Hello Amir.
On Wed Apr 30 09:08:02 2014, Amir Banaei Esfahani wrote:
> Thank you so much for your help. Oh, Sorry, but I had sent my request
> to '[email protected]' but I got the following answer:
yes. you need to subscribe to post. An invite should now be in your
inbox.
> Your script is really nice but I have two problem with it. Is it
> possible to modify this?
It's a script - so you can change it as you see fit !
> 1)I need to have something like that the script produces but I need
> also to know name of each sequences before the features. Something
> like the following pattern:
>
> Name_of_seq1 feature_type1
> feature_Description1 index_of_feature_in_aligned_file1
You can get the name of the sequence with 'getName()'. Change the print
statement to:
println([sq.getName(), sf.getType(),sf.getDescription(),
sq.findIndex(sf.getBegin()), sq.findIndex(sf.getEnd())].join("\t")+"\n")
> 2)It doesn’t allow me to see all the features, I think the output
> panel has limitation in number of line (I have 64 sequences) and I can
> just see last part of result.
Hmm - really ? I guess you'll need to write it to a file.
This is the quickest way of doing that:
1. add the following line to the top of the script:
def outfile = new File("file_to_write.tsv");
2. Change the println statement to outfile.writeLine :
outfile.writeLine( [sq.getName(), sf.getType(),sf.getDescription(),
sq.findIndex(sf.getBegin()), sq.findIndex(sf.getEnd())].join("\t"))
You can find out more about groovy scripting here:
http://groovy.codehaus.org/Input+Output
Jim.
The University of Dundee is a registered Scottish Charity, No: SC015096
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