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Top Forums Shell Programming and Scripting Search for a pattern,extract value(s) from next line, extract lines having those extracted value(s) Post 302676021 by AshwaniSharma09 on Tuesday 24th of July 2012 02:35:01 AM
Old 07-24-2012
Thanks Corona688 for the reply. Files containing CYTOCHROME C are treating your script very well. Above I took examples of those files which are throwing errors. The only difference here is, I am searching for pattern "LYSOZYME" instead of CYTOCHROME C. The script on a file (with extension .pdb) goes like this:
Code:
cat test.sh 
awk -F":" '(!RGX) && /LYSOZYME/ && !/ANTIBODY/ && (NF == 2){
        getline
        gsub(/[;, ]*/, "");
        RGX="[" $2 "]"
        FS=" ";
} RGX && ($5 ~ RGX) && /ATOM/' 1G7H.pdb

My little understanding tells me that your speculation is right. Something is messing up with RGX variable. I think ":" symbol just 1 line above to the line mentioned in error. As in file 132L.pdb, error mentions line 4 and I can see a ":" in line 3 and matching pattern in left hand side of it. Just to be clear, I don't want to extract line 3 or 4 here.

Thanks and Regards,
Ashwani

Quote:
Originally Posted by Corona688
I can't tell. CYTOCHROME C isn't anywhere in that file, so I have no idea what it's supposed to match. It must be picking up regex-like characters from the string it's trying to catch, which foul up the RGX variable when it's created.

You can put the script in a file easily enough like this:

Code:
$ cat script.awk

(!RGX) && ($0 ~ RMATCH) && (NF==2) {
         getline
         gsub(/[;, ]*/, "");
         RGX="[" $2 "]"
         FS=" ";
} RGX && ($5 ~ RGX) && /ATOM/

$ awk -v RMATCH="CYTOCHROME C" -f script.awk file

...

$

I'm probably out for the rest of the day unfortunately. I'll check this evening if I can, for further details on your difficulty.
 

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MU-EXTRACT(1)						      General Commands Manual						     MU-EXTRACT(1)

NAME
mu_extract - display and save message parts (attachments), and open them with other tools. SYNOPSIS
mu extract [options] <file> mu extract [options] <file> <pattern> DESCRIPTION
mu extact is the mu sub-command for extracting MIME-parts (e.g., attachments) from mail messages. It works on message files, and does not require the message to be indexed in the database. For attachments, the file name used when saving it, is the name of the attachment in the message. If there is no such name, or when saving non-attachment MIME-parts, a name is derived from the message-id of the message. If you specify a pattern (a case-insensitive regular expression) as the second argument, all attachments with filenames matching that pat- tern will be extracted. The regular expressions are Perl-compatible (as per the PCRE-library). Without any options, mu extract simply outputs the list of leaf MIME-parts in the message. Only 'leaf' MIME-parts (including RFC822 attach- ments) are considered, multipart/* etc. are ignored. OPTIONS
-a, --save-attachments save all MIME-parts that look like attachments. --save-all save all non-multipart MIME-parts. --parts=<parts> only consider the following numbered parts (comma-separated list).The numbers for the parts can be seen from running mu extract without any options but only the message file. --target-dir=<dir> save the parts in the target directory rather than the current working directory. --overwrite overwrite existing files with the same name; by default overwriting is not allowed. --play Try to 'play' (open) the attachment with the default application for the particular file type. On MacOS, this uses the open program, on other platforms is uses xdg-open. You can choose a different program by setting the MU_PLAY_PROGRAM environment variable. EXAMPLES
To display information about all the MIME-parts in a message file: $ mu extract msgfile To extract MIME-part 3 and 4 from this message, overwriting existing files with the same name: $ mu extract --parts=3,4 --overwrite msgfile To extract all files ending in '.jpg' (case-insensitive): $ mu extract msgfile '.*.jpg' To extract an mp3-file, and play it in the the default mp3-playing application. $ mu extract --play msgfile 'whoopsididitagain.mp3' BUGS
Please report bugs if you find them: http://code.google.com/p/mu0/issues/list AUTHOR
Dirk-Jan C. Binnema <djcb@djcbsoftware.nl> SEE ALSO
mu(1) User Manuals February 2012 MU-EXTRACT(1)
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