10-15-2009
Emergency work question for a Unix dummy
Im trying to awk two values from each a line (about 40000 lines in the file):
e.g.
gi|10580442|gb|AAG19320.1| inosine-5'-monophosphate dehydrogenase-like [Halobacterium sp. NRC-1]
I want to get the value between the first set of pipes and then the value between square brackets separated by a tab, i.e.
10580442 Halobacterium sp. NRC-1
How do I do it? Im trying to look for awk FS= something something but im lost.
After this (in a separate expression) I want to pick the lines or numbers that have a certain string as the second variable, i.e. Homo sapiens or something else. Im quite sure this part can be accomplished by grep?
Thanks anyone!
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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 Also
ex(1), sed(1), sh(1)
grep(1)