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Contents

  • How it works
    • General requirements for primers
    • VariantPrimerGenerator
    • ExonPrimerGenerator
    • GenePrimerGenerator
    • GenomicPositionPrimerGenerator
  • Resources used
    • Primer3
    • genomepy
    • hgvs.parser

Package

  • primertool
    • primertool package
      • Submodules
      • primertool.exceptions module
        • InSilicoPCRError
        • InSilicoPCRRequestError
        • PrimertoolError
        • PrimertoolExonLengthError
        • PrimertoolGenomeError
        • PrimertoolInputError
        • PrimertoolIntronicPositionError
        • PrimertoolMutalyzerError
        • PrimertoolNoPrimerFoundError
      • primertool.functions module
        • calculate_targets()
        • correct_intronic_variant()
        • filter_unique_primers()
        • find_sequence_positions()
        • get_gene_information()
        • get_snps()
        • mask_snps()
        • mutalyzer_error_handler()
        • parse_mutation()
        • purge_primer_pair()
        • reduce_numbers_in_string()
        • remove_whitespaces()
        • split_nm()
      • primertool.insilicopcr module
        • InSilicoPCR
      • primertool.logger module
        • CustomFormatter
        • init_logger()
      • primertool.primertool module
        • ExonPrimerGenerator
        • ExonPrimerPair
        • GenePrimerGenerator
        • GenomicPositionPrimerGenerator
        • GenomicPositionPrimerPair
        • PrimerGenerator
        • PrimerPair
        • VariantPrimerGenerator
      • primertool.ucsc_database module
        • query()
      • primertool.unittest module
        • PrimertoolTest
      • Module contents
    • streamlit module
      • streamlit_custom_components
        • feedback()
        • generate_primers()
        • kuerzel_check()
      • streamlit_help
      • streamlit_main
      • streamlit_primertool

Setup and Deployment

  • Setup
    • Streamlit
    • Docker
    • Log access
  • Local UCSC database
    • Download database tables
    • Create and populate local database
    • Create new user to access the database
  • Deployment using proxy
primertool
  • Overview: module code

All modules for which code is available

  • primertool.exceptions
  • primertool.functions
  • primertool.insilicopcr
  • primertool.logger
  • primertool.primertool
  • primertool.ucsc_database
  • primertool.unittest
  • streamlit_custom_components

© Copyright 2024, Simon Michau, Daniela Dey, Carlos Classen.

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