Perl: Printing Multiple Lines after pattern match Post: 302333256

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Top Forums Shell Programming and Scripting Perl: Printing Multiple Lines after pattern match Post 302333256 by durden_tyler on Sunday 12th of July 2009 12:25:08 AM

07-12-2009

Registered User

Quote:

Originally Posted by Deep9000

...
PROBLEM:
Capture/finding the Ids stored in File1 from file2 is trivial.
What I need to capture "also" is the remaining part.
For example:
This part of the code gives me the line when it has found the match: Query= 009463_3922_1827 length=252 uaccno=FIFOXZ216JUM5H
...
...
Now how can I get to the other lines below this (Query= 009463_3922_1827 length=252 uaccno=FIFOXZ216JUM5H) line.
For example, everything until
Query= 009525_3967_2963 length=249 uaccno=FIFOXZ216JYL81
(249 letters)
...

Since you've solved the first part of the problem, given below is one way to solve the second part.

Assuming that you *know* your ID (from file1), the perl one-liner below fetches the multiline pattern associated with it:

Code:

$ 
$ cat file2
Query= 009463_3922_1827 length=252
(252 letters)

Sequences producing significant alignments: (bits) Value

ref|NZ_ACCL02000008.1| Bryantella formatexigens DSM 14469 B_form... 153 2e-37

Query: 243 cccgcacacg 252
|||||||||
Sbjct: 89219 accgcacacg 89228
More stufff here

Query= 009525_3967_2963 length=249 uaccno=FIFOXZ216JYL81
(249 letters)
AND MORE STUFF HERE 
$ 
$ # try the first ID
$ perl -ne 'BEGIN{undef $/; $x="009463_3922_1827"}{while (/(Query= $x.*)Query=|(Query= $x.*)/msg){ print $1 eq "" ? $2 : $1 }}' file2
Query= 009463_3922_1827 length=252
(252 letters)

Sequences producing significant alignments: (bits) Value

ref|NZ_ACCL02000008.1| Bryantella formatexigens DSM 14469 B_form... 153 2e-37

Query: 243 cccgcacacg 252
|||||||||
Sbjct: 89219 accgcacacg 89228
More stufff here

$ 
$ # another ID
$ perl -ne 'BEGIN{undef $/; $x="009525_3967_2963"}{while (/(Query= $x.*)Query=|(Query= $x.*)/msg){ print $1 eq "" ? $2 : $1 }}' file2
Query= 009525_3967_2963 length=249 uaccno=FIFOXZ216JYL81
(249 letters)
AND MORE STUFF HERE 
$ 
$

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head

HEAD(1) 								FSF								   HEAD(1)

NAME

       head - output the first part of files

SYNOPSIS

       head [OPTION]... [FILE]...

DESCRIPTION

       Print  first  10 lines of each FILE to standard output.	With more than one FILE, precede each with a header giving the file name.  With no
       FILE, or when FILE is -, read standard input.

       Mandatory arguments to long options are mandatory for short options too.

       -c, --bytes=SIZE
	      print first SIZE bytes

       -n, --lines=NUMBER
	      print first NUMBER lines instead of first 10

       -q, --quiet, --silent
	      never print headers giving file names

       -v, --verbose
	      always print headers giving file names

       --help display this help and exit

       --version
	      output version information and exit

       SIZE may have a multiplier suffix: b for 512, k for 1K, m for 1 Meg.

AUTHOR

       Written by David MacKenzie.

REPORTING BUGS

       Report bugs to <bug-coreutils@gnu.org>.

COPYRIGHT

       Copyright (C) 2002 Free Software Foundation, Inc.
       This is free software; see the source for copying conditions.  There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICU-
       LAR PURPOSE.

SEE ALSO

       The  full documentation for head is maintained as a Texinfo manual.  If the info and head programs are properly installed at your site, the
       command

	      info head

       should give you access to the complete manual.

head (coreutils) 4.5.3						   February 2003							   HEAD(1)

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