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GenomicMedLab / cool-seq-tool

https://coolseqtool.readthedocs.io
MIT License
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Allow initialization of writeable SeqRepo instance #282

Open jsstevenson opened 6 months ago

jsstevenson commented 6 months ago

Just need to add an extra param

jsstevenson commented 6 months ago

It's not that complicated to just do this manually

from biocommons.seqrepo import SeqRepo
from cool_seq_tool.app import CoolSeqTool

sr = SeqRepo("/usr/local/share/seqrepo/latest", writeable = True)
CoolSeqTool(sr=sr)

Not sure if it's worth adding writeable as a param to SeqRepoAccess or if we think it's fine the way it is. Maybe we could also add a method that makes this a little simpler:

    alias_dict_list = [{'namespace': 'ga4gh', 'alias': sequence_id}]
    get_seqrepo().sr.store(sequence, nsaliases = alias_dict_list)
github-actions[bot] commented 3 months ago

This issue is stale because it has been open 45 days with no activity. Please make a comment for triaging or closing the issue.