Converting sam to color space

[loituna]

Hi,

Does anybody know if a tool exists for converting sam (or bam) back to original csfasta file?
I know that the color space information is included in the sam format, but I can't find a tool that does the conversion.
So far, from what I read, neither samtool view nor picard tool have that option.
That would be great if it existed, I really don't want to do it myself

Thanks!

[nilshomer]

Seems like time for a perl one liner. Try this:

cat <in.sam> | grep -v "^@" | perl -ne '$_ =~ s/\t.*CS:Z:([^\t]+).*/\n$1/g; print ">$_";'

[loituna]

Thanks!
But I am not sure it is making exactly what I want :
The problem is that I want to get the original read, as they were output from the sequencer.
So if part of the read was cut because the end was considered not matching I would like to put them back together. Same as if the read was align not continously on the genome (part of a read was matching somewhere and the other part somewhere else, because eg of rearrangement).
I am not sure the solution is trivial to write especially a fast solution. or is it?

And I am not entirely sure either that the problem I am describing is correct, and there might be other issue I don't see right now...

what do you think?

[nilshomer]

The CS tag should give ALL the colors, not just the aligned portion.

[loituna]

Great!

Then that solve my problem..

Thanks