search

wheretrue / biobear

Work with bioinformatic files using Arrow, Polars, and/or DuckDB
https://www.wheretrue.dev/docs/exon/biobear/
MIT License
163 stars 9 forks source link

Can not read ".fq" file #163

Closed xiasijian closed 3 months ago

xiasijian commented 4 months ago

image

xiasijian commented 4 months ago

image maybe you can update it, thanks.

tshauck commented 4 months ago

Hi @xiasijian, sorry that's giving you issues. Can you try using read_fastq_file on the session context. It should be able to infer the file extension. See https://github.com/wheretrue/biobear/blob/8d4f8f19174631a79f431cbed6cb37b9818f9a38/python/tests/test_session.py#L143-L158 for the test case.

tshauck commented 3 months ago

@xiasijian I'm gonna close this, but feel free to reopen if read_fastq_file doesn't work for you.

xiasijian commented 2 months ago

image It is OK, Thanks a lot~