Add autopkgtest after adding packages with the needed data

Notes on how this package can be tested.

────────────────────────────────────────

This package can be tested by running the provided test.  You need

to install kaptive-data and kaptive-example package before you can run

    sh run-unit-test

in order to confirm its integrity.

Homepage: https://github.com/katholt/Kaptive

Package: kaptive

Architecture: any

Architecture: all

Depends: ${python3:Depends},

         ${misc:Depends},

         python3-biopython

         python3-biopython,

         ncbi-blast+

Suggests: kaptive-data,

          kaptive-example

Description: obtain information about K and O types for Klebsiella genome assemblies

 Kaptive reports information about K and O types for Klebsiella genome

 assemblies.

 to you! Very poor assemblies can confound the results, so be sure to

 closely examine any case where the locus sequence in your assembly is

 broken into multiple pieces.

Package: kaptive-data

Architecture: all

Depends: ${misc:Depends}

Enhances: kaptive

Description: reference data for kaptive for Klebsiella genome assemblies

 Kaptive reports information about K and O types for Klebsiella genome

 assemblies.

 .

 Given a novel genome and a database of known loci (K or O), Kaptive will

 help a user to decide whether their sample has a known or novel locus.

 It carries out the following for each input assembly:

 .

  * BLAST for all known locus nucleotide sequences (using blastn) to

    identify the best match ('best' defined as having the highest

    coverage).

  * Extract the region(s) of the assembly which correspond to the BLAST

    hits (i.e. the locus sequence in the assembly) and save it to a

    FASTA file.

  * BLAST for all known locus genes (using tblastn) to identify which

    expected genes (genes in the best matching locus) are present/missing

    and whether any unexpected genes (genes from other loci) are present.

  * Output a summary to a table file.

 .

 In cases where your input assembly closely matches a known locus,

 Kaptive should make that obvious. When your assembly has a novel type,

 that too should be clear. However, Kaptive cannot reliably extract or

 annotate locus sequences for totally novel types - if it indicates a

 novel locus is present then extracting and annotating the sequence is up

 to you! Very poor assemblies can confound the results, so be sure to

 closely examine any case where the locus sequence in your assembly is

 broken into multiple pieces.

 .

 This package contains a reference database.  Its not necessarily used

 to run kaptive since you can use your own database.

Package: kaptive-example

Architecture: all

Depends: ${misc:Depends}

Enhances: kaptive

Description: example data for kaptive for Klebsiella genome assemblies

 Kaptive reports information about K and O types for Klebsiella genome

 assemblies.

 .

 Given a novel genome and a database of known loci (K or O), Kaptive will

 help a user to decide whether their sample has a known or novel locus.

 It carries out the following for each input assembly:

 .

  * BLAST for all known locus nucleotide sequences (using blastn) to

    identify the best match ('best' defined as having the highest

    coverage).

  * Extract the region(s) of the assembly which correspond to the BLAST

    hits (i.e. the locus sequence in the assembly) and save it to a

    FASTA file.

  * BLAST for all known locus genes (using tblastn) to identify which

    expected genes (genes in the best matching locus) are present/missing

    and whether any unexpected genes (genes from other loci) are present.

  * Output a summary to a table file.

 .

 In cases where your input assembly closely matches a known locus,

 Kaptive should make that obvious. When your assembly has a novel type,

 that too should be clear. However, Kaptive cannot reliably extract or

 annotate locus sequences for totally novel types - if it indicates a

 novel locus is present then extracting and annotating the sequence is up

 to you! Very poor assemblies can confound the results, so be sure to

 closely examine any case where the locus sequence in your assembly is

 broken into multiple pieces.

 .

 This package contains some example data.

reference_database	usr/share/kaptive/

sample_data/*	usr/share/doc/kaptive/examples

README*

debian/tests/run-unit-test

debian/README.test