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pha4ge / primaschema

Infrastructure for tiled amplicon PCR primer scheme definitions
MIT License
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Add subcommand to print intervals spanned by primers #21

Closed pvanheus closed 4 months ago

pvanheus commented 6 months ago

Given a primer.bed file like:

MN908947.3  25  50  SARS-CoV-2_1_LEFT   1   +   AACAAACCAACCAACTTTCGATCTC
MN908947.3  324 344 SARS-CoV-2_2_LEFT   2   +   TTTACAGGTTCGCGACGTGC
MN908947.3  408 431 SARS-CoV-2_1_RIGHT  1   -   CTTCTACTAAGCCACAAGTGCCA
MN908947.3  705 727 SARS-CoV-2_2_RIGHT  2   -   ATAAGGATCAGTGCCAAGCTCG

The new intervals subcommand prints:

MN908947.3      25      431     SARS-CoV-2_1
MN908947.3      324     727     SARS-CoV-2_2

Code is designed to work with PHA4GE-standard primer schemes and can deal with alt primers.

bede commented 5 months ago

Sorry for delay, useful! Seems to work nicely for some ARTICs but not for Midnight or the most recent ARTICs. Happy to merge, but a heads up in case you want to try and accommodate these naming conventions. Presumably the latest naming is what's being used going forwards. Just let me know