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[HELP] regexp that covers the whole text

acpguedes
Novice

Oct 16, 2011, 10:20 AM

Post #1 of 7 (15964 views)

[HELP] regexp that covers the whole text	Can't Post

I have problem with this script:

Code

#!/usr/bin/perl  
  
  
use strict;  
  
use warnings;  
  
print "Write input arquive name\n\t";  
my $input = <STDIN>;  
print "Write max energy. Like: -28\n\t";  
my $min = <STDIN>;  
print "Write min energy. Like: -30\n\t";  
my $max = <STDIN>;  
print "Write output arquive name\n\t";  
my $output = <STDIN>;  
  
  
open IN, $input or die "cannot open input";   
open OUT,">". $output or die usage ();  
  
  
while(<IN>){  
    if($_ =~ m/(mfe:s+(-?d.*.?d.*?)s+kcal/mol)/gi){  
        if($2 <= $min && $2 >= $max){   
            print OUT " $1.$/ ";  
              
        }  
    }  
}

I need a regex that covers the whole text below as it is repeated several times and I want to get all of the text according to the value of "mfe:"

Code

----------------------------------------------------------------  
miRNA:  hsa-miR-92b*  #variable is here! Start here 
  
Hybrid:  
mfe: -29.5 kcal/mol     #variable is here!  this is the important value 
  
position  29     #variable is here!  
target 5' U    A     A    U    C 3'         #variable is here!  
           GCUG ACUGC UUCC UCCC    #variable is here!  
           UGAC UGGCG AGGG AGGG    #variable is here!  
miRNA  3' G    G     C    C    A 5'       #variable is here!  
  
  
Miranda:  
  
Position: 29      #variable is here!  
  
   Query:    3' guGACGUGGCGCAGGGCAGGGa 5'          #variable is here!  
                  ||| ||:|| |:|| ||||                                                                #variable is here!  
   Ref:      5' tgCTGAACTGCATTCCTTCCCc 3'                 #variable is here!  
  
   Energy:  -24.110001 kCal/Mol #variable is here!  
  
  
Rybrid vs miRanda:  OK  #Finish here 
----------------------------------------------------------------  
miRNA:  hsa-miR-4689          #variable is here!  
  
Hybrid:  
mfe: -34.0 kcal/mol       #variable is here!  
  
position  3                   #variable is here!  
target 5' U  G         ACCC  U      U 3'                #variable is here!  
           GU CCCACCAUG    UC UCCUCA    #variable is here!  
           CG GGGUGGUAC    AG AGGAGU    #variable is here!  
miRNA  3' C  G                      U 5'                     #variable is here!  
  
Miranda:  
  
Position: 3                   #variable is here!  
  
   Query:    3' ccggGGGUGGUAC----A-GAGGAGUu 5' #variable is here!  
                    |||||||||    | :||||||                                                       #variable is here!  
   Ref:      5' tgtgCCCACCATGACCCTCTTCCTCAt 3'  #variable is here!  
  
   Energy:  -29.650000 kCal/Mol       #variable is here!  
  
  
Rybrid vs miRanda:  OK

I did a search regexp that the value of "mfe:" but I wanted the output file would leave all text

Code

/(mfe:s+(-?d.*.?d.*?)s+kcal/mol)/

--------------------------------------
I'm looking for one that represents the entire regexp text above in order to say "Here begins the text, here are some lines with text, text in that part of the value should be in the range request, the text ends here"
like:
/(miRNA:)....(mfe:s+(-?d.*.?d.*?)s+kcal/mol)......((Rybrid)s+(vs)s+(miRanda)s+(OK))
^this is a eg
--------------------------------------

I'm wating some help

tanks

(This post was edited by acpguedes on Oct 16, 2011, 10:41 AM)

wickedxter
User

Oct 18, 2011, 3:56 AM

Post #2 of 7 (15754 views)

Re: [acpguedes] [HELP] regexp that covers the whole text [In reply to]	Can't Post

as i c you are going threw the file a line at a time, so youll have to setup multi. regex for the different matches your looking for.

you can just use if elsif to match each line your looking for and return the information you want to save.

(This post was edited by wickedxter on Oct 18, 2011, 3:57 AM)

acpguedes
Novice

Oct 18, 2011, 6:15 AM

Post #3 of 7 (15749 views)

Re: [wickedxter] [HELP] regexp that covers the whole text [In reply to]	Can't Post

What I want is this:

I have a list of results, including the results are separated by "------------------------------------ ---------------------------------------------"

a sample list is below

Code

---------------------------------------------------------------- 
miRNA:  hsa-miR-92b* 
 
Hybrid: 
mfe: -29.5 kcal/mol 
 
position  29 
target 5' U    A     A    U    C 3' 
           GCUG ACUGC UUCC UCCC     
           UGAC UGGCG AGGG AGGG     
miRNA  3' G    G     C    C    A 5' 
 
 
Miranda: 
 
Position: 29 
 
   Query:    3' guGACGUGGCGCAGGGCAGGGa 5' 
                  ||| ||:|| |:|| ||||  
   Ref:      5' tgCTGAACTGCATTCCTTCCCc 3' 
 
   Energy:  -24.110001 kCal/Mol 
 
 
Rybrid vs miRanda:  OK 
---------------------------------------------------------------- 
miRNA:  hsa-miR-4689 
 
Hybrid: 
mfe: -34.0 kcal/mol 
 
position  3 
target 5' U  G         ACCC  U      U 3' 
           GU CCCACCAUG    UC UCCUCA     
           CG GGGUGGUAC    AG AGGAGU     
miRNA  3' C  G                      U 5' 
 
 
Miranda: 
 
Position: 3 
 
   Query:    3' ccggGGGUGGUAC----A-GAGGAGUu 5' 
                    |||||||||    | :||||||  
   Ref:      5' tgtgCCCACCATGACCCTCTTCCTCAt 3' 
 
   Energy:  -29.650000 kCal/Mol 
 
 
Rybrid vs miRanda:  OK

this list, for example, has 3 results.

dai, I want a script where he writes on a result by result output file
but each result will be written only if the value of "mfe: blablabla kcal / mol" is within a range.

example, if I set the range is between -28 and -30 it will write the output file so the second result, looks like this:

Code

miRNA:  hsa-miR-92b* 
 
Hybrid: 
mfe: -29.5 kcal/mol 
 
position  29 
target 5' U    A     A    U    C 3' 
           GCUG ACUGC UUCC UCCC     
           UGAC UGGCG AGGG AGGG     
miRNA  3' G    G     C    C    A 5' 
 
 
Miranda: 
 
Position: 29 
 
   Query:    3' guGACGUGGCGCAGGGCAGGGa 5' 
                  ||| ||:|| |:|| ||||  
   Ref:      5' tgCTGAACTGCATTCCTTCCCc 3' 
 
   Energy:  -24.110001 kCal/Mol 
 
 
Rybrid vs miRanda:  OK

* Note that this result only from the list the "mfe:" is between -28 and -30

I'm waiting some help

Thanks

FishMonger
Veteran / Moderator

Oct 18, 2011, 7:59 AM

Post #4 of 7 (15742 views)

Re: [acpguedes] [HELP] regexp that covers the whole text [In reply to]	Can't Post

Is this what you're looking for?

Code

#!/usr/bin/perl 
 
use strict; 
use warnings; 
 
my $min = -28; 
my $max = -30; 
my $file = 'input.txt'; 
$/ = '----------------------------------------------------------------'; 
 
#open my $fh, $file, or die "can't open '$file' $!"; 
 
while ( my $record = <DATA> ) { 
    if ( $record =~ m~\nmfe:\s+(\S+)\s+kcal/mol~ ) { 
        if ( $1 <= $min and $1 >= $max ) { 
            print $record; 
        } 
    } 
} 
 
__DATA__ 
---------------------------------------------------------------- 
miRNA:  hsa-miR-92b* 
 
Hybrid: 
mfe: -29.5 kcal/mol 
 
position  29 
target 5' U    A     A    U    C 3' 
           GCUG ACUGC UUCC UCCC     
           UGAC UGGCG AGGG AGGG     
miRNA  3' G    G     C    C    A 5' 
 
 
Miranda: 
 
Position: 29 
 
   Query:    3' guGACGUGGCGCAGGGCAGGGa 5' 
                  ||| ||:|| |:|| ||||  
   Ref:      5' tgCTGAACTGCATTCCTTCCCc 3' 
 
   Energy:  -24.110001 kCal/Mol 
 
 
Rybrid vs miRanda:  OK 
---------------------------------------------------------------- 
miRNA:  hsa-miR-4689 
 
Hybrid: 
mfe: -34.0 kcal/mol 
 
position  3 
target 5' U  G         ACCC  U      U 3' 
           GU CCCACCAUG    UC UCCUCA     
           CG GGGUGGUAC    AG AGGAGU     
miRNA  3' C  G                      U 5' 
 
 
Miranda: 
 
Position: 3 
 
   Query:    3' ccggGGGUGGUAC----A-GAGGAGUu 5' 
                    |||||||||    | :||||||  
   Ref:      5' tgtgCCCACCATGACCCTCTTCCTCAt 3' 
 
   Energy:  -29.650000 kCal/Mol 
 
 
Rybrid vs miRanda:  OK

acpguedes
Novice

Oct 18, 2011, 8:21 AM

Post #5 of 7 (15733 views)

Re: [FishMonger] [HELP] regexp that covers the whole text [In reply to]	Can't Post

Wow, man, you helped me a lot.
I'm not very good at perl, so me more help.
In this algorithm, I would like to indicate the path of an input file, if the input file contains a list of result sets.

something like
my $ input = <STDIN>;

FishMonger
Veteran / Moderator

Oct 18, 2011, 8:32 AM

Post #6 of 7 (15730 views)

Re: [acpguedes] [HELP] regexp that covers the whole text [In reply to]	Can't Post

No problem, just use your original method when assigning the input vars, but remember to 'chomp' those vars before using them.

Code

print "Write input arquive name\n\t";  
chomp(my $input = <STDIN>);  
 
print "Write max energy. Like: -28\n\t";  
chomp(my $min = <STDIN>;)  
 
print "Write min energy. Like: -30\n\t";  
chomp(my $max = <STDIN>);  
 
print "Write output arquive name\n\t";  
chomp(my $output = <STDIN>);

acpguedes
Novice

Oct 18, 2011, 12:40 PM

Post #7 of 7 (15719 views)

Re: [FishMonger] [HELP] regexp that covers the whole text [In reply to]	Can't Post

thank you....
now it's ok

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