teilab.seedmatch module¶

teilab.seedmatch.get_matched_mRNAs(seedseq: str) → pandas.core.frame.DataFrame[source]¶

Get a list of mRNAs with seedseq in 3’UTR

Parameters: seedseq (str) – A query sequence.
Returns: A data frame with a column named "SystematicName" meaning Accession numbers for each mRNA and a column named "NumHits" meaning how many seedseq sequences are in its 3’UTR
Return type: pd.DataFrame

Examples

>>> from teilab.seedmatch import get_matched_mRNAs
>>> df_matched_mRNAs = get_matched_mRNAs(seedseq="gagttca")
>>> print(df_matched_mRNAs.to_markdown())
|      | SystematicName   |   NumHits |
|-----:|:-----------------|----------:|
|    0 | NM_001004713     |         1 |
|    1 | NM_173860        |         1 |
|    2 | NM_001005493     |         1 |
|    : |     :            |         : |
| 3643 | NM_015139        |         1 |
| 3644 | NM_015463        |         1 |
| 3645 | NM_007189        |         1 |
>>> from teilab.utils import now_str
>>> now_str()
'2021-06-10@23.36.12'

You can also get the data with the command like curl .

$ curl -d "seedseq=gagttca" <SEEDMATCH_URL>