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orthodb-refseq-mapper's Introduction

Mapping orthoDB to RefSeq RNA

Species

Name dog elephant horse human monkey platypus rabbit mouse cow
TAX_ID 9615 9785 9796 9606 9544 9258 9986 10090 9913

Download the required data

bash prepare_species.sh

Map any species

python analyse.py <species_name> <species_tax_id>

Run flags:

  • --detailed-report generate detailed report.
  • --deep-search activate deep search option. (Explained in Methods)

Check mapping quality

python check_mapping_quality.py <species_name> <species_tax_id>

You can add species as much as you can.

Mapping is not guaranteed to be PERFECT.

Not all transcripts are mapped.

Running with Pypy Will speed up the process significantly.

orthodb-refseq-mapper's People

Contributors

drtamermansour avatar mr-eyes avatar

Stargazers

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Watchers

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orthodb-refseq-mapper's Issues

Match description by similarity

Genes description matching could be enhanced by using string similarity.

Ex:

from difflib import SequenceMatcher
def similar(a, b):
    return SequenceMatcher(None, a, b).ratio()

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