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Top Forums Shell Programming and Scripting How to extract some parts of a file to create some outfile Post 302314431 by iammitra on Friday 8th of May 2009 09:49:38 AM
Old 05-08-2009
How to extract some parts of a file to create some outfile

Hi All,
I am very new in programming. I need some help.
I have one input file like:

Number of disabled taxa: 9
Loading mapping file: ncbi.map
Load mapping:
taxId2TaxLevel: 469951
--- Subsample reads (20%): 66680 of 334386
Processing: tree-from-summary
Running tree-from-summary algorithm
Taxonomy:
Gammaproteobacteria: 2767
Alphaproteobacteria: 4123
Deltaproteobacteria: 1343
Epsilonproteobacteria: 26
Not assigned: 1445
No hits: 220253
+++++++++++End of summary for file: B-Red-sum.txt
--- Subsample reads (20%): 67037 of 334386
Processing: tree-from-summary
Running tree-from-summary algorithm
Taxonomy:
Gammaproteobacteria: 2809
Alphaproteobacteria: 4001
Deltaproteobacteria: 1208
Epsilonproteobacteria: 15
Not assigned: 299
No hits: 461890
+++++++++++End of summary for file: B-Red-sum.txt

::::: and so on

I want to create some output like:
Out file1.txt(which grep from, next line of "Taxonomy:" upto "+++++++++++End" ) with no space in front of line and so on.

So the desired ouput will be:
outfile1.txt
Gammaproteobacteria: 2767
Alphaproteobacteria: 4123
Deltaproteobacteria: 1343
Epsilonproteobacteria: 26
Not assigned: 1445
No hits: 220253

outfile2.txt
Gammaproteobacteria: 2809
Alphaproteobacteria: 4001
Deltaproteobacteria: 1208
Epsilonproteobacteria: 15
Not assigned: 299
No hits: 461890

and so on.

Can anybody please help me in this matter?

I tried with some code like this. But didn't workout.
--------------------------------------------------------------------------
#!/bin/tcsh
if $#argv != "1" then
echo "Usage: process-file-script 1st-output-file-as-inputfile"
exit 0
endif

FIL_NM=$1

str=""
cat $FIL_NM | while read LINE
do
if [ "`echo $LINE | awk '{print $1}'`" = "+++++++++++Begin" ] ; then
n=1
c=1
fi
if [ "`echo $LINE |grep Gamma`"] ; then
NEW_FIL_NM=$FIL_NM"_"$n.txt"
fi

fi
if [ "`echo $LINE | awk '{print $1}'`" = "+++++++++++End" ] ; then
n=0
fi
done
--------------------------------------------------------
Please help...
Many thanks in advance...
Best wishes,
Mitra
 

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XCLIP-COPYFILE(1)					      General Commands Manual						 XCLIP-COPYFILE(1)

NAME
xclip-copyfile, xclip-cutfile, xclip-pastefile - copy and move files via the X clipboard SYNOPSIS
xclip-copyfile [-p] FILES... xclip-cutfile [-p] FILES... xclip-pastefile DESCRIPTION
xclip-copyfile copies files into the X clipboard, recursing into directories. xclip-cutfile copies the files, but also deletes them afterwards. -p preserve path formation xclip-pastefile pastes the files out of the clipboard EXAMPLES
Copying a file to a remote host [maggie.lkpg.cendio.se ~]$ echo "A file created on ${HOSTNAME}" > file1 [maggie.lkpg.cendio.se ~]$ xclip-copyfile file1 [sofie.homeip.net ~/doc]$ xclip-pastefile file1 [sofie.homeip.net ~/doc]$ cat file1 A file created on maggie.lkpg.cendio.se Copying an entire tree structure [sofie.homeip.net ~]$ xclip-copyfile doc [maggie.lkpg.cendio.se ~/tmp]$ xclip-pastefile doc/ doc/letter-mom-april.txt doc/file1 doc/letter-dad-march.txt Copying files with preserved path information [maggie.lkpg.cendio.se ~]$ xclip-copyfile -p /etc/sysconfig/grub tar: Removing leading `/' from member names [sofie.homeip.net ~/tmp]$ xclip-pastefile etc/sysconfig/grub [sofie.homeip.net ~/tmp]$ ls etc/sysconfig/grub etc/sysconfig/grub Moving files [sofie.homeip.net ~]$ ls letter-brother-may.txt letter-brother-may.txt [sofie.homeip.net ~]$ xclip-cutfile letter-brother-may.txt [sofie.homeip.net ~]$ ls letter-brother-may.txt ls: cannot access letter-brother-may.txt: No such file or directory [sofie.homeip.net ~]$ cd doc [sofie.homeip.net ~/doc]$ xclip-pastefile letter-brother-may.txt AUTHORS
This manual page was written by Maximilian Gass <mxey@cloudconnected.org> for the Debian project. It may be used for everything else, of course. XCLIP-COPYFILE(1)
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