[med-svn] [Git][med-team/kaptive][master] Add autopkgtest after adding packages with the needed data

Andreas Tille gitlab at salsa.debian.org
Tue Sep 24 20:39:15 BST 2019 


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

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View it on GitLab: https://salsa.debian.org/med-team/kaptive/commit/1cd87a9d8420842ad0ef6487b751ebd246aff9ce
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