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

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