How to extract some parts of a file to create some outfile


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# 1  
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
# 2  
Code:
nawk '
    /^Taxonomy/ {p=6;close(out);out="output" ++cnt ".txt";next}
    p &&p-- { print > out }' myInputFile

# 3  
if you have Python, here's an alternative solution
Code:
f=0;i=0
for line in open("file"):
    line=line.strip()
    if line.startswith("+++++++++++"): 
        f=0
        o.close()
    if "Taxonomy:" in line: 
        f=1;i=i+1
        o=open("out_"+str(i)+".txt","w")
    if f:
        print >>o, line

# 4  
Hallo ghostdog74,
Thanks for your reply. But I am sorry to say that I forgot to mention : in my input file there are not always only 6 lines. I just copied some lines.. This lines varies from 100 to 200. So it is necessary for the program to read +++++++++End.

Thanks a lot,
Mitra.
# 5  
And here's a perl solution:

Code:
$
$
$ cat input.txt
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
$
$
$
$ perl -ne '{$/=""; $i=1;
>   while (/^Taxonomy:.(.*?)\+{11}/msgi) {
>     open(OUT,">outfile".$i++.".txt"); print OUT $1; close(OUT);
>   }}' input.txt
$
$
$ cat outfile1.txt
Gammaproteobacteria: 2767
Alphaproteobacteria: 4123
Deltaproteobacteria: 1343
Epsilonproteobacteria: 26
Not assigned: 1445
No hits: 220253
$
$
$ cat outfile2.txt
Gammaproteobacteria: 2809
Alphaproteobacteria: 4001
Deltaproteobacteria: 1208
Epsilonproteobacteria: 15
Not assigned: 299
No hits: 461890
$
$

tyler_durden
# 6  
Code:
nawk '
   /^Taxonomy/ {p++;close(out);out="output" ++cnt ".txt";next}
   /^[+]+End/ { p=0}
   p { print > out }' myInputFile

# 7  
Quote:
Originally Posted by iammitra
Hallo ghostdog74,
Thanks for your reply. But I am sorry to say that I forgot to mention : in my input file there are not always only 6 lines. I just copied some lines.. This lines varies from 100 to 200. So it is necessary for the program to read +++++++++End.

Thanks a lot,
Mitra.
well, i am not sure i get you, but i see other solutions include "End', therefore if you are sure that ++++++++ is not unique, you can add "End"
Code:
....
if line.startswith("+++++++++++End"): 
....

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