09-10-2008
Yeah, using a number for the group was where I originally wanted to be but the problem is that it tells a biologist little beyond the fact that "you just reached Group_10000289".
My next step (which I know how to do) is to substitute the group ID's w. the name of the gene. Now a biologist knows (s)he can look for "geneX" of his interest to see how many groups and how many members per group the gene has. And once I have merged that information I can use it to create interfaces for my analysis where people can come and query or manipulate or add to or analyze the results, etc.
Again, thanks for the valuable discussions. This helps me keep my project ideas clear in both the near and long term.
More after trying the code.
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GREP(1) General Commands Manual GREP(1)
NAME
grep, egrep, fgrep - search a file for a pattern
SYNOPSIS
grep [ option ] ... expression [ file ] ...
egrep [ option ] ... [ expression ] [ file ] ...
fgrep [ option ] ... [ strings ] [ file ]
DESCRIPTION
Commands of the grep family search the input files (standard input default) for lines matching a pattern. Normally, each line found is
copied to the standard output. Grep patterns are limited regular expressions in the style of ex(1); it uses a compact nondeterministic
algorithm. Egrep patterns are full regular expressions; it uses a fast deterministic algorithm that sometimes needs exponential space.
Fgrep patterns are fixed strings; it is fast and compact. The following options are recognized.
-v All lines but those matching are printed.
-x (Exact) only lines matched in their entirety are printed (fgrep only).
-c Only a count of matching lines is printed.
-l The names of files with matching lines are listed (once) separated by newlines.
-n Each line is preceded by its relative line number in the file.
-b Each line is preceded by the block number on which it was found. This is sometimes useful in locating disk block numbers by con-
text.
-i The case of letters is ignored in making comparisons -- that is, upper and lower case are considered identical. This applies to
grep and fgrep only.
-s Silent mode. Nothing is printed (except error messages). This is useful for checking the error status.
-w The expression is searched for as a word (as if surrounded by `<' and `>', see ex(1).) (grep only)
-e expression
Same as a simple expression argument, but useful when the expression begins with a -.
-f file
The regular expression (egrep) or string list (fgrep) is taken from the file.
In all cases the file name is shown if there is more than one input file. Care should be taken when using the characters $ * [ ^ | ( ) and
in the expression as they are also meaningful to the Shell. It is safest to enclose the entire expression argument in single quotes ' '.
Fgrep searches for lines that contain one of the (newline-separated) strings.
Egrep accepts extended regular expressions. In the following description `character' excludes newline:
A followed by a single character other than newline matches that character.
The character ^ matches the beginning of a line.
The character $ matches the end of a line.
A . (period) 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 newline 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 [] then *+? then concatenation then | and newline.
Ideally there should be only one grep, but we don't know a single algorithm that spans a wide enough range of space-time tradeoffs.
SEE ALSO
ex(1), sed(1), sh(1)
DIAGNOSTICS
Exit status is 0 if any matches are found, 1 if none, 2 for syntax errors or inaccessible files.
BUGS
Lines are limited to 256 characters; longer lines are truncated.
4th Berkeley Distribution April 29, 1985 GREP(1)