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