Andreas Tille pushed to branch master at Debian Med / kaptive
Commits: 1cd87a9d by Andreas Tille at 2019-09-24T19:38:37Z Add autopkgtest after adding packages with the needed data - - - - - 8 changed files: - + debian/README.test - debian/control - + debian/kaptive-data.install - + debian/kaptive-example.install - + debian/kaptive.docs - + debian/kaptive.install - + debian/tests/control - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,9 @@ +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. ===================================== debian/control ===================================== @@ -14,10 +14,13 @@ Vcs-Git: https://salsa.debian.org/med-team/kaptive.git 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. @@ -45,3 +48,72 @@ Description: obtain information about K and O types for Klebsiella genome assemb 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. ===================================== debian/kaptive-data.install ===================================== @@ -0,0 +1 @@ +reference_database usr/share/kaptive/ ===================================== debian/kaptive-example.install ===================================== @@ -0,0 +1 @@ +sample_data/* usr/share/doc/kaptive/examples ===================================== debian/kaptive.docs ===================================== @@ -0,0 +1,3 @@ +README* +debian/tests/run-unit-test +debian/README.test ===================================== debian/kaptive.install ===================================== @@ -0,0 +1 @@ +kaptive.py usr/bin ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @ +Restrictions: allow-stderr ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,17 @@ +#!/bin/bash +set -e + +pkg=kaptive + +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM +fi + +cp -a /usr/share/doc/${pkg}/examples/* "${AUTOPKGTEST_TMP}" + +cd "${AUTOPKGTEST_TMP}" + +gunzip -r * + +kaptive.py -a exact_match.fasta -k /usr/share/${pkg}/reference_database/Klebsiella_k_locus_primary_reference.gbk -o output/test View it on GitLab: https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce -- View it on GitLab: https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce You're receiving this email because of your account on salsa.debian.org.
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