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  • RR MISHRA
    Hi Everybody, Can any body give me idea about the use of subroutines and bugs.If any body have the tutorials or sample examples about it then plz send me.I am
    Message 1 of 19 , Jun 5 9:02 AM
      Hi Everybody,
      Can any body give me idea about the use of subroutines and bugs.If any body have the tutorials or sample examples about it then plz send me.I am also want to know how subroutines and bugs are helpful in bioinformatics work.Plz guide me.I need your guidance.
      Thanx in advance.
      Regards.



      ---------------------------------
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      [Non-text portions of this message have been removed]
    • DigiDoc
      I need to write some code that will take an ID from File-1 and see if it exists on File-2. If it does, then I want to write out the record from File-2 to
      Message 2 of 19 , Jun 5 10:37 AM
        I need to write some code that will take an ID from File-1 and see if it
        exists on File-2. If it does, then I want to write out the record from
        File-2 to another file.

        File-1 is just IDs, and File-2 is the ID plus a bunch of other fields
        comma delimited. The ID however is variable length. The files are
        ASCII. File-1 will only contain a small number of records (about 1K),
        while File-2 will be about 100K records.

        I have no idea how to do this (I'm a total Perl novice) and could
        greatly use help.


        Thanks!


        ~~Kevin~


        [Non-text portions of this message have been removed]
      • a_z0_9_blah
        ... if it ... from ... fields ... are ... 1K), ... Could you show some sample lines from the first file and from the second file?
        Message 3 of 19 , Jun 5 12:27 PM
          --- In perl-beginner@yahoogroups.com, DigiDoc <DigiDoc@...> wrote:
          >
          > I need to write some code that will take an ID from File-1 and see
          if it
          > exists on File-2. If it does, then I want to write out the record
          from
          > File-2 to another file.
          >
          > File-1 is just IDs, and File-2 is the ID plus a bunch of other
          fields
          > comma delimited. The ID however is variable length. The files
          are
          > ASCII. File-1 will only contain a small number of records (about
          1K),
          > while File-2 will be about 100K records.
          >
          > I have no idea how to do this (I'm a total Perl novice) and could
          > greatly use help.
          >
          >
          > Thanks!
          >
          >
          > ~~Kevin~
          >


          Could you show some sample lines from the first file and from the
          second file?
        • Charles K. Clarkson
          ... Read the perlsub file in the Perl documentation. ... Goto http://rt.perl.org/perlbug/ and click on the Current Perl 5 Issues link. Charles K. Clarkson --
          Message 4 of 19 , Jun 5 12:37 PM
            RR MISHRA wrote:

            :Can any body give me idea about the use of subroutines

            Read the 'perlsub' file in the Perl documentation.


            : and bugs.

            Goto http://rt.perl.org/perlbug/ and click on the
            Current Perl 5 Issues link.



            Charles K. Clarkson
            --
            Mobile Homes Specialist
            Free Market Advocate
            Web Programmer

            254 968-8328

            Don't tread on my bandwidth. Trim your posts.
          • DigiDoc
            File-1 ... abc bg cd1234 File-2 ... abc,john,doe,1234,9999 addathk,kathy,smith,3453,5629 bg,joe,shmo,4532,5343 cd1234,jane,madle,5432,0932
            Message 5 of 19 , Jun 5 1:22 PM
              File-1
              -------
              abc
              bg
              cd1234


              File-2
              -------
              abc,john,doe,1234,9999
              addathk,kathy,smith,3453,5629
              bg,joe,shmo,4532,5343
              cd1234,jane,madle,5432,0932
              dkk32,marge,hasbro,2345,1234


              Note: Data layout in File-2 may vary from time to time, but will always
              start with the ID.


              ~~Kevin~


              a_z0_9_blah wrote:
              > --- In perl-beginner@yahoogroups.com, DigiDoc <DigiDoc@...> wrote:
              >
              >> I need to write some code that will take an ID from File-1 and see
              >>
              > if it
              >
              >> exists on File-2. If it does, then I want to write out the record
              >>
              > from
              >
              >> File-2 to another file.
              >>
              >> File-1 is just IDs, and File-2 is the ID plus a bunch of other
              >>
              > fields
              >
              >> comma delimited. The ID however is variable length. The files
              >>
              > are
              >
              >> ASCII. File-1 will only contain a small number of records (about
              >>
              > 1K),
              >
              >> while File-2 will be about 100K records.
              >>
              >> I have no idea how to do this (I'm a total Perl novice) and could
              >> greatly use help.
              >>
              >>
              >> Thanks!
              >>
              >>
              >> ~~Kevin~
              >>
              >>
              >
              >
              > Could you show some sample lines from the first file and from the
              > second file?
              >
              >
              >
              >
              >


              [Non-text portions of this message have been removed]
            • a_z0_9_blah
              ... always ... see ... record ... (about ... could ... the ... You could try the following code on your sample data. If you will be massaging the data in
              Message 6 of 19 , Jun 5 5:50 PM
                --- In perl-beginner@yahoogroups.com, DigiDoc <DigiDoc@...> wrote:
                >
                >
                > Note: Data layout in File-2 may vary from time to time, but will
                always
                > start with the ID.
                >
                >
                > ~~Kevin~
                >
                >
                > a_z0_9_blah wrote:
                > > --- In perl-beginner@yahoogroups.com, DigiDoc <DigiDoc@> wrote:
                > >
                > >> I need to write some code that will take an ID from File-1 and
                see
                > >>
                > > if it
                > >
                > >> exists on File-2. If it does, then I want to write out the
                record
                > >>
                > > from
                > >
                > >> File-2 to another file.
                > >>
                > >> File-1 is just IDs, and File-2 is the ID plus a bunch of other
                > >>
                > > fields
                > >
                > >> comma delimited. The ID however is variable length. The files
                > >>
                > > are
                > >
                > >> ASCII. File-1 will only contain a small number of records
                (about
                > >>
                > > 1K),
                > >
                > >> while File-2 will be about 100K records.
                > >>
                > >> I have no idea how to do this (I'm a total Perl novice) and
                could
                > >> greatly use help.
                > >>
                > >>
                > >> Thanks!
                > >>
                > >>
                > >> ~~Kevin~
                > >>
                > >>
                > >
                > >
                > > Could you show some sample lines from the first file and from
                the
                > > second file?
                > >
                > File-1
                > -------
                > abc
                > bg
                > cd1234
                >
                >
                > File-2
                > -------
                > abc,john,doe,1234,9999
                > addathk,kathy,smith,3453,5629
                > bg,joe,shmo,4532,5343
                > cd1234,jane,madle,5432,0932
                > dkk32,marge,hasbro,2345,1234
                >

                You could try the following code on your sample data.

                If you will be 'massaging' the data in file-2,
                you might consider treating your second
                file as a database (using DBD::CSV).


                #!/usr/bin/perl
                use strict;
                use warnings;

                my %ids;

                open my $id, "<", "o33.txt" or die "Unable to open o33.txt $!";

                while (<$id>) {
                chomp;
                $ids{$_} = 1;
                }

                close $id or die $!;

                open my $data, "<", "o44.txt" or die "Unable to open o44.txt $!";
                open my $out, ">", "o55.txt" or die "Couldn't write results $!";

                while (<$data>) {
                my $key = (split /,/)[0];
                if ($ids{$key}) {
                print $out $_;
                }
                }

                close $data or die $!;
                close $out or die $!;
              • DigiDoc
                Great, thanks for the reply. I think I understand the majority of this code. I ll research the DBD::CSV as well. I definitely would not have known about that
                Message 7 of 19 , Jun 5 7:16 PM
                  Great, thanks for the reply.

                  I think I understand the majority of this code. I'll research the
                  DBD::CSV as well. I definitely would not have known about that without
                  your help. THANK YOU!!!!!

                  I can read a fair amount of Perl code, but am just not up to quickly
                  putting code together yet (and probably not for some time). It takes me
                  forever.

                  This helps me out immensely.

                  Dumb question. If I read this correctly, you've hard coded the files,
                  how would I set it up to make these variables?

                  Thanks!

                  ~~Kevin~
                  >
                  >
                  > You could try the following code on your sample data.
                  >
                  > If you will be 'massaging' the data in file-2,
                  > you might consider treating your second
                  > file as a database (using DBD::CSV).
                  >
                  >
                  > #!/usr/bin/perl
                  > use strict;
                  > use warnings;
                  >
                  > my %ids;
                  >
                  > open my $id, "<", "o33.txt" or die "Unable to open o33.txt $!";
                  >
                  > while (<$id>) {
                  > chomp;
                  > $ids{$_} = 1;
                  > }
                  >
                  > close $id or die $!;
                  >
                  > open my $data, "<", "o44.txt" or die "Unable to open o44.txt $!";
                  > open my $out, ">", "o55.txt" or die "Couldn't write results $!";
                  >
                  > while (<$data>) {
                  > my $key = (split /,/)[0];
                  > if ($ids{$key}) {
                  > print $out $_;
                  > }
                  > }
                  >
                  > close $data or die $!;
                  > close $out or die $!;
                  >
                  >
                  >
                  >
                  >
                  >


                  [Non-text portions of this message have been removed]
                • Alan_C
                  On Monday 05 June 2006 19:16, DigiDoc wrote: [ . . ] ...
                  Message 8 of 19 , Jun 6 1:18 AM
                    On Monday 05 June 2006 19:16, DigiDoc wrote:
                    [ . . ]
                    > Dumb question. If I read this correctly, you've hard coded the files,
                    > how would I set it up to make these variables?

                    http://groups.google.com/group/perl.beginners/browse_thread/thread/69865c81985c57f4/7d45c2b46cb7ba2b#7d45c2b46cb7ba2b

                    Take a look at the code in that it uses shift

                    A command line example:

                    perlscript file1

                    in that above command line example, file1 will be opened as filehandle OLD

                    if need to, can be set up to shift more than one file off the command line.

                    Further search topics be: shift, commandline, command line, ARGV, @ARGV,
                    $ARGV, $ARGV[0], $ARGV[1]

                    try search at <http://learn.perl.org/first-response> too likely turn up lots
                    yet even more.

                    --
                    Alan.
                  • DigiDoc
                    Thanks for all the help to this question. I ve got it working with the $ARGV stuff. I ve got more tweaks I want to make, but the base code you provided really
                    Message 9 of 19 , Jun 6 12:45 PM
                      Thanks for all the help to this question.

                      I've got it working with the $ARGV stuff. I've got more tweaks I want
                      to make, but the base code you provided really helps me out.

                      I'm thinking I'll want to make a GUI out of it now. I was doing some
                      research and found "The GUI Loft". It's a front end that uses
                      Win32::GUI. I haven't used it yet, but it seems like what I need. If
                      anyone has a better suggestion, please let me know.

                      I can't tell me how much time you've saved me, not to mention that I've
                      learned a few things as well. Code examples help me out a great deal, I
                      tend to learn faster from them.

                      Thanks!



                      [Non-text portions of this message have been removed]
                    • Ken Shail
                      ... From: DigiDoc ; DigiDoc To: perl-beginner@yahoogroups.com Sent: Tuesday, June 06, 2006 8:45 PM Subject: Re: [PBML] Re: File lookup? Thanks for all the help
                      Message 10 of 19 , Jun 6 12:55 PM
                        ----- Original Message -----
                        From: DigiDoc ; DigiDoc
                        To: perl-beginner@yahoogroups.com
                        Sent: Tuesday, June 06, 2006 8:45 PM
                        Subject: Re: [PBML] Re: File lookup?


                        Thanks for all the help to this question.

                        I've got it working with the $ARGV stuff. I've got more tweaks I want
                        to make, but the base code you provided really helps me out.

                        I'm thinking I'll want to make a GUI out of it now. I was doing some
                        research and found "The GUI Loft". It's a front end that uses
                        Win32::GUI. I haven't used it yet, but it seems like what I need. If
                        anyone has a better suggestion, please let me know.

                        I can't tell me how much time you've saved me, not to mention that I've
                        learned a few things as well. Code examples help me out a great deal, I
                        tend to learn faster from them.

                        Thanks!

                        Perl Tk - works on Linux and windoze
                        http://dc.pm.org/talks/tk/home.html
                        http://www.perltk.org/index.php?option=com_frontpage&Itemid=1
                        http://phaseit.net/claird/comp.lang.perl.tk/ptkFAQ.html
                      • DigiDoc
                        Thanks for the links. I was looking at that, but couldn t find a nice front end that lets you work visually. The GUI Loft let s you do things visually, then
                        Message 11 of 19 , Jun 6 1:24 PM
                          Thanks for the links.

                          I was looking at that, but couldn't find a nice front end that lets you
                          work visually. The GUI Loft let's you do things visually, then
                          generates the code for you. Is there something in tk that does that, or
                          am I missing something? Or at the very least, some application that has
                          some kind of code snippets that are easy to insert?

                          My goal is to develop code as rapidly as possible since I'll have a lot
                          to crank out.


                          Ken Shail wrote:
                          >
                          >
                          > ----- Original Message -----
                          > From: DigiDoc ; DigiDoc
                          > To: perl-beginner@yahoogroups.com
                          > <mailto:perl-beginner%40yahoogroups.com>
                          > Sent: Tuesday, June 06, 2006 8:45 PM
                          > Subject: Re: [PBML] Re: File lookup?
                          >
                          > Thanks for all the help to this question.
                          >
                          > I've got it working with the $ARGV stuff. I've got more tweaks I want
                          > to make, but the base code you provided really helps me out.
                          >
                          > I'm thinking I'll want to make a GUI out of it now. I was doing some
                          > research and found "The GUI Loft". It's a front end that uses
                          > Win32::GUI. I haven't used it yet, but it seems like what I need. If
                          > anyone has a better suggestion, please let me know.
                          >
                          > I can't tell me how much time you've saved me, not to mention that I've
                          > learned a few things as well. Code examples help me out a great deal, I
                          > tend to learn faster from them.
                          >
                          > Thanks!
                          >
                          > Perl Tk - works on Linux and windoze
                          > http://dc.pm.org/talks/tk/home.html <http://dc.pm.org/talks/tk/home.html>
                          > http://www.perltk.org/index.php?option=com_frontpage&Itemid=1
                          > <http://www.perltk.org/index.php?option=com_frontpage&Itemid=1>
                          > http://phaseit.net/claird/comp.lang.perl.tk/ptkFAQ.html
                          > <http://phaseit.net/claird/comp.lang.perl.tk/ptkFAQ.html>
                          >
                          >


                          [Non-text portions of this message have been removed]
                        • Alan_C
                          ... [ Perl Tk - works on Linux and windoze ] (if you quote a bit of context, it makes it easier for me (+ probably some others) to track this thread and to
                          Message 12 of 19 , Jun 6 2:06 PM
                            On Tuesday 06 June 2006 13:24, DigiDoc wrote:
                            > Thanks for the links.

                            [ > > Perl Tk - works on Linux and windoze ]

                            (if you quote a bit of context, it makes it easier for me (+ probably some
                            others) to track this thread and to then offer any help if I have any help to
                            offer.

                            > I was looking at that, but couldn't find a nice front end that lets you
                            > work visually. The GUI Loft let's you do things visually, then
                            > generates the code for you. Is there something in tk that does that, or
                            > am I missing something? Or at the very least, some application that has
                            > some kind of code snippets that are easy to insert?
                            >
                            > My goal is to develop code as rapidly as possible since I'll have a lot
                            > to crank out.

                            There's WX Widgets. It has drag and drop (for the builder). It's cross
                            platform ie Win, Linux, etc. There's article on WX Widgets in the
                            latest "The Perl Review" (for subscribers) hey it's reasonable enough and I
                            look forward to each issue's arrival. (I've no affiliation, just a
                            subscriber).

                            http://www.theperlreview.com/

                            The summer issue has article on WX Widgets.

                            Other than what I've shared, I know nothing about WX. I want to try it but
                            it'll be + few weeks until I do due to other business currently.

                            > > I'm thinking I'll want to make a GUI out of it now. I was doing some
                            > > research and found "The GUI Loft". It's a front end that uses
                            > > Win32::GUI. I haven't used it yet, but it seems like what I need. If
                            > > anyone has a better suggestion, please let me know.

                            --
                            Alan.
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