Re^4: compare lines within a file

[kennethk]

Define "doesn't work". Please provide your input file (wrapped in <code> tags) as well as your observed and expected outputs.

One problem is that you have written '\t' in place of "\t". These mean different things in Perl. Double quotes interpolate, whereas single quotes do not. This means '\t' yields the literal string of a backslash followed by a t; "\t" yields a tab character. There is a list of escape sequences in the link I have provided.

[garyboyd]

I tried the code but I get an error: Use of uninitialized value in printf at parse_result.txt.pl line 23, <$fh> line 45.

If I change the code '\t' in place of "\t" I still get the error

The input file is:

HWUSI-EAS95L_0025_FC:3:1:2031:1075#0/1    +    2770970    2771005    
HWUSI-EAS95L_0025_FC:3:1:2031:1075#0/2    +    2771158    2771190    
HWUSI-EAS95L_0025_FC:3:1:2229:1075#0/1    -    1449587    1449620    
HWUSI-EAS95L_0025_FC:3:1:2229:1075#0/2    -    1449425    1449460    
HWUSI-EAS95L_0025_FC:3:1:5001:1079#0/1    -    1449311    1449346    
HWUSI-EAS95L_0025_FC:3:1:5001:1079#0/2    -    1449301    1449336    
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/1    -    1449586    1449619    
HWUSI-EAS95L_0025_FC:3:1:5232:1082#0/2    -    1449544    1449577    
HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/1    -    4744083    4744113    
HWUSI-EAS95L_0025_FC:3:1:6417:1078#0/2    -    4744011    4744042    
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/1    -    4867122    4867157    
HWUSI-EAS95L_0025_FC:3:1:6539:1083#0/2    -    4866942    4866977    
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/1    +    1930232    1930266    
HWUSI-EAS95L_0025_FC:3:1:10260:1083#0/2    +    1930354    1930389    
HWUSI-EAS95L_0025_FC:3:1:10916:1076#0/1    -    4874098    4874133    
HWUSI-EAS95L_0025_FC:3:1:10916:1076#0/2    -    4874089    4874121    
HWUSI-EAS95L_0025_FC:3:1:11022:1076#0/1    +    749842    749877    
HWUSI-EAS95L_0025_FC:3:1:11022:1076#0/2    +    749905    749936    
HWUSI-EAS95L_0025_FC:3:1:11305:1077#0/1    +    2083459    2083494    
HWUSI-EAS95L_0025_FC:3:1:11305:1077#0/2    +    2083661    2083696    
HWUSI-EAS95L_0025_FC:3:1:11824:1080#0/1    +    1930341    1930376    
HWUSI-EAS95L_0025_FC:3:1:11824:1080#0/2    +    1930373    1930408    
HWUSI-EAS95L_0025_FC:3:1:12409:1075#0/1    -    4359407    4359442    
HWUSI-EAS95L_0025_FC:3:1:12409:1075#0/2    -    4359384    4359419    
HWUSI-EAS95L_0025_FC:3:1:15014:1078#0/1    +    742090    742125    
HWUSI-EAS95L_0025_FC:3:1:15014:1078#0/2    +    742134    742168    
HWUSI-EAS95L_0025_FC:3:1:15074:1080#0/1    -    2697450    2697485    
HWUSI-EAS95L_0025_FC:3:1:15074:1080#0/2    -    2697347    2697381    
HWUSI-EAS95L_0025_FC:3:1:15895:1077#0/1    -    3870810    3870845    
HWUSI-EAS95L_0025_FC:3:1:15895:1077#0/2    -    3870798    3870832    
HWUSI-EAS95L_0025_FC:3:1:16241:1078#0/1    +    3726316    3726351    
HWUSI-EAS95L_0025_FC:3:1:16241:1078#0/2    +    3726444    3726479    
HWUSI-EAS95L_0025_FC:3:1:16990:1084#0/1    +    4485745    4485780    
HWUSI-EAS95L_0025_FC:3:1:16990:1084#0/2    +    4485764    4485797    
HWUSI-EAS95L_0025_FC:3:1:1360:1089#0/1    -    4848206    4848241    
HWUSI-EAS95L_0025_FC:3:1:2719:1087#0/1    -    1449535    1449570    
HWUSI-EAS95L_0025_FC:3:1:2719:1087#0/2    -    1449425    1449460    
HWUSI-EAS95L_0025_FC:3:1:2763:1085#0/1    -    1449423    1449458    
HWUSI-EAS95L_0025_FC:3:1:2763:1085#0/2    -    1449427    1449460    
HWUSI-EAS95L_0025_FC:3:1:3151:1099#0/1    -    4867745    4867773    
HWUSI-EAS95L_0025_FC:3:1:3151:1099#0/2    -    4867750    4867774    
HWUSI-EAS95L_0025_FC:3:1:4137:1088#0/1    -    4359723    4359758    
HWUSI-EAS95L_0025_FC:3:1:4137:1088#0/2    -    4359622    4359657    
HWUSI-EAS95L_0025_FC:3:1:4196:1093#0/1    +    2145336    2145371    
HWUSI-EAS95L_0025_FC:3:1:4196:1093#0/2    +    2145456    2145490

I was hoping to get the output something like 2770970 and 2771190 for the first 2 entries......etc

Hope that makes sense!

[kennethk]

The line

    if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0//E}) {

should have read

    if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0/\E}) {

There is a typo in the original code with an incorrect slash before the trailing E. The escaped pair \Q and \E tells Perl (when interpolating) to escape all characters that have special meaning in a regular expression - see Quote and Quote like Operators in perlop. The typo was of course mine, and I have corrected the original post accordingly. With that change, I get the output: 1449586    1449577. Obviously, you should be modifying that matching condition to fit your requirements.

[garyboyd]

Thanks kennethk, this works, but I cannot figure out how to incorporate this into a program that can take a list and then check each line of the list to see if subsequent entries compare and if they do to then print out.

It is possible to do this if the name is specified in the code

if ($row->[0] =~ m{\QHWUSI-EAS95L_0025_FC:3:1:5232:1082#0/\E}) {

but how to do this if you do not know what each line is??

I tried using the following regex, which will match each line:

         if ($header2 =~  m{HWUSI-EAS95L_0025_FC:3:1:\d*:\d*#0/}) {

but not sure how to take it from there.....