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

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Top Forums Shell Programming and Scripting How to extract some parts of a file to create some outfile
# 8  
Old 05-08-2009
Hallo durden_tyler,
your perl code works. Thanks a lot. But there is still one problem.
As I told in my input file there are several amount of spaces in front desired lines.
Is there any possibility to get rid of these space directly?
Now it is giving:
Code:
mitra:~ mitra$ cat outfile1.txt
          Gammaproteobacteria: 2767
       Alphaproteobacteria: 4123
         Deltaproteobacteria: 1343
                         Epsilonproteobacteria: 26
     Betaproteobacteria: 397
                        unclassified Proteobacteria: 48
                  Spirochaetes (class): 15
        Nitrospira (class): 1
        Bacilli: 25
  Not assigned: 1445
  No hits: 220253

Thank you very much for your help.
Best Wishes,
Mitra.
Last edited by Franklin52; 05-10-2009 at 01:07 PM.. Reason: adding code tags
# 9  
Old 05-08-2009
Sorry, I don't know why all the spaces disappears here. But there are several spaces (not equal for all lines)in front of desired lines.
# 10  
Old 05-08-2009
Hallo ghostdog74,
I will try with this modification. If it works.
Thank you very much.
Best,
Mitra.
# 11  
Old 05-09-2009
Quote:
Originally Posted by iammitra
...
As I told in my input file there are several amount of spaces in front desired lines.
Is there any possibility to get rid of these space directly?
...
Here's one way to do it:

Code:
perl -ne '{$/=""; $i=1;
  while (/^Taxonomy:.(.*?)\+{11}/msgi) {
    $x = $1; $x =~ s/(^|\n)\s+/\1/g;
    open(OUT,">outfile".$i++.".txt"); print OUT $x; close(OUT);
  }}' input.txt

Testing on sample data:

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) {
    $x = $1; $x =~ s/(^|\n)\s+/\1/g;
    open(OUT,">outfile".$i++.".txt"); print OUT $x; 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
$
$

Hope that helps,
tyler_durden

____________________________________________________________
"This is your life and it's ending one minute at a time."
# 12  
Old 05-09-2009
Quote:
Originally Posted by iammitra
Sorry, I don't know why all the spaces disappears here. ...
The spaces disappear here because you do not enclose your file data or code within the "code" tags. (Notice how the actual code posted by the forum members has a nice little box around it with the title "Code:" at the top.)

If you sandwich the desired text within "code" tags, without any space between "code", "]", "[" and "/" :

[ code ] <your_text_here> [ / code ]

then the leading spaces will be preserved.

Alternatively, if you are feeling lazy to actually type the "code" tags, then you can do this -
(a) select the desired text, and
(b) click on the "#" icon in your Message Box right above the response area
The dynamic script associated with the web page will put the "code" tags for you.

HTH,
tyler_durden

____________________________________________________________
"This is your life and it's ending one minute at a time."
# 13  
Old 05-10-2009
Hallo durden_tyler,
At first I want to thank you for your help. Thanks a lot...I am very new in scripting. Can you please explain the filed (.*?)\+{11}/msgi) for your code in my thread help?

Actually I am trying to learn. So it will be really helpful. And one more question How can I make this script executable.

My try was:
#!/usr/bin/perl -w

$#ARGV==1 or die "Usage: 2ndprocess-script 1st-output-file-as-inputfile\n";

$input=shift;

perl -ne '{$/=""; $i=1;
while (/^Taxonomy:.(.*?)\+{11}/msgi) {
$x = $1; $x =~ s/(^|\n)\s+/\1/g;
open(OUT,">outfile".$i++.".txt"); print OUT $x; close(OUT);
}}' $1;

-----------------------------
which didn't work.
Can you please help me to learn this?
Thank you very much once again.
Have anice time.
Best wishes,
Mitra
# 14  
Old 05-10-2009
Hallo durden_tyler,
At first I want to thank you for your help. Thanks for the help in writing also. Now I can use that.Thanks a lot...I am very new in scripting. Can you please explain the filed (.*?)\+{11}/msgi) for your code in my thread help?

Actually I am trying to learn. So it will be really helpful. And one more question How can I make this script executable.

My try was:

Quote:
#!/usr/bin/perl -w

$#ARGV==1 or die "Usage: 2ndprocess-script 1st-output-file-as-inputfile\n";

$input=shift;

perl -ne '{$/=""; $i=1;
while (/^Taxonomy:.(.*?)\+{11}/msgi) {
$x = $1; $x =~ s/(^|\n)\s+/\1/g;
open(OUT,">outfile".$i++.".txt"); print OUT $x; close(OUT);
}}' $1;
-----------------------------
which didn't work.
Can you please help me to learn this?
Thank you very much once again.
Have anice time.
Best wishes,
Mitra
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