Question: Text Manipulation
gravatar for Felix Hammer
7.8 years ago by
Felix Hammer200
Felix Hammer200 wrote:
Hi, is there a way to manipulate the different values in the column of a tab sepparated file (i.e. change all chr1@sdfasdfasdfasdf to chr1 using regexp). thx, Felix
ADD COMMENTlink modified 7.8 years ago by Jennifer Hillman Jackson25k • written 7.8 years ago by Felix Hammer200
gravatar for Jennifer Hillman Jackson
7.8 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Felix, "Text Manipulation -> Convert delimiters to TAB" could split one field into more than one, but the delimiter has to be in the list ("@" is not). "Text Manipulation -> Cut columns" from a table is similar, but it will not split on a "@" either. "Text Manipulation -> Trim leading or trailing characters" could be use for this specific case, since you can trim off the end of a column based on a position (but again, not a specified delimiter). To prep for an entire genome, you would need to break up the starting query so that the chromosome name lengths in any derivative queries are of a consistent length, then merge back together. Perhaps the "@" was just an example and one of these tools will work for you. If you are customizing, additions to the Tool Shed that expand the native tools are always welcome! Thanks for using Galaxy and for bringing up an interesting use case, Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.8 years ago by Jennifer Hillman Jackson25k
I've been planning to write a Galaxy tool to split a column on a given delimiter (e.g. @ for this example, or | for NCBI style identifiers), which would solve this use case nicely. I haven't done it yet though - so if anyone else wants to write such a tool first, please go ahead. Specifically I would be aiming to expose the Python split and rsplit string method functionality, so the user would have to specify the number of splits (or perhaps more intuitively the number of columns to make) and if it should start on the left (default) or on the right. Peter
ADD REPLYlink written 7.8 years ago by Peter Cock1.4k
Hi Peter, sounds nice, would be a great feature. For everyone else how is not using a custom server: if you are lucky you can use the trim tool on tabs to solve your problem. If you want to add text to the beginning or end of a column: - Use add column and add the text as a new column - Then use cut to get everything in the right order - finally join the new column with the column you want to add the text to I hope you get what I mean and is helpful to someone Using these tricks I have created a work flow that serves as my custom sam to gff converter. Of course its terribly inefficient, but it gets the job done. thx, Felix
ADD REPLYlink written 7.8 years ago by Felix Hammer200
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