[BiO BB] perl help

[Dan Bolser]

not sure about the genbank format, but could you do something like


while(<>){                     # itterate through file given on command line...

  if (/^ORIGIN(.*)/){
    $sequence .= $1;
  }
}

$rand = rand( length($sequence) );

substr ( $rand, 100, $sequence) );




Matt McCormick said:
> Please allow me to elaborate a bit more.  I'm trying to pull a random 100 kb
> section from the chromosomal sequence(in genbank format,
> Accession NC_003070).  The chromosome sequence is 30494425 bp long, and the
> positions x and y represent the base i want my sequence to start and end
> respectively.  I'm just beginning to use perl, and for me to use substr function,
> i would have to find and join all the lines starting at the ORIGIN.  I m not sure
> on the best way to do this.  Any help would be appreciated. Thank you.
>
>
> On Sat, 2003-11-15 at 19:47, Joe Landman wrote:
>> Hi Matt:
>>
>>
>> On Sat, 2003-11-15 at 19:33, Matt McCormick wrote:
>> > Hi,
>> > I am trying to construct a sequence, with start position x and end position y,
>> from A.thaliana chromosome 1.  Does anyone have any code they would be willing
>> to share that would do this? I have the current perl and bioperl modules
>> installed.  Thank you.
>>
>>    I might suggest giving a better specification of the problem.  You
>> have the chromosome 1 data in some format, and you need to extract a particular
>> section from it?  If this is the case, then is there a particular reason why the
>> substr function will not work?
>>
>> 	my $small = substr $sequence,$x,$y-$x+1 ;
>>
>> Joe
>>
>> >
>> > -Matt McCormick
>> >
>> >
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>
>
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