Grabing line from file

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  • pallabtrue
    New Member
    • Jun 2010
    • 11
    #1

    Grabing line from file

    Hi my original file looks like this-
    >P1;208,D-
    208,D-5 - (MOUSE) mouse
    DVLMTQTPPSLPVSL GDQASISCRSSQTIV HSDGNTYLEW
    YLQKPGQSPKLLIYK VSNRFSGVPDRFSGS GSGTDFTLKI
    SRVEAEDLGLYYCFQ GSHVPPTFGGGTKLE IKR*
    VQLLEESGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
    PEKRLEWFATISDGG SHTYYPDSVKGRFTI SRDNAKNNLY
    LQMSCLRSEDTAMYY CTRDSLDFYGMDYWG QGTSVTVSS*
    >P1;MN14C1
    MN14C11.6 - (MOUSE) mouse
    DILMTQTPLSLPVSL GDQASISCRSSQSLV HSNGNTYLHW
    YLQKPGQSPKLLIYT VSNRFSGVPDRFSGS GSGTDFTLKI
    SRVEAEDLGLYFCSQ STHLPPTFGGGTKLD IKR*
    DVHLLVSGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
    PEKRLEWVATISDGG AHTYYPDSVKGRFTI SRDNAKNNLY
    LHMNSLKSEDTAMYY CARDPLEYYGMDYWG QGTAVTV*
    >P1;scFv40
    scFv40 - (MOUSE) mouse
    DVQIIQTTASLSASV GETVTITCRASEHIY SYLAWYQQKQ
    GKSPQLLVYSAKTLA EGVPSRFSGSGSGTQ FSLKINSLQP
    EDFGSYYCQHHYDTP RTFGGGTKLEIRRA*
    VDQVQQPGAELVRSG ASVKMSCKASGYTFT SYNMHWVKQT
    PGQGLEWIGYIYPGN GGTIYNQKFKGKATL TADTSSSTAN
    MQISSLTSEDSAVYF CARGDYRNDPFDFWG QGTTLTVSS*

    After that I created new file by perl and its looks like this -
    >P1|208,D
    DVLMTQTPPSLPVSL GDQASISCRSSQTIV HSDGNTYLEW
    YLQKPGQSPKLLIYK VSNRFSGVPDRFSGS GSGTDFTLKI
    SRVEAEDLGLYYCFQ GSHVPPTFGGGTKLE IKR*
    VQLLEESGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
    PEKRLEWFATISDGG SHTYYPDSVKGRFTI SRDNAKNNLY
    LQMSCLRSEDTAMYY CTRDSLDFYGMDYWG QGTSVTVSS*
    >P1|MN14C1
    DILMTQTPLSLPVSL GDQASISCRSSQSLV HSNGNTYLHW
    YLQKPGQSPKLLIYT VSNRFSGVPDRFSGS GSGTDFTLKI
    SRVEAEDLGLYFCSQ STHLPPTFGGGTKLD IKR*
    DVHLLVSGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
    PEKRLEWVATISDGG AHTYYPDSVKGRFTI SRDNAKNNLY
    LHMNSLKSEDTAMYY CARDPLEYYGMDYWG QGTAVTV*
    >P1|scFv40
    DVQIIQTTASLSASV GETVTITCRASEHIY SYLAWYQQKQ
    GKSPQLLVYSAKTLA EGVPSRFSGSGSGTQ FSLKINSLQP
    EDFGSYYCQHHYDTP RTFGGGTKLEIRRA*
    VDQVQQPGAELVRSG ASVKMSCKASGYTFT SYNMHWVKQT
    PGQGLEWIGYIYPGN GGTIYNQKFKGKATL TADTSSSTAN
    MQISSLTSEDSAVYF CARGDYRNDPFDFWG QGTTLTVSS*


    So want to grab lines in two ways

    one is
    >P1|208,D
    DVLMTQTPPSLPVSL GDQASISCRSSQTIV HSDGNTYLEW
    YLQKPGQSPKLLIYK VSNRFSGVPDRFSGS GSGTDFTLKI
    SRVEAEDLGLYYCFQ GSHVPPTFGGGTKLE IKR*


    2nd way is
    >P1|208,D
    *
    VQLLEESGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
    PEKRLEWFATISDGG SHTYYPDSVKGRFTI SRDNAKNNLY
    LQMSCLRSEDTAMYY CTRDSLDFYGMDYWG QGTSVTVSS*

    I was thinking about regular expression but its not working. Anyone can plz help me....

    Thanks
    Pallab
    Tags: None
    • toolic
      Recognized Expert New Member
      • Sep 2009
      • 70
      #2
      Code:
      use warnings;
use strict;

my $start;
my $flag = 0;
while (<DATA>) {
    print;
    if (/^>/) {
        $start = $_;
        $flag = 1;
    }
    elsif (/\*/) {
        print "$start*\n" if $flag;
        $flag = 0;
    }
}

__DATA__
>P1|208,D
DVLMTQTPPSLPVSLGDQASISCRSSQTIVHSDGNTYLEW
YLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYYCFQGSHVPPTFGGGTKLEIKR*
VQLLEESGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWFATISDGGSHTYYPDSVKGRFTISRDNAKNNLY
LQMSCLRSEDTAMYYCTRDSLDFYGMDYWGQGTSVTVSS*
>P1|MN14C1
DILMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHW
YLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYFCSQSTHLPPTFGGGTKLDIKR*
DVHLLVSGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWVATISDGGAHTYYPDSVKGRFTISRDNAKNNLY
LHMNSLKSEDTAMYYCARDPLEYYGMDYWGQGTAVTV*
>P1|scFv40
DVQIIQTTASLSASVGETVTITCRASEHIYSYLAWYQQKQ
GKSPQLLVYSAKTLAEGVPSRFSGSGSGTQFSLKINSLQP
EDFGSYYCQHHYDTPRTFGGGTKLEIRRA*
VDQVQQPGAELVRSGASVKMSCKASGYTFTSYNMHWVKQT
PGQGLEWIGYIYPGNGGTIYNQKFKGKATLTADTSSSTAN
MQISSLTSEDSAVYFCARGDYRNDPFDFWGQGTTLTVSS*
      Prints out:

      Code:
      >P1|208,D
DVLMTQTPPSLPVSLGDQASISCRSSQTIVHSDGNTYLEW
YLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYYCFQGSHVPPTFGGGTKLEIKR*
>P1|208,D
*
VQLLEESGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWFATISDGGSHTYYPDSVKGRFTISRDNAKNNLY
LQMSCLRSEDTAMYYCTRDSLDFYGMDYWGQGTSVTVSS*
>P1|MN14C1
DILMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHW
YLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYFCSQSTHLPPTFGGGTKLDIKR*
>P1|MN14C1
*
DVHLLVSGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWVATISDGGAHTYYPDSVKGRFTISRDNAKNNLY
LHMNSLKSEDTAMYYCARDPLEYYGMDYWGQGTAVTV*
>P1|scFv40
DVQIIQTTASLSASVGETVTITCRASEHIYSYLAWYQQKQ
GKSPQLLVYSAKTLAEGVPSRFSGSGSGTQFSLKINSLQP
EDFGSYYCQHHYDTPRTFGGGTKLEIRRA*
>P1|scFv40
*
VDQVQQPGAELVRSGASVKMSCKASGYTFTSYNMHWVKQT
PGQGLEWIGYIYPGNGGTIYNQKFKGKATLTADTSSSTAN
MQISSLTSEDSAVYFCARGDYRNDPFDFWGQGTTLTVSS*

        Comment

        • pallabtrue
          New Member
          • Jun 2010
          • 11
          #3
          Originally posted by toolic
          Code:
          use warnings;
use strict;

my $start;
my $flag = 0;
while (<DATA>) {
    print;
    if (/^>/) {
        $start = $_;
        $flag = 1;
    }
    elsif (/\*/) {
        print "$start*\n" if $flag;
        $flag = 0;
    }
}

__DATA__
>P1|208,D
DVLMTQTPPSLPVSLGDQASISCRSSQTIVHSDGNTYLEW
YLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYYCFQGSHVPPTFGGGTKLEIKR*
VQLLEESGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWFATISDGGSHTYYPDSVKGRFTISRDNAKNNLY
LQMSCLRSEDTAMYYCTRDSLDFYGMDYWGQGTSVTVSS*
>P1|MN14C1
DILMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHW
YLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYFCSQSTHLPPTFGGGTKLDIKR*
DVHLLVSGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWVATISDGGAHTYYPDSVKGRFTISRDNAKNNLY
LHMNSLKSEDTAMYYCARDPLEYYGMDYWGQGTAVTV*
>P1|scFv40
DVQIIQTTASLSASVGETVTITCRASEHIYSYLAWYQQKQ
GKSPQLLVYSAKTLAEGVPSRFSGSGSGTQFSLKINSLQP
EDFGSYYCQHHYDTPRTFGGGTKLEIRRA*
VDQVQQPGAELVRSGASVKMSCKASGYTFTSYNMHWVKQT
PGQGLEWIGYIYPGNGGTIYNQKFKGKATLTADTSSSTAN
MQISSLTSEDSAVYFCARGDYRNDPFDFWGQGTTLTVSS*
          Prints out:

          Code:
          >P1|208,D
DVLMTQTPPSLPVSLGDQASISCRSSQTIVHSDGNTYLEW
YLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYYCFQGSHVPPTFGGGTKLEIKR*
>P1|208,D
*
VQLLEESGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWFATISDGGSHTYYPDSVKGRFTISRDNAKNNLY
LQMSCLRSEDTAMYYCTRDSLDFYGMDYWGQGTSVTVSS*
>P1|MN14C1
DILMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHW
YLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYFCSQSTHLPPTFGGGTKLDIKR*
>P1|MN14C1
*
DVHLLVSGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWVATISDGGAHTYYPDSVKGRFTISRDNAKNNLY
LHMNSLKSEDTAMYYCARDPLEYYGMDYWGQGTAVTV*
>P1|scFv40
DVQIIQTTASLSASVGETVTITCRASEHIYSYLAWYQQKQ
GKSPQLLVYSAKTLAEGVPSRFSGSGSGTQFSLKINSLQP
EDFGSYYCQHHYDTPRTFGGGTKLEIRRA*
>P1|scFv40
*
VDQVQQPGAELVRSGASVKMSCKASGYTFTSYNMHWVKQT
PGQGLEWIGYIYPGNGGTIYNQKFKGKATLTADTSSSTAN
MQISSLTSEDSAVYFCARGDYRNDPFDFWGQGTTLTVSS*
          Thanks for your answer

            Comment

            • pallabtrue
              New Member
              • Jun 2010
              • 11
              #4
              Originally posted by toolic
              Code:
              use warnings;
use strict;

my $start;
my $flag = 0;
while (<DATA>) {
    print;
    if (/^>/) {
        $start = $_;
        $flag = 1;
    }
    elsif (/\*/) {
        print "$start*\n" if $flag;
        $flag = 0;
    }
}

__DATA__
>P1|208,D
DVLMTQTPPSLPVSLGDQASISCRSSQTIVHSDGNTYLEW
YLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYYCFQGSHVPPTFGGGTKLEIKR*
VQLLEESGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWFATISDGGSHTYYPDSVKGRFTISRDNAKNNLY
LQMSCLRSEDTAMYYCTRDSLDFYGMDYWGQGTSVTVSS*
>P1|MN14C1
DILMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHW
YLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYFCSQSTHLPPTFGGGTKLDIKR*
DVHLLVSGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWVATISDGGAHTYYPDSVKGRFTISRDNAKNNLY
LHMNSLKSEDTAMYYCARDPLEYYGMDYWGQGTAVTV*
>P1|scFv40
DVQIIQTTASLSASVGETVTITCRASEHIYSYLAWYQQKQ
GKSPQLLVYSAKTLAEGVPSRFSGSGSGTQFSLKINSLQP
EDFGSYYCQHHYDTPRTFGGGTKLEIRRA*
VDQVQQPGAELVRSGASVKMSCKASGYTFTSYNMHWVKQT
PGQGLEWIGYIYPGNGGTIYNQKFKGKATLTADTSSSTAN
MQISSLTSEDSAVYFCARGDYRNDPFDFWGQGTTLTVSS*
              Prints out:

              Code:
              >P1|208,D
DVLMTQTPPSLPVSLGDQASISCRSSQTIVHSDGNTYLEW
YLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYYCFQGSHVPPTFGGGTKLEIKR*
>P1|208,D
*
VQLLEESGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWFATISDGGSHTYYPDSVKGRFTISRDNAKNNLY
LQMSCLRSEDTAMYYCTRDSLDFYGMDYWGQGTSVTVSS*
>P1|MN14C1
DILMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHW
YLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKI
SRVEAEDLGLYFCSQSTHLPPTFGGGTKLDIKR*
>P1|MN14C1
*
DVHLLVSGGGLVKPGGSLKLSCAASGFTFSDYYMFWVRQT
PEKRLEWVATISDGGAHTYYPDSVKGRFTISRDNAKNNLY
LHMNSLKSEDTAMYYCARDPLEYYGMDYWGQGTAVTV*
>P1|scFv40
DVQIIQTTASLSASVGETVTITCRASEHIYSYLAWYQQKQ
GKSPQLLVYSAKTLAEGVPSRFSGSGSGTQFSLKINSLQP
EDFGSYYCQHHYDTPRTFGGGTKLEIRRA*
>P1|scFv40
*
VDQVQQPGAELVRSGASVKMSCKASGYTFTSYNMHWVKQT
PGQGLEWIGYIYPGNGGTIYNQKFKGKATLTADTSSSTAN
MQISSLTSEDSAVYFCARGDYRNDPFDFWGQGTTLTVSS*
              hi
              can u plz explain me about function of variable $flag.
              and other thing is that if I try to print only

              >P1|208,D
              DVLMTQTPPSLPVSL GDQASISCRSSQTIV HSDGNTYLEW
              YLQKPGQSPKLLIYK VSNRFSGVPDRFSGS GSGTDFTLKI
              SRVEAEDLGLYYCFQ GSHVPPTFGGGTKLE IKR*

              >P1|MN14C1
              DILMTQTPLSLPVSL GDQASISCRSSQSLV HSNGNTYLHW
              YLQKPGQSPKLLIYT VSNRFSGVPDRFSGS GSGTDFTLKI
              SRVEAEDLGLYFCSQ STHLPPTFGGGTKLD IKR*

              >P1|scFv40
              DVQIIQTTASLSASV GETVTITCRASEHIY SYLAWYQQKQ
              GKSPQLLVYSAKTLA EGVPSRFSGSGSGTQ FSLKINSLQP
              EDFGSYYCQHHYDTP RTFGGGTKLEIRRA*


              Or only I if I try to printout this format

              >P1|208,D
              *
              VQLLEESGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
              PEKRLEWFATISDGG SHTYYPDSVKGRFTI SRDNAKNNLY
              LQMSCLRSEDTAMYY CTRDSLDFYGMDYWG QGTSVTVSS*

              >P1|MN14C1
              *
              DVHLLVSGGGLVKPG GSLKLSCAASGFTFS DYYMFWVRQT
              PEKRLEWVATISDGG AHTYYPDSVKGRFTI SRDNAKNNLY
              LHMNSLKSEDTAMYY CARDPLEYYGMDYWG QGTAVTV*

              >P1|scFv40
              *
              VDQVQQPGAELVRSG ASVKMSCKASGYTFT SYNMHWVKQT
              PGQGLEWIGYIYPGN GGTIYNQKFKGKATL TADTSSSTAN
              MQISSLTSEDSAVYF CARGDYRNDPFDFWG QGTTLTVSS*

              so for this one what I have to change in previous programme

              Thanks
              Pallab

                Comment

                • toolic
                  Recognized Expert New Member
                  • Sep 2009
                  • 70
                  #5
                  $flag is used as a state variable.
                  It is set when a line begins with ">".
                  It is cleared when a line ends with "*".
                  I admit that it is not the best name for a variable,
                  but you can change it to be more meaningful for you.

                  I don't understand the rest of yuor question.

                    Comment

                    • pallabtrue
                      New Member
                      • Jun 2010
                      • 11
                      #6
                      Originally posted by toolic
                      $flag is used as a state variable.
                      It is set when a line begins with ">".
                      It is cleared when a line ends with "*".
                      I admit that it is not the best name for a variable,
                      but you can change it to be more meaningful for you.

                      I don't understand the rest of yuor question.
                      Thanks for your feedback....... ..Actually in every Sequence there are two parts which is divided by *...* so that means
                      >P1|BD-8
                      FHFHFJHFJFDJJHF JF
                      HFJHFJKFJKFJKFJ KF                      *
                      GFHFHJFJFJFJKFJ KF
                      HJFHJFJFJKFJKFJ KF                      *

                      So bold is part1 of that sequence and thats lies between > and first *

                      and 2nd part lies between first * and second *

                      so my job is to grab part1 of all sequence and print them
                      and second job is that grab par2 of all sequence and print them with header line.

                      Thanks
                      Pallab

                        Comment

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