Greetings all,
Thank you for all your answers.
What I want to do is ,after modifying callbases, I need to use the
sequences with 'phrad' foro DNA assembly.For 'phrad', I need to give
Fasta files and Quality files.
I can modify callbases using my chromatogram editor , and save the new
sequence in Fasta file.But my problem is , If I change the original
callbases from AB1 file ,does it effect the Qualitiy files also? Or can
I use the original Quality files generated by 'phred' with the new
callbases.
Here is a image demonstrating my scenario:
http://img3.imageshack.us/img3/3564/f92df0815fab523f3c72aa3qx7.png
Step (2) Ab1 files are passed into 'phred' and Fasta,Quality files are
generated.
Step (3) If user want to edit callbases , he can use the chromatogram
editor.Then the Fasta files generated by 'phred' are replaced with new
onces generated by editor.
My problem is can I use the same Quality files ,with the modified
callbases ?
Sorry if this is off the topic.
Thanks in advance,
Umanga
Andy Yates wrote:
Hi Umanga,
Unfortunately there is no write feature available in the BioJava API. My
advice would be to store these new basecalls in a separate file & look
into using the Staden IO package which does support write functions (not
sure if it will write into AB1 but it will do SCF & ZTR). Sadly this is
written in C so you will have to write either some glue code with JNI to
get it working or write a small C program to munge an AB1 trace & your
new file together.
Sorry I can't be of any more help,
Andy
Ashika Umanga Umagiliya wrote:
Greetings all,
I was able to display chromatogram using ABIFChromatogram class .
Now what I want to implement is a chromatogram Editor,where user can
edit base calls and save aback to AB1 files.
Is there a way to do this in BioJava?
Best Regards,
umanga
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
_______________________________________________
Biojava-l mailing list - [email protected]
http://lists.open-bio.org/mailman/listinfo/biojava-l
