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Top Forums Shell Programming and Scripting [Solved] Editing the alphabet's based on position information Post 302821991 by RudiC on Sunday 16th of June 2013 01:06:06 PM
Old 06-16-2013
Try this
Code:
awk     'NR==FNR        {F[$1]=$2; R[$1]=$3; next}
                        {for (i=1; i<=NF; i++) if ($i == F[++CNT]) $i=R[CNT]}
         1
        ' file2 FS="" OFS="" file1
ATGTTCCTTCGCTACGTAACAAGTAGAAAAAA
AGCGCTAGCATTGAAGCGGAGGAGAGGAAGA
TGCGATGATGACCCAGTATAAAGAGTGATGAT

 

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string(n)						       Tcl Built-In Commands							 string(n)

__________________________________________________________________________________________________________________________________________________

NAME
string - Manipulate strings SYNOPSIS
string option arg ?arg ...? _________________________________________________________________ DESCRIPTION
Performs one of several string operations, depending on option. The legal options (which may be abbreviated) are: | string bytelength string | Returns a decimal string giving the number of bytes used to represent string in memory. Because UTF-8 uses one to three bytes to | represent Unicode characters, the byte length will not be the same as the character length in general. The cases where a script | cares about the byte length are rare. In almost all cases, you should use the string length operation. Refer to the Tcl_NumUt- | fChars manual entry for more details on the UTF-8 representation. | string compare ?-nocase? ?-length int? string1 string2 | Perform a character-by-character comparison of strings string1 and string2. Returns -1, 0, or 1, depending on whether string1 is lexicographically less than, equal to, or greater than string2. If -length is specified, then only the first length characters are | used in the comparison. If -length is negative, it is ignored. If -nocase is specified, then the strings are compared in a case- | insensitive manner. | string equal ?-nocase? ?-length int? string1 string2 | Perform a character-by-character comparison of strings string1 and string2. Returns 1 if string1 and string2 are identical, or 0 | when not. If -length is specified, then only the first length characters are used in the comparison. If -length is negative, it is | ignored. If -nocase is specified, then the strings are compared in a case-insensitive manner. | string first string1 string2 ?startIndex? | Search string2 for a sequence of characters that exactly match the characters in string1. If found, return the index of the first character in the first such match within string2. If not found, return -1. If startIndex is specified (in any of the forms | accepted by the index method), then the search is constrained to start with the character in string2 specified by the index. For | example, | string first a 0a23456789abcdef 5 | will return 10, but | string first a 0123456789abcdef 11 | will return -1. | string index string charIndex Returns the charIndex'th character of the string argument. A charIndex of 0 corresponds to the first character of the string. | charIndex may be specified as follows: | integer | The char specified at this integral index | end | The last char of the string. | end-integer | The last char of the string minus the specified integer offset (e.g. end-1 would refer to the "c" in "abcd"). | If charIndex is less than 0 or greater than or equal to the length of the string then an empty string is returned. | string is class ?-strict? ?-failindex varname? string | Returns 1 if string is a valid member of the specified character class, otherwise returns 0. If -strict is specified, then an empty | string returns 0, otherwise and empty string will return 1 on any class. If -failindex is specified, then if the function returns | 0, the index in the string where the class was no longer valid will be stored in the variable named varname. The varname will not | be set if the function returns 1. The following character classes are recognized (the class name can be abbreviated): | alnum | Any Unicode alphabet or digit character. | alpha | Any Unicode alphabet character. | ascii | Any character with a value less than u0080 (those that are in the 7-bit ascii range). | boolean | Any of the forms allowed to Tcl_GetBoolean. | control | Any Unicode control character. | digit | Any Unicode digit character. Note that this includes characters outside of the [0-9] range. | double | Any of the valid forms for a double in Tcl, with optional surrounding whitespace. In case of under/overflow in the value, | 0 is returned and the varname will contain -1. | false | Any of the forms allowed to Tcl_GetBoolean where the value is false. | graph | Any Unicode printing character, except space. | integer | Any of the valid forms for an integer in Tcl, with optional surrounding whitespace. In case of under/overflow in the | value, 0 is returned and the varname will contain -1. | lower | Any Unicode lower case alphabet character. | print | Any Unicode printing character, including space. | punct | Any Unicode punctuation character. | space | Any Unicode space character. | true | Any of the forms allowed to Tcl_GetBoolean where the value is true. | upper | Any upper case alphabet character in the Unicode character set. | wordchar | Any Unicode word character. That is any alphanumeric character, and any Unicode connector punctuation characters (e.g. | underscore). | xdigit | Any hexadecimal digit character ([0-9A-Fa-f]). | In the case of boolean, true and false, if the function will return 0, then the varname will always be set to 0, due to the varied | nature of a valid boolean value. | string last string1 string2 ?startIndex? | Search string2 for a sequence of characters that exactly match the characters in string1. If found, return the index of the first character in the last such match within string2. If there is no match, then return -1. If startIndex is specified (in any of the | forms accepted by the index method), then only the characters in string2 at or before the specified startIndex will be considered by | the search. For example, | string last a 0a23456789abcdef 15 | will return 10, but | string last a 0a23456789abcdef 9 | will return 1. | string length string Returns a decimal string giving the number of characters in string. Note that this is not necessarily the same as the number of bytes used to store the string. | string map ?-nocase? charMap string | Replaces characters in string based on the key-value pairs in charMap. charMap is a list of key value key value ... as in the form | returned by array get. Each instance of a key in the string will be replaced with its corresponding value. If -nocase is speci- | fied, then matching is done without regard to case differences. Both key and value may be multiple characters. Replacement is done | in an ordered manner, so the key appearing first in the list will be checked first, and so on. string is only iterated over once, | so earlier key replacements will have no affect for later key matches. For example, | string map {abc 1 ab 2 a 3 1 0} 1abcaababcabababc | will return the string 01321221. | string match ?-nocase? pattern string | See if pattern matches string; return 1 if it does, 0 if it doesn't. If -nocase is specified, then the pattern attempts to match | against the string in a case insensitive manner. For the two strings to match, their contents must be identical except that the following special sequences may appear in pattern: * Matches any sequence of characters in string, including a null string. ? Matches any single character in string. [chars] Matches any character in the set given by chars. If a sequence of the form x-y appears in chars, then any character between x and y, inclusive, will match. When used with -nocase, the end points of the range are converted to lower case | first. Whereas {[A-z]} matches '_' when matching case-sensitively ('_' falls between the 'Z' and 'a'), with -nocase this | is considered like {[A-Za-z]} (and probably what was meant in the first place). x Matches the single character x. This provides a way of avoiding the special interpretation of the characters *?[] in pattern. string range string first last Returns a range of consecutive characters from string, starting with the character whose index is first and ending with the charac- ter whose index is last. An index of 0 refers to the first character of the string. first and last may be specified as for the | index method. If first is less than zero then it is treated as if it were zero, and if last is greater than or equal to the length of the string then it is treated as if it were end. If first is greater than last then an empty string is returned. | string repeat string count | Returns string repeated count number of times. | string replace string first last ?newstring? | Removes a range of consecutive characters from string, starting with the character whose index is first and ending with the charac- | ter whose index is last. An index of 0 refers to the first character of the string. First and last may be specified as for the | index method. If newstring is specified, then it is placed in the removed character range. If first is less than zero then it is | treated as if it were zero, and if last is greater than or equal to the length of the string then it is treated as if it were end. | If first is greater than last or the length of the initial string, or last is less than 0, then the initial string is returned | untouched. | string tolower string ?first? ?last? | Returns a value equal to string except that all upper (or title) case letters have been converted to lower case. If first is speci- | fied, it refers to the first char index in the string to start modifying. If last is specified, it refers to the char index in the | string to stop at (inclusive). first and last may be specified as for the index method. | string totitle string ?first? ?last? | Returns a value equal to string except that the first character in string is converted to its Unicode title case variant (or upper | case if there is no title case variant) and the rest of the string is converted to lower case. If first is specified, it refers to | the first char index in the string to start modifying. If last is specified, it refers to the char index in the string to stop at | (inclusive). first and last may be specified as for the index method. | string toupper string ?first? ?last? | Returns a value equal to string except that all lower (or title) case letters have been converted to upper case. If first is speci- | fied, it refers to the first char index in the string to start modifying. If last is specified, it refers to the char index in the | string to stop at (inclusive). first and last may be specified as for the index method. string trim string ?chars? Returns a value equal to string except that any leading or trailing characters from the set given by chars are removed. If chars is not specified then white space is removed (spaces, tabs, newlines, and carriage returns). string trimleft string ?chars? Returns a value equal to string except that any leading characters from the set given by chars are removed. If chars is not speci- fied then white space is removed (spaces, tabs, newlines, and carriage returns). string trimright string ?chars? Returns a value equal to string except that any trailing characters from the set given by chars are removed. If chars is not speci- fied then white space is removed (spaces, tabs, newlines, and carriage returns). | string wordend string charIndex | Returns the index of the character just after the last one in the word containing character charIndex of string. charIndex may be | specified as for the index method. A word is considered to be any contiguous range of alphanumeric (Unicode letters or decimal dig- | its) or underscore (Unicode connector punctuation) characters, or any single character other than these. | string wordstart string charIndex | Returns the index of the first character in the word containing character charIndex of string. charIndex may be specified as for | the index method. A word is considered to be any contiguous range of alphanumeric (Unicode letters or decimal digits) or underscore | (Unicode connector punctuation) characters, or any single character other than these. SEE ALSO
expr(n), list(n) KEYWORDS
case conversion, compare, index, match, pattern, string, word, equal, ctype Tcl 8.1 string(n)
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