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Load bcalm2's output into our bigraph #2

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18 tasks done
sebschmi opened this issue May 25, 2020 · 0 comments · Fixed by #26
Closed
18 tasks done

Load bcalm2's output into our bigraph #2

sebschmi opened this issue May 25, 2020 · 0 comments · Fixed by #26
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enhancement New feature or request
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Load bigraph from...

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sebschmi commented May 25, 2020 •
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Implement this functionality in the context of the verify command.

  • Create genome-graph crate for the IO functions
  • Load the output, perhaps with support of the bio crate
    • Store the genome string
    • Compute reverse complements
    • Add error handling using error-chain
    • Implement DynamicBigraph::add_partner_nodes()
    • Implement DynamicBigraph::add_mirror_edges()
    • parse a single node from bcalm2
    • parse all the nodes from bcalm2 into a graph
    • add the edges to the graph
    • add the partner nodes and mirror edges to the graph
  • Save the output again, such that we can verify that it gets loaded correctly
    • plan this
    • write a method that serialises a single node including its out-edges
    • write a method that serialises all nodes, but skips nodes whose partner has already been serialised

Also add tests for

  • DynamicBigraph::add_partner_nodes()
  • DynamicBigraph::add_mirror_edges()
  • One full test case with a tiny bcalm2 file (artificially made) that checks if the resulting graph is completely correct
@sebschmi sebschmi added the enhancement New feature or request label May 25, 2020
@sebschmi sebschmi added this to the Load bigraph from bcalm2 milestone May 25, 2020
@sebschmi sebschmi assigned sebschmi and unassigned sebschmi May 25, 2020
@sebschmi sebschmi self-assigned this Jul 20, 2020
sebschmi added a commit that referenced this issue Jul 20, 2020
@sebschmi
Add genome-graph crate
d69dabd 
Relates to #2
sebschmi added a commit that referenced this issue Jul 20, 2020
@sebschmi
Add methods to open bcalm2 output (.fasta file).
1082509 
Relates to #2
sebschmi added a commit that referenced this issue Jul 20, 2020
@sebschmi
Attach fasta file opening function to cli verify command.
79af0b8 
The command now opens the file and prints the first line, and panics afterwards.

Relates to #2
sebschmi added a commit that referenced this issue Jul 20, 2020
@sebschmi
Load bcalm2's nodes into struct with error handling.
f3a12f8 
Error handling is done with error-chain that was added in this commit.

Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Implement DynamicBigraph and add_partner_nodes() for `NodeBigraph…
8ff30cf 
…Wrapper`.

Also added a trait `BidirectedNodeData` with a function `reverse_complement` that can be used instead of the `binode_mapping_function` parameter of some methods.
The test case for `add_partner_nodes()` currently fails, because `StaticBigraph::new_unchecked()` is unimplemented.

Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Read bcalm2 nodes into digraph data structure.
81bea01 
+ Implement `DynamicBigraph` and `add_partner_nodes()` for `NodeBigraphWrapper`
+ Implement `new_unchecked` for `NodeBigraphWrapper`
+ Add trait `BidirectedNodeData` with a function `reverse_complement` that can be used instead of the `binode_mapping_function` parameter of some methods
* Fix partner node: Return none if invalid

Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Complete loading of bcalm2's bigraph.
1cf589c 
+ implement `add_mirror_edges`
+ add partner nodes to the graph
+ add edges to the graph
+ add mirror edges to the graph

Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Implement test for add_mirror_edges.
44c8f11 
Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Add functions to write a bigraph into bcalm2 format.
28bbf8f 
Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Write bigraph to disk in verify.
bf8dc30 
This allows us to verify that the bigraph was loaded correctly.

Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Make add test case comparing between our and bcalm2's format.
c36b5d2 
* bcalm2 seems to output the edges without system, therefore we had to sort them manually
* we were missing some edges, they are output now
* the test case can be reproduced manually with the `verify.sh` script

Relates to #2
sebschmi added a commit that referenced this issue Jul 21, 2020
@sebschmi
Add success/failure message to verify.sh.
3ecc010 
Relates to #2
sebschmi added a commit that referenced this issue Jul 22, 2020
@sebschmi
Add test case for bcalm2 reading and writing.
baa7611 
Read from a string, write it again and check if it is the same.

Relates to #2
@sebschmi sebschmi mentioned this issue Jul 22, 2020
Merged
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Sebschmi/i2 load bcalm algbio/practical-omnitigs
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