[Biococoa-dev] BioCocoa linux install

paolo siniselli paolo_siniselli at yahoo.it
Fri Mar 28 11:23:10 EDT 2008


Hi Scott,
I gave the command below. I don't if it is look good
or not. Should I change something or just keep going?
Anyway I appreciated your time.
Thanks
Paolo


debian:/home/kei/biococoa_ultraconserved/Ultraconserved.r132/trunk/obj#
./print_sarray outputchr1 | more
.:3: validity error : Validation failed: no DTD found
!
<plist version="0.9">
                    ^
.:3: validity error : Validation failed: no DTD found
!
<plist version="0.9">
                    ^
.:3: validity error : Validation failed: no DTD found
!
<plist version="0.9">
                    ^
offset: 237262 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTAT
...
offset: 237263 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATC
...
offset: 237264 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCT
...
offset: 237265 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTT
...
offset: 237266 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTC
...
offset: 237267 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCA
...
offset: 237268 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCAT
...
offset: 237269 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCATA
...
offset: 237270 strand: R id: chr1
AAAAAAAAAAAAAAAAAAAAAAAAAAAAGAAGAATGTGTCTATCTTCATAA
...
offset: 237271 strand: R id: chr1




--- Scott Christley <schristley at mac.com> wrote:

> Anyways, you created a suffix array file with your
> chromosome, try  
> using the "print_sarray" command to output the
> contents of that  
> suffix array.


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