noted that not only will the caret (^) behave differently within the brackets, it will have the opposite result of placing it outside of the brackets. Placing the caret where you have it will search for all strings NOT beginning with the content you placed within the brackets. You also would want to place a period before the asterisk in between your brackets as with grep, it also acts as a "wildcard".
grep ^[.rwx].*[0-9]$
This should work for you, I noticed that some posters used a character class in their expressions which is an effective method as well, but you were not using any in your original expression so I am trying to get one as close to yours as possible explaining every minor change along the way so that it is better understood. How can we learn otherwise?
You probably want egrep. Try:
egrep '^[d-]rwx.*[0-9]$' usrLog.txt
are you parsing output of ls -l?
If you are, and you just want to get the file name
find . -iname "*[0-9]"
If you have no choice because usrLog.txt is created by something/someone else and you absolutely must use this file, other options include
awk '/^[-d].*[0-9]$/' file
Ruby(1.9+)
ruby -ne 'print if /^[-d].*[0-9]$/' file
Bash
while read -r line ; do case $line in [-d]*[0-9] ) echo $line; esac; done < file
Many answers provided for this question. Just wanted to add one more which uses bashism-
#! /bin/bash
while read -r || [[ -n "$REPLY" ]]; do
[[ "$REPLY" =~ ^(-rwx|drwx).*[[:digit:]]+$ ]] && echo "Got one -> $REPLY"
done <"$1"
#kurumi answer for bash, which uses case is also correct but it will not read last line of file if there is no newline sequence at the end(Just save the file without pressing 'Enter/Return' at the last line).