in reply to Re^8: Read, match string and print
in thread Read, match string and print

Nowhere in that source code does the word value appear, so I highly doubt that the program ever outputs the string Ignoring unknown value. I put the following line into the program:

warn "Ignoring unknown line [$_]\n";

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in there so you know what parts of the input get discarded. In that line, I even output the part that gets discarded. If you determine that a certain line is never of use, just add another rule ignoring it.

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Re^10: Read, match string and print
by sophix (Sexton) on Feb 08, 2010 at 10:38 UTC
    So I turned off the warnings 
    #!/usr/bin/perl
use strict;
use warnings;

my %info; # here we collect all information
my @columns = qw(gi version cds); # The name and order of the columns 
+we want to print

my $data = '/PRBB/Practice.gb'; # GenBank file is located at C:\PRBB
open INFILE, '<', $data or die "Please insert a new coin!\n";

while (<INFILE>) {
    if (m!GI:(\d+)!) {
        if ($info{cds}) { # we are in a CDS block
            $info{gi} = $1;
        };
    } elsif (m!^\s+CDS\s+(.*)!) {
        # a new gene information has started
        flush_info();

        # now remember the CDS
        $info{cds} = $1
    } elsif (m!^VERSION.*\w:(\d+)! ) {
        $info{ version } = $1;
    #} else {warn "Ignoring unknown line [$_]\n";};
};}

# Output any leftover information:
flush_info();

sub flush_info {
    # print out all information:
    print join '*', @info{@columns};

    # and forget the collected information
    %info = ();
};

    [download]
    This gives an error at print join '*', @info{@columns}; And it prints all the matchings into one single line. How is it possible to print them out as would be in the following structure: 
    if ( defined $cds && defined $gi && defined $version ) { # Print only 
+when all variables are defined
        print "$gi\t$version\t$cds\n";
        $gi = $cds = undef; # Get ready for the next loop
        }

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    Thanks for sparing time!
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      If comparing two print statements and then modifying one so it works like the other exceeds your current skills, I recommend learning some more Perl. It's not really hard:

      @info{ @columns } is equivalent to $info{ gi }, $info{ version } and $info{ cds }, because that's what @columns contains.

      The join function joins a list with a string. I chose * as the string, but you might want to choose a different separator.

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        No doubt I should learn Perl more (and programming in general). I guess I managed to handle the print statement. Now, the code is: 
        #!/usr/bin/perl
use strict;
use warnings;

my %info; # here we collect all information
my @columns = qw(gi version cds); # The name and order of the columns 
+we want to print

my $data = '/DATA/GenBankFile.gb'; # GenBank file is located at C:\DAT
+A
open INFILE, '<', $data or die "Cannot!\n";

while (<INFILE>) {
    if (m!GI:(\d+)!) {
        if ($info{cds}) { # we are in a CDS block
            $info{gi} = $1;
        };
    } elsif (m!^\s+CDS\s+(.*)!) {
        # a new gene information has started
        flush_info();

        # now remember the CDS
        $info{cds} = $1
    } elsif (m!^VERSION.*\w:(\d+)! ) {
        $info{ version } = $1;
    #} else {warn "Ignoring unknown line [$_]\n";};
};}

# Output any leftover information:
#flush_info();

sub flush_info {
    # print out all information:
    print "$info{gi}"."\t"."$info{version}"."\t"."$info{cds}\n";
    
    # and forget the collected information
    %info = ();
};
>

        [download]
        And here is some part of the output: 
        Use of uninitialized value $info{"gi"} in string at C:\Perl\bin\wtf14.
+pl line 32, <INFILE> line 154.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 154.
Use of uninitialized value $info{"cds"} in concatenation (.) or string
+ at C:\Perl\bin\wtf14.pl line 32, <INFILE> line 154.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 180.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 206.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 232.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 258.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 284.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 314.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 345.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 374.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 404.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 434.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 481.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 498.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 534.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 600.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 617.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 634.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 667.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 710.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 721.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 746.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 773.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 836.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 848.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 860.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 892.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 938.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 952.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 996.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1009.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1046.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1070.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1098.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1131.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1174.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1188.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1216.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1256.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1269.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1329.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1344.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1360.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1403.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1415.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1445.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1490.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1505.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1533.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1591.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1606.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1621.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1710.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1767.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1781.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1795.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1827.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1865.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1899.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1934.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1982.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 1998.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2048.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2083.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2119.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2264.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2282.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2300.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2337.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2382.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2419.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2450.
Use of uninitialized value $info{"version"} in string at C:\Perl\bin\w
+tf14.pl line 32, <INFILE> line 2459.
        
30061484        join(68351..68408,76646..77058)
30061486        join(123270..123327,126056..126333)
83582801        join(138186..138234,139415..139665)
30061487        complement(join(168527..168759,170216..170264))
197245446        join(207930..207987,209919..210412)
23943927        join(238420..238477,239718..239947)
55769555        complement(join(251848..251908,256609..256727,
21264338        278228..279439
197245445        306569..307516
41327717        join(330288..330476,333854..334279)
144953899        join(368655..368945,371931..372223,376842..377334)
5454168        join(389383..389423,398170..398263,398376..398574,
111185943        join(389402..389423,390525..390669,398170..398263,
47419901        complement(join(419230..419485,419752..419939,
4503095        complement(join(464605..464720,467020..467106,
29570791        complement(join(464605..464720,467020..467106,
48255908        complement(join(464605..464720,467020..467106,
22129777        complement(join(585235..585309,590357..590881))
22129778        complement(join(629358..629561,633620..633829))
197245441        join(629536..629555,633613..634228,642601..643113)
156564358        complement(join(644315..645105,656113..656245))
108389007        complement(join(741670..741882,742345..742468,
46391104        825448..826335
108389127        825448..826335
21328453        825448..826335
83722283        complement(join(853603..853763,854927..855057,
90970328        complement(join(941000..941109,947817..947957,
145611425        complement(join(941000..941109,944578..944763,
145611430        join(1099417..1099545,1106141..1106293,1108069..11081
+51,

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