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katholt / srst2

Short Read Sequence Typing for Bacterial Pathogens
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Extract new allele sequence #13

Closed ConstantinV closed 10 years ago

ConstantinV commented 10 years ago

Thanks a lot for this perfect tool! But I can't figure out is it possible to extract new allele sequence after it's identification by mapping?

swlong commented 10 years ago

I have done this manually by reviewing the pileup file and identifying the SNP loci, but an automated method would be handy.

hdashnow commented 10 years ago

I've implemented the code for this and submitted a pull request. @katholt Would you like to check it and add it in if you're happy with it?

katholt commented 10 years ago

Hi guys, sorry we have had this coded up for a while (thanks Harriet) but I've not had time to test it! This is now available in the master branch, please let me know if it is working for you and it will be included in the next release. If you are really interested in novel alleles though, I recommend assembling the mapped reads (in the bam files output by srst2) and inspecting manually. This should be considered essential if there are indels reported (ie in the 'mismatches' column of MLST output); if it's just a SNP or 2 then consensus called from mapping should be fine.

ConstantinV commented 10 years ago

Sorry for long response. Thanks for answers and dissolution.
@katholt Is this option available in README. If not how to pass this option in command line? And how to update your package? Just type again sudo pip install git+https://github.com/katholt/srst2 or uninstall the previous version?

katholt commented 10 years ago

OK I've pushed these changes to the master branch.

You can update using: sudo pip install git+https://github.com/katholt/srst2

Usage instructions are now in the README https://github.com/katholt/srst2#printing-consensus-sequences