read and paste two files

[darkknight18]

I need help in reading and pasting two files.
File list 1 - list of files ex: d3jf_fh_xyz and so on
File list 2 - list of files ex: d3jf_fh_abc

each file has one line of numbers separated by spaces. If the beginning part of the file name in list 1 matches file name in list 2 (i.e d3jf_fh), I want to paste the two lines into one output file for all files.

Since I am new to Perl, suggestions would be appreciated

 

[MillerH]

http://perldoc.perl.org/perlintro.html

- Miller

 

[darkknight18]

I've written the following, it is very crude but works till the last step, where it has to paste two lines only if their ID's are the same.





#!/usr/bin/perl -w

use warnings;

######## READING FILE ONE ##########
$[ = 1;
open(DATA, "< list1") or die "Failed to open list1";
open(MYOUT1, "> out1") or die "Failed to open file1";
#print MYOUT "aa bb cc\n";
while (<DATA>){
@lines1 = <DATA>;
foreach $line1 (@lines1){
open (DATA1, "<$line1") or die "Failed to open $line1\n";
while (<DATA1>){
if ($. > 0){
chomp;
$ID1 = substr($line1, 1, 7);
open (FILE, "$line1");
@FId = split(' ', $_, -1);
$cor = $FId[1];
$icor = $FId[2];
$ocor = $FId[3];

}
}
printf MYOUT1 "$ID1 $cor $icor $ocor\n" ;
}
}
close (DATA);
close (DATA1);
close (FILE);
close (MYOUT1);

####### READING FILE TWO ##########

open(DATA, "< list2" ) or die "Failed to open list1";
open(MYOUT2, "> out2") or die "Failed to open file2";
while (<DATA>){
@lines2 = <DATA>;
foreach $line2 (@lines2){
open (DATA1, "<$line2") or die "Failed to open $line2\n";
while (<DATA1>){
if ($. > 0){
chomp;
$ID1 = substr($line2, 1, 7);
open (FILE, "$line2");
@FId = split(' ', $_, -1);
$cor = $FId[1];
$icor = $FId[2];
$ocor = $FId[3];
}
}
printf MYOUT2 "$ID1 $cor $icor $ocor\n" ;
}
}

close (DATA);
close (DATA1);
close (FILE);
close (MYOUT2);

######### PASTING THE TWO FILES TOGETHER ######

open(VCOR, "< out1" ) or die "Failed to open vcor";
open(DAT, "< out2" ) or die "Failed to open data";
open(MYOUT, "> megafitfile") or die "Failed to open ";
while (<VCOR>){
if ($.> 0){
chomp;
@FId = split(' ', $_, -1);
$a=$FId[1];
$b=$FId[2] ;
$c=$FId[3] ;
}
while (<DAT>){
if ($.> 0){
chomp;
@FId = split(' ', $_, -1);
$d=$FId[1];
$e=$FId[2] ;
$f=$FId[3] ;

}
}
#### THIS PART DOES NOT WORK ######

if ($a eq $d){
print MYOUT "$a $b $c $d $e $f\n" ;
}
else {print MYOUT "$a $b $c\n";}

}

close(VCOR);
close(DAT);
close(MYOUT);

 

[prex1]

You need to rewind the second file each time you read a line from the first one, otherwise the second file is read only once. I assume of course that you need to fully check the second file against every line read from the first one.
Add the line
[tt]seek DAT,0,0;[/tt]
before
[tt]while(<DAT){[/tt]
Also note that it is deprecated to use [tt]$a[/tt] and [tt]$b[/tt] as variable names.
And please provide a properly formatted code putting it between [ignore]

[/ignore] tags:
[tt][ignore][code][/ignore][i]your code here...[/i][ignore]

[/ignore][/tt]

Franco

http://www.xcalcs.com

: Online engineering calculations

http://www.megamag.it

: Magnetic brakes for fun rides

http://www.levitans.com

: Air bearing pads

 

[darkknight18]

Thanks prex1,

That works but I get a few errors such as

Use of uninitialized value $_ in scalar chomp at ./trial line 11, <DATA> line 5.
readline() on closed filehandle FILE at ./trial line 14
Use of uninitialized value $ID1 in string eq at ./trial line 64, <DAT> line 1


The files I'm using are :

list1
1aw7_AB.fit => 1 2 3
1bjw_AB.fit
1biq_AB.fit
1bsr_AB.fit

list2
1aw7_AB.vcor => 4 5 6
1bjw_AB.vcor
1biq_AB.vcor

with each file in the list containing a line of numbers.

So I want the output to be 1aw7_AB 1 2 3 1aw7_AB 4 5 6 and so on

The problem with the script is that the else command does not work.
Here's my code

#!/usr/bin/perl -w

use warnings;

######## READING FILE ONE ##########
$[ = 1;
open(DATA, "<list1") ;
open(MYOUT1, "> out1") ;
  @lines1 = <DATA>;
  foreach $line1 (@lines1){
    chomp;
    $ID1 = substr($line1, 1, 7);
    open (FILE, "<$line1");
      while(<FILE>){
      chomp;
     ($line2)=$_;

   }

printf MYOUT1 "$ID1 $line2\n" ;
  }
close (DATA);
close (FILE);
close (MYOUT1);
  
####### READING FILE TWO ##########

open(DATA, "< list2" ) or die "Failed to open list1";
open(MYOUT2, "> out2") or die "Failed to open file2";
  @lines2 = <DATA>;
  foreach $line2 (@lines2){
   chomp;
   $ID1 = substr($line2, 1, 7);
   open (FILE, "<$line2");
       while(<FILE>){
       chomp;
       ($line2)=$_;
  }

printf MYOUT2 "$ID1 $line2\n" ;
 }
 close (DATA);
 close (FILE);
 close (MYOUT2);
 
########## PASTING THE TWO FILES TOGETHER IF IDs MATCH ######

open(VCOR, "< out1" ) or die "Failed to open vcor";
open(DAT, "< out2" ) or die "Failed to open data";
open(MYOUT, "> megafitfile") or die "Failed to open ";
while (<VCOR>){
   chomp;
   ($line3)=$_;
   @FId = split(' ', $_, -1);
   $ID1=$FId[1];
seek DAT,0,0;

while (<DAT>){
    chomp;
    @FId = split(' ', $_, -1);
    $ID2=$FId[1];
    ($line4)=$_;

if ($ID1 eq $ID2){
print MYOUT  "$line3 $line4\n" ;
else {print MYOUT "$line3\n";} 
}
}
}

close(VCOR);
close(DAT);
close(MYOUT);

 

[Annihilannic]

I'd do this in shell:

for fit in $(<list1) ; do vcor=${fit%.fit}.vcor ; if grep -qx $vcor list2 ; then echo ${fit%.fit} $(cat $fit) ${fit%.fit} $(cat $vcor) ; fi ; done

You could of course implement the same algorithm in perl.

Annihilannic.