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Top Forums Shell Programming and Scripting Outputting characters after a given string and reporting the characters in the row below --sed Post 303028723 by Don Cragun on Monday 14th of January 2019 02:20:01 AM
Old 01-14-2019
Quote:
Originally Posted by Xterra
Don
Thanks!
PS. If I would like to search for more than one string (GCATGAAAACATACA and TTTCCAGAAATTGT) and report different number characters (3 and 6. I should be able to do it passing the strings and number of charters as variables, right?

Code:
awk -vlen="3 6" -vstr="GCATGAAAACATACA TTTCCAGAAATTGT" '
BEGIN {	for (MX=n=split (str, TMP); n>0; n--) SRCH[TMP[n]] = n
	String = n
	StringLen = length(String)
}
/^@/ {	matchline = NR + 1
	qualityline = NR + 3
	next
}
NR == matchline {
	if(spot = index($0, String))
		printf("Codon:\t%s\tQuality Score:\t",
		    substr($0, spot + StringLen, len))
	else	qualityline = 0
	next
}
NR == qualityline {
	printf("%s\n", substr($0, spot + StringLen, len))
}' test.txt

I'm pretty sure that the code you have shown us above won't do what you want to do, but from your new description I'm not sure what it is that you're trying to do.

The String variable in my code needs to be a string; not a number representing an index into the TMP[] and/or SRC[] arrays. If you're looking for multiple strings on the 2nd line of each group of input lines you're processing, you need to perform more than one index() operation to search for those strings.

If you could give us a clearer description and show us the output you hope to produce from your new requirements, maybe we could help.
This User Gave Thanks to Don Cragun For This Post:
 

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StringLabels(3) 						   OCaml library						   StringLabels(3)

NAME
StringLabels - String operations. Module Module StringLabels Documentation Module StringLabels : sig end String operations. val length : string -> int Return the length (number of characters) of the given string. val get : string -> int -> char String.get s n returns character number n in string s . The first character is character number 0. The last character is character number String.length s - 1 . You can also write s.[n] instead of String.get s n . Raise Invalid_argument index out of bounds if n is outside the range 0 to (String.length s - 1) . val set : string -> int -> char -> unit String.set s n c modifies string s in place, replacing the character number n by c . You can also write s.[n] <- c instead of String.set s n c . Raise Invalid_argument index out of bounds if n is outside the range 0 to (String.length s - 1) . val create : int -> string String.create n returns a fresh string of length n . The string initially contains arbitrary characters. Raise Invalid_argument if n < 0 or n > Sys.max_string_length . val make : int -> char -> string String.make n c returns a fresh string of length n , filled with the character c . Raise Invalid_argument if n < 0 or n > Sys.max_string_length . val copy : string -> string Return a copy of the given string. val sub : string -> pos:int -> len:int -> string String.sub s start len returns a fresh string of length len , containing the characters number start to start + len - 1 of string s . Raise Invalid_argument if start and len do not designate a valid substring of s ; that is, if start < 0 , or len < 0 , or start + len > StringLabels.length s . val fill : string -> pos:int -> len:int -> char -> unit String.fill s start len c modifies string s in place, replacing the characters number start to start + len - 1 by c . Raise Invalid_argu- ment if start and len do not designate a valid substring of s . val blit : src:string -> src_pos:int -> dst:string -> dst_pos:int -> len:int -> unit String.blit src srcoff dst dstoff len copies len characters from string src , starting at character number srcoff , to string dst , start- ing at character number dstoff . It works correctly even if src and dst are the same string, and the source and destination chunks overlap. Raise Invalid_argument if srcoff and len do not designate a valid substring of src , or if dstoff and len do not designate a valid sub- string of dst . val concat : sep:string -> string list -> string String.concat sep sl concatenates the list of strings sl , inserting the separator string sep between each. val iter : f:(char -> unit) -> string -> unit String.iter f s applies function f in turn to all the characters of s . It is equivalent to f s.[0]; f s.[1]; ...; f s.[String.length s - 1]; () . val iteri : f:(int -> char -> unit) -> string -> unit Same as String.iter , but the function is applied to the index of the element as first argument (counting from 0), and the character itself as second argument. Since 4.00.0 val map : f:(char -> char) -> string -> string String.map f s applies function f in turn to all the characters of s and stores the results in a new string that is returned. Since 4.00.0 val trim : string -> string Return a copy of the argument, without leading and trailing whitespace. The characters regarded as whitespace are: ' ' , '12' , ' ' , ' ' , and ' ' . If there is no whitespace character in the argument, return the original string itself, not a copy. Since 4.00.0 val escaped : string -> string Return a copy of the argument, with special characters represented by escape sequences, following the lexical conventions of OCaml. If there is no special character in the argument, return the original string itself, not a copy. val index : string -> char -> int String.index s c returns the position of the leftmost occurrence of character c in string s . Raise Not_found if c does not occur in s . val rindex : string -> char -> int String.rindex s c returns the position of the rightmost occurrence of character c in string s . Raise Not_found if c does not occur in s . val index_from : string -> int -> char -> int Same as StringLabels.index , but start searching at the character position given as second argument. String.index s c is equivalent to String.index_from s 0 c . val rindex_from : string -> int -> char -> int Same as StringLabels.rindex , but start searching at the character position given as second argument. String.rindex s c is equivalent to String.rindex_from s (String.length s - 1) c . val contains : string -> char -> bool String.contains s c tests if character c appears in the string s . val contains_from : string -> int -> char -> bool String.contains_from s start c tests if character c appears in the substring of s starting from start to the end of s . Raise Invalid_argument if start is not a valid index of s . val rcontains_from : string -> int -> char -> bool String.rcontains_from s stop c tests if character c appears in the substring of s starting from the beginning of s to index stop . Raise Invalid_argument if stop is not a valid index of s . val uppercase : string -> string Return a copy of the argument, with all lowercase letters translated to uppercase, including accented letters of the ISO Latin-1 (8859-1) character set. val lowercase : string -> string Return a copy of the argument, with all uppercase letters translated to lowercase, including accented letters of the ISO Latin-1 (8859-1) character set. val capitalize : string -> string Return a copy of the argument, with the first character set to uppercase. val uncapitalize : string -> string Return a copy of the argument, with the first character set to lowercase. type t = string An alias for the type of strings. val compare : t -> t -> int The comparison function for strings, with the same specification as Pervasives.compare . Along with the type t , this function compare allows the module String to be passed as argument to the functors Set.Make and Map.Make . OCamldoc 2014-06-09 StringLabels(3)
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