Random sequence creator with range

ashnator has asked for the wisdom of the Perl Monks concerning the following question:

Dear Monks,

1) I have a fasta raw sequence file which contains A,C,G,T charaters i
+n a single string like this:-

AAAAAAAAAAAAACTGCTGACTAGCATAGTTAAAAAAAAAAAAAAAAGTTTTTTTA....

2) I want to create multiple fasta files using this file giving a user
+ defined range like :- Range of minimum length 10 and maximum length 
+of 40 suppose and then create short sequence in this range of 10 - 40
+ without losing the original positional information randomly.

3) I mean my result should be like this from above 

>seq1 length 10
AAAAAAAAAA
>seq2 length 18
AAACTGCTGACTAGCATA
>seq3 length 28
GTTAAAAAAAAAAAAAAAAGTTTTTTTA

..... 

4) How can I do this in perl. I need help fast.

I would be obliged to get help from Monks..

Thanks..
[download]

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Re: Random sequence creator with range by ikegami (Patriarch) on Sep 17, 2008 at 03:20 UTC
`my $seq = ...; my $len = ...; die if $len > length($seq); my $start = rand( length($seq) - $len + 1 ); my $subseq = substr( $seq, $start, $len );` [download] I presume you know how to create and write to a file.	[reply] [d/l]
Re: Random sequence creator with range by repellent (Priest) on Sep 17, 2008 at 03:38 UTC
This creates files `seq001`, `seq002`, `seq003`, etc. `perl -e '$file = "seq001"; for (@ARGV) { if (10 <= $_ && $_ <= 40) { r +ead STDIN, my $seq, $_; open my $FH, ">", $file++; print $FH $seq } } +' 10 18 28 < fasta.txt` [download]	[reply] [d/l] [select]