[med-svn] [Git][med-team/scrappie][master] 3 commits: Add autopkgtest
Nilesh Patra
gitlab at salsa.debian.org
Sun Oct 25 14:46:58 GMT 2020
Nilesh Patra pushed to branch master at Debian Med / scrappie
Commits:
201d0528 by Nilesh Patra at 2020-10-25T19:59:11+05:30
Add autopkgtest
- - - - -
afa9159a by Nilesh Patra at 2020-10-25T14:39:15+00:00
Add manpages
- - - - -
a973b0d3 by Nilesh Patra at 2020-10-25T20:16:43+05:30
Update changelog
- - - - -
7 changed files:
- debian/changelog
- + debian/createmanpages
- + debian/manpages
- + debian/scrappie.1
- + debian/tests/control
- + debian/tests/run-unit-test
- + debian/tests/simple_test.py
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+scrappie (1.4.2-3) unstable; urgency=medium
+
+ * Team upload.
+ * Add autopkgtest
+ * Add manpage
+
+ -- Nilesh Patra <npatra974 at gmail.com> Sun, 25 Oct 2020 20:01:22 +0530
+
scrappie (1.4.2-2) unstable; urgency=medium
* Team upload.
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,28 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=${PROGNAME}
+help2man --no-info --no-discard-stderr --help-option="help" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/scrappie.1
=====================================
@@ -0,0 +1,32 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.16.
+.TH SCRAPPIE "1" "October 2020" "scrappie 1.4.2" "User Commands"
+.SH NAME
+scrappie \- basecaller for Nanopore sequencer
+.SH DESCRIPTION
+Scrappie is a technology demonstrator for the Oxford Nanopore Technologies
+Limited Research Algorithms group.
+.PP
+Basic usage:
+* scrappie events Base call from event based data.
+* scrappie help Print general help or help about specific Scrappie command.
+* scrappie licence Print licensing information.
+* scrappie raw Base call directly from raw signal.
+* scrappie version Print version information.
+* scrappie squiggle Create approximate squiggle for sequence
+* scrappie mappy Map signal to approximate squiggle
+* scrappie seqmappy Map signal to sequence via basecall posteriors
+* scrappie event_table Output table of events for read
+.PP
+This project began life as a proof (bet) that a base caller could be written
+in a low level language in under 8 hours. Some of the poor and just plain odd
+design decisions, along with the lack of documentation, are a result of its
+inception. In keeping with ONT's fish naming policy, the project was originally
+called Crappie.
+.PP
+Scrappie's purpose is to demonstrate the next generation of base calling and, as
+such, may change drastically between releases and breaks backwards
+compatibility. Newer versions may drop support of current features or change their
+behaviour.
+.SH AUTHOR
+ This manpage was written by Nilesh Patra for the Debian distribution and
+ can be used for any other usage of the program.
=====================================
debian/tests/control
=====================================
@@ -0,0 +1,2 @@
+Tests: run-unit-test
+Depends: @, python3
=====================================
debian/tests/run-unit-test
=====================================
@@ -0,0 +1,37 @@
+#!/bin/bash
+set -e
+
+pkg="scrappie"
+CUR_DIR=`pwd`
+
+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 ${CUR_DIR}/reads $AUTOPKGTEST_TMP
+cp -a ${CUR_DIR}/misc $AUTOPKGTEST_TMP
+
+cd $AUTOPKGTEST_TMP
+gunzip -r *
+
+echo "Test functionality"
+
+echo "Test 1"
+scrappie raw -f sam reads --min_prob=0.1 --format=FASTA --output=test1.fa
+[ -s test1.fa ]
+head -n 1 test1.fa
+echo "PASS"
+
+echo "Test 2"
+scrappie events reads > test2.fa
+head -n 1 test2.fa
+[ -s test2.fa ]
+echo "PASS"
+
+echo "Test 3"
+scrappie raw reads | tee test2.fa | grep '^>' | cut -d ' ' -f 2- | python3 misc/json_to_tsv.py > test3.tsv
+[ -s test3.tsv ]
+cat test3.tsv
+echo "PASS"
+
=====================================
debian/tests/simple_test.py
=====================================
@@ -0,0 +1,16 @@
+from dnapilib.apred import adapter_prediction
+from dnapilib.apred import iterative_adapter_prediction
+
+def test_functional():
+ iterative_result = iterative_adapter_prediction("good.fq", [1.2, 1.3, 1.4], [9, 11], 50000)
+ single_result = adapter_prediction("good.fq", 1.4, 9, 50000)
+
+
+ assert(iterative_result[0][0] == 'TGGAATTCTCGG')
+ assert(single_result[0][0] == 'TGGAATTCTCGGGTGCCAAGGAACTCC')
+
+ iterative_result = iterative_adapter_prediction("processed.fq", [1.2, 1.3, 1.4], [9, 11], 50000)
+ single_result = adapter_prediction("processed.fq", 1.4, 9, 50000)
+
+ assert([x[0] for x in iterative_result] == ['TCTGCCCAGTGCTCTG', 'TAATACTGCCTG', 'TGGCAGTGTCTT'])
+ assert([x[0] for x in single_result] == ['TAATACTGCCTGGTAATGATG', 'TGGCAGTGTCTTAGCTGGTTG', 'CTGCCCAGTGCTCTGAA'])
View it on GitLab: https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a
--
View it on GitLab: https://salsa.debian.org/med-team/scrappie/-/compare/ed80ed3e2ac44a1d5311c8e2c3e556b1214a8a00...a973b0d3f3f93bd5df3b3a9898c1de58fa395d1a
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