No, that will not fly. This new sed code will match multiple lines per file, but whether you use global or not, this will still only one occurrence of a regular match or one reversed/complemented match per line, the latter only if there is no regular match on that line...
--
You could limit to 10 matches per file, like so, try:
Code:
awk -v len=4 -v string=AATTCCGG -v max=10 '
BEGIN {
FS=RS; RS=">"; OFS=""
C["A"]="T"; C["T"]="A"; C["C"]="G"; C["G"]="C"
}
function reverse_complement(s, t,i,n,F) {
n=split(s,F,"")
for(i=1;i<=n;i++)
t=C[F[i]] t
return t
}
FNR==1{
split(FILENAME, F, ".")
c=1
next
}
{
label=$1
$1=""
rec=$0 FS reverse_complement($0)
while(c<=max && match(rec,string)) {
print F[1] ":" label ":" substr(rec,RSTART+RLENGTH, len)
rec=substr(rec, RSTART+RLENGTH+len)
c++
}
}
' file*.txt
Last edited by Scrutinizer; 04-12-2016 at 11:00 PM..
Reason: Swapped Function for the faster option...
I need help to strip out the first two characters of the variable $FileName. Please help.
FileName=`find . -mtime +0 -name '*'`
Contents of variable $FileName:
./SRIZVI4.MCR_IDEAS_REPORT.LAST.052705.075405.csv
I want to strip out "./" and place the contents in another variable. How do I... (3 Replies)
Can someone please help me figure out what the command syntax I need to use is?
Here is what I am wanting to do.
I have hundreds of thousands of files I need to look for a specific search string in.
These files are spread across multiple subdirectories from one main directory.
I would like... (4 Replies)
Hello everyone,
I'm writing a script to add a string to an XML file, right after a specified string that only occurs once in the file. For testing purposes I created a file 'testfile' that looks like this:
1
2
3
4
5
6
6
7
8
9
And this is the script as far as I've managed:
... (2 Replies)
This is a pretty straight-forward question. Within a program of mine, I have a string that's going to be used as a filename, but it might have some invalid characters in it that wouldn't be valid in a filename. If there are any invalid characters, I want to get rid of them and essentially squeeze... (4 Replies)
Hi Everyone,
I have a.txt
12341" <sip:191@vo.my>;asdf=q"
116aaaa<sip:00091@vo.my>;penguin
would like to get the output
191
00091
Please advice.
Thanks (4 Replies)
Hi all,
I like to know how to get the count of each character in a given word. Using the commands i can easily get the output. How do it without using the commands ( in shell programming or any programming)
if you give outline of the program ( pseudo code )
i used the following commands
... (3 Replies)
Hello. How can i put all of the special characters on my keyboard into a string in c++ ?
I tried this but it doesn't work.
string characters("~`!@#$%^&*()_-+=|\}]{
How can i accomplish this?
Thanks in advance. (1 Reply)
Hello Folks..
I need your help ..
here the example of my problem..i know its easy..i don't all the commands in unix to do this especiallly sed...here my string..
dwc2_dfg_ajja_dfhhj_vw_dec2_dfgh_dwq
desired output is..
dwc2_dfg_ajja_dfhhj
it's a simple task with tail... (5 Replies)
Hi All,
I am trying to extract only characters from a string value eg: abcdedg1234.cnf
How can I extract only characters abcdedg and assign to a variable.
Please help.
Thanks (2 Replies)
I have this fastq file:
@M04961:22:000000000-B5VGJ:1:1101:9280:7106 1:N:0:86
GGGGGGGGGGGGCATGAAAACATACAAACCGTCTTTCCAGAAATTGTTCCAAGTATCGGCAACAGCTTTATCAATACCATGAAAAATATCAACCACACCA
+test-1
GGGGGGGGGGGGGGGGGCCGGGGGFF,EDFFGEDFG,@DGGCGGEGGG7DCGGGF68CGFFFGGGG@CGDGFFDFEFEFF:30CGAFFDFEFF8CAF;;8... (10 Replies)
Discussion started by: Xterra
10 Replies
LEARN ABOUT ULTRIX
grep
grep(1) General Commands Manual grep(1)Name
grep, egrep, fgrep - search file for regular expression
Syntax
grep [option...] expression [file...]
egrep [option...] [expression] [file...]
fgrep [option...] [strings] [file]
Description
Commands of the family search the input files (standard input default) for lines matching a pattern. Normally, each line found is copied
to the standard output.
The command patterns are limited regular expressions in the style of which uses a compact nondeterministic algorithm. The command patterns
are full regular expressions. The command uses a fast deterministic algorithm that sometimes needs exponential space. The command pat-
terns are fixed strings. The command is fast and compact.
In all cases the file name is shown if there is more than one input file. Take care when using the characters $ * [ ^ | ( ) and in the
expression because they are also meaningful to the Shell. It is safest to enclose the entire expression argument in single quotes ' '.
The command searches for lines that contain one of the (new line-separated) strings.
The command accepts extended regular expressions. In the following description `character' excludes new line:
A followed by a single character other than new line matches that character.
The character ^ matches the beginning of a line.
The character $ matches the end of a line.
A . (dot) matches any character.
A single character not otherwise endowed with special meaning matches that character.
A string enclosed in brackets [] matches any single character from the string. Ranges of ASCII character codes may be abbreviated
as in `a-z0-9'. A ] may occur only as the first character of the string. A literal - must be placed where it can't be mistaken as
a range indicator.
A regular expression followed by an * (asterisk) matches a sequence of 0 or more matches of the regular expression. A regular
expression followed by a + (plus) matches a sequence of 1 or more matches of the regular expression. A regular expression followed
by a ? (question mark) matches a sequence of 0 or 1 matches of the regular expression.
Two regular expressions concatenated match a match of the first followed by a match of the second.
Two regular expressions separated by | or new line match either a match for the first or a match for the second.
A regular expression enclosed in parentheses matches a match for the regular expression.
The order of precedence of operators at the same parenthesis level is the following: [], then *+?, then concatenation, then | and new
line.
Options-b Precedes each output line with its block number. This is sometimes useful in locating disk block numbers by context.
-c Produces count of matching lines only.
-e expression
Uses next argument as expression that begins with a minus (-).
-f file Takes regular expression (egrep) or string list (fgrep) from file.
-i Considers upper and lowercase letter identical in making comparisons and only).
-l Lists files with matching lines only once, separated by a new line.
-n Precedes each matching line with its line number.
-s Silent mode and nothing is printed (except error messages). This is useful for checking the error status (see DIAGNOSTICS).
-v Displays all lines that do not match specified expression.
-w Searches for an expression as for a word (as if surrounded by `<' and `>'). For further information, see only.
-x Prints exact lines matched in their entirety only).
Restrictions
Lines are limited to 256 characters; longer lines are truncated.
Diagnostics
Exit status is 0 if any matches are found, 1 if none, 2 for syntax errors or inaccessible files.
See Alsoex(1), sed(1), sh(1)grep(1)