[gt-users] How to create a node_stream and gff3 file from scratch (not from existing file)

[La Rota, Mauricio]

Hi all,

I am a bit lost here as it seems genometools (or at least from its python perspective) assumes that node_streams (or genome_streams, feature_streams) are always created from an existing GFF3 file.  Or at least, this is how I am understanding the code.

I have a set of annotation data (in older flat table as gff2 or tables in SQL db), I want to output valid GFF3 from it and think that genometools would be great to help me keep track of parent/children objects and their relationships and to create IDs for them (not good on gff2).

This is what I am thinking to do:

1) Create new Feature Nodes from scratch with data at hand, add children to parents as I read them from data.

As new Features are made..

2) Make a FeatureIndex, then add nodes (FeatureNodes) to it with gt_feature_index_add_feature_node() (not implemented in python, I think)

3) Figure out how to "stream" the FeatureIndex and FeatureNodes to some Node/Feature stream stream.. 


4) open a gff3_ouput_stream and feed the stream from 3)  or directly from 2) if it turns out I don't need a FeatureIndex.

5) pull the Features through the Feature Stream

I found this email (http://genometools.org/pipermail/gt-users/2009-January/000027.html) helpful but it did not explain step 3) above.

Thanks all,

Mauricio

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