Hi Jen,
It works, thanks!
I am wondering why using Text Manipulation/Compute function, galaxy
changes brackets '[' to '__ob__' and '__cb__' for ']', so
for this: str(c1)[1:2] --> str(c1)__ob__1:2__cb__
thanks a lot,
michal
Hi
Michal,
The tool "Fetch Sequences -> Extract Genomic DNA" can be used
to extract fasta sequences. The coordinates can be BED, GTF, etc.
and the "genome" doesn't necessarily have to be an actual genome,
just a fasta file in your history.
To subset a data string, the tool "Text Manipulation -> Trim"
might be helpful. This would only work if you want to use the same
rules for an entire file (or split your file up and run the tool
on those subfiles using different rules). Practical for some
cases, but not all.
And the final option is for coordinate data - tools in "Operate on
Genomic Intervals". Once you have the final coordinate set, going
back and using the "Fetch Sequences" tool can capture the
associated result fasta sequence, from a native genome or a fasta
file in your history, as described above.
Hopefully this gives you an option that will work for your
project,
Best,
Jen
Galaxy team
On 6/5/11 7:14 AM, Michal Stuglik wrote:
Hi all,
I am wondering if galaxy has tool to substring/extract
sequence/text
from another sequence/text based on coordinates in columns
(start, end
column) or how to do it in Text Manipulation/Compute?
all the best,
michal