blakesweeney/infer-rfamy-rna-types

Some work to figure out how to improve the inference of RNA types from Rfam

Improving Rfam's RNA Types

This is some code to try to improve the ISNDC type that Rfam families get.

Logic

The script in bin/infer.py will infer an INSDC RNA type for all Rfam families. It has a series of different methods for selecting the name. In the order they are attempted:

manual

Check if there is a manually assigned RNA type for the family. Currently there are none.

name

Check if the name contains a descriptive string like Y_RNA.

so-term

Check if the SO terms assigned to the family have an RNA type assigned.

rna-type

Use Rfam's RNA type to infer an INSDC RNA type.

so-search

Use the given SO terms and look up the tree to find the nearest parent SO term(s) that have been assigned an RNA type.

The assignments to RNA types are found in data/manual-assignments.json. Most families have an inferred type (though other is a common one) with this method. The last stage, searching the attached SO terms, is a minor contribution to the inferred names, and can probably be ignored in general.

Also note that in theory it is possible (and correct) to infer more than one ISNDC RNA type for some families. For example family []() is a snoRNA that can act as an miRNA, so both types are correct. Here we use as the RNA type.

Results

The inferred types are in data/infered-types.txt. A few quick summaries:

$ xsv select method data/infered-types.txt | sort | uniq -c
    479 fallbacks
      1 method
     36 name
   1056 rna-type
     15 so-search
   1002 so-term
$ xsv select rna_types data/infered-types.txt | sort | uniq -c
    479 ""
      2 RNase_MRP_RNA
      5 RNase_P_RNA
      9 SRP_RNA
      4 Y_RNA
     33 antisense_RNA
     10 autocatalytically_spliced_intron
      5 hammerhead_ribozyme
    217 lncRNA
    484 other
    530 precursor_RNA
     15 rRNA
     12 ribozyme
      1 rna_types
     18 snRNA
    753 snoRNA
      2 tRNA
      4 telomerase_RNA
      5 tmRNA
      1 vault_RNA

The method called fallbacks means no INSDC type could be found.

Requirements

• python3
• make
• wget
• gzip

You must also install the requirments in requirements.txt.

$ pip install -r requirements.txt

Usage

To produce a csv of family to INSDC RNA types in data/infered-types.txt.

$ make