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Full Discussion: Running a program multiple times to search pattern and assign structure
Top Forums Shell Programming and Scripting Running a program multiple times to search pattern and assign structure Post 302762005 by bioinfo on Sunday 27th of January 2013 05:08:38 PM
Old 01-27-2013
Running a program multiple times to search pattern and assign structure
Hi all,
I have a big file (n.txt) with following pattern:

Code:
ATOM      1  N    SER A   1     122.392 152.261 138.190  1.00  0.00     N  
ATOM      2  CA  SER A   1     122.726 151.241 139.183  1.00  0.00     C  
TER
ENDMDL
ATOM      1  N    SER A   1     114.207 142.287 135.439  1.00  0.00      N  
ATOM      2  CA  SER A   1     113.667 143.509 134.894  1.00  0.00      C 
TER
ENDMDL

I am using following script to read pattern and assign structure to them using another program st giving 2 output files-fn.str -m.mol:
Code:
pattern_txt=n.txt
npattern=`grep -c ENDMDL $pattern_txt`
echo $npattern patterns. Assigning_structure:
echo $npattern > st_input
seq -w 1 $npattern >> st_input
st $pattern_txt -fn.str -mn.mol

But this script is reading only first pattern and giving structure of that pattern by running st program. I wish to have structure for all patterns.

Please guide.
 

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LEARN ABOUT X11R4

zgrep

ZGREP(1)                                                      General Commands Manual                                                     ZGREP(1)

NAME

       zgrep - search possibly compressed files for a regular expression

SYNOPSIS

       zgrep [ grep_options ] [ -e ] pattern filename...

DESCRIPTION

       Zgrep  invokes  grep  on  compressed  or  gzipped  files.   These  grep  options  will  cause  zgrep  to  terminate  with  an  error  code:
       (-[drRzZ]|--di*|--exc*|--inc*|--rec*|--nu*).  All other options specified are passed directly to grep.  If no file is specified,  then  the
       standard input is decompressed if necessary and fed to grep.  Otherwise the given files are uncompressed if necessary and fed to grep.

       If the GREP environment variable is set, zgrep uses it as the grep program to be invoked.

EXIT CODE

       2 - An option that is not supported was specified.

AUTHOR

       Charles Levert (charles@comm.polymtl.ca)

SEE ALSO

       grep(1), gzexe(1), gzip(1), zdiff(1), zforce(1), zmore(1), znew(1)

                                                                                                                                          ZGREP(1)
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