Comments (3)
This should be doable now.
You can use the internal function graph.get_path(chromosome)
that takes the chromosome name similar to the SN
tag as input and returns a list with the path nodes. If the list is empty, then something went wrong and you need to check the warning messages.
Still need to add a test case for this.
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Thanks Fawaz, it seems to be working fine. However, we are missing the orientation of the nodes. After sorting, we might need to check the respective "L" lines to find the edges (unless you already have them in your data structure and get the orientation so that we have an output such as s1>s2s19....>s151
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@asylvz I just pushed a new function that takes the path returned by graph.get_path(chromosome)
and returns a string with node orientation but in the GFA path line format, i.e. node1+,node2-,node3+ and so on. This format is described here.
The function is called return_gfa_path
, and takes as input a list of nodes in the path that you get from get_path
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Related Issues (13)
- SNP calling HOT 1
- can not found gfa_sort function in sort.py HOT 4
- gaftools convert places strand column in 4th field HOT 1
- Feature Request: Orient a GFA HOT 1
- Integrating GFA class HOT 4
- Issue running gaftools stat on gzip compressed file HOT 4
- Bug in order_gfa after merging PR14 HOT 18
- Let order_gfa output nodes and edges in an order corresponding to BO and NO tags HOT 10
- order_gfa with minigraph-cactus HOT 4
- Possible to use GFA 1.0 as input to gaftools index? HOT 1
- Gaftools stat does not work with a GAF file as input HOT 6
- Improve order_gfa documentation HOT 2
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