Pranav Ballaney pushed to branch master at Debian Med / fitgcp
Commits: bef30559 by Pranav Ballaney at 2020-05-11T21:24:27+05:30 Add examples - - - - - db3098de by Pranav Ballaney at 2020-05-11T21:25:26+05:30 Add autopkgtests - - - - - 25451d29 by Pranav Ballaney at 2020-05-11T21:57:11+05:30 Some changes that 2to3 probably missed - - - - - 6c6449c5 by Pranav Ballaney at 2020-05-11T23:23:45+05:30 Install sources and docs - - - - - 3b470dc3 by Pranav Ballaney at 2020-05-12T02:31:23+05:30 Add more autopkgtests - - - - - a1b3c6db by Pranav Ballaney at 2020-05-12T02:32:57+05:30 Update changelog - - - - - 10 changed files: - + debian/README.test - debian/changelog - debian/docs - + debian/examples - + debian/patches/2to3_additions.patch - debian/patches/series - + debian/tests/README.test_data - + debian/tests/control - + debian/tests/data/NC_004830.2.sam - + debian/tests/run-unit-test Changes: ===================================== debian/README.test ===================================== @@ -0,0 +1,8 @@ +Notes on how this package can be tested. +──────────────────────────────────────── + +This package can be tested by running the provided test: + + sh run-unit-test + +in order to confirm its integrity. ===================================== debian/changelog ===================================== @@ -1,3 +1,20 @@ +fitgcp (0.0.20150429-4) UNRELEASED; urgency=medium + + [ Steffen Möller ] + * Could not find ref to conda + + [ Steffen Moeller ] + * d/u/metadata: yamllint + + [ Pranav Ballaney ] + * Add examples + * Add autopkgtests + * Some changes that 2to3 probably missed + * Install sources and docs + * Add more autopkgtests + + -- Pranav Ballaney <[email protected]> Tue, 12 May 2020 02:32:07 +0530 + fitgcp (0.0.20150429-3) unstable; urgency=medium * Use 2to3 to port to Python3 ===================================== debian/docs ===================================== @@ -1 +1,4 @@ README* +debian/README.test +debian/tests/run-unit-test +debian/tests/README.test_data \ No newline at end of file ===================================== debian/examples ===================================== @@ -0,0 +1 @@ +debian/tests/data/* \ No newline at end of file ===================================== debian/patches/2to3_additions.patch ===================================== @@ -0,0 +1,56 @@ +Description: Some changes that 2to3 probably missed +Author: Pranav Ballaney <[email protected]> +Last-Update: Tue, 11 May 2020 21:53:00 +0530 + +--- a/fitGCP.py ++++ b/fitGCP.py +@@ -128,7 +128,7 @@ class NBinom(Distribution): + return stats.nbinom.pmf(x,self._p1,self._p2) + + def estimate_par(self, data, weights=None): +- if weights == None: ++ if weights is None: + weights = data*0. + 1. + norm = np.sum(weights) + mean = np.sum(data*weights)/(norm + 10**(-25)) +@@ -338,7 +338,7 @@ class DataSet: + + def read_from_pickle(self,filename): + """ read a genome coverage profile from a pickle file. """ +- data = pickle.load(open(filename,'r')) ++ data = pickle.load(open(filename,'rb')) + + self.cov = np.array(data[0],dtype=np.int) + self.count = np.array(data[1],dtype=np.int) +@@ -363,7 +363,7 @@ class DataSet: + if not read.is_unmapped: + r_start = start_pos[read.tid] + read.pos # start position + r_end = start_pos[read.tid] + read.pos + read.qlen # end +- cov[r_start:r_end] += 1 ++ cov[int(r_start):int(r_end)] += 1 + num_reads += 1 + read_length += r_end-r_start + self.fname = filename +@@ -376,7 +376,7 @@ class DataSet: + def write_to_pickle(self, filename): + """ store dataset in a pickle file. """ + return pickle.dump([self.cov, self.count, self.rlen, self.rds, +- self.glen, self.fname], open(filename,'w')) ++ self.glen, self.fname], open(filename,'wb')) + + + +@@ -446,11 +446,11 @@ def iterative_fitting(data_set, mixture_ + + # maximum CDF difference + xs = np.arange(np.max(data_set.cov)+1) +- ref_pdf = np.zeros((np.max(data_set.cov)+1,)) ++ ref_pdf = np.zeros((int(np.max(data_set.cov))+1,)) + for dist in mixture_model: + ref_pdf += dist.pmf(xs)*dist.alpha + +- obs_pdf = np.zeros((np.max(data_set.cov)+1,)) ++ obs_pdf = np.zeros((int(np.max(data_set.cov))+1,)) + obs_pdf[data_set.cov.astype(np.int)] = data_set.count/float(np.sum(data_set.count)) + max_cdf_diff = np.max(np.abs(np.cumsum(ref_pdf)-np.cumsum(obs_pdf))) + ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ 2to3.patch +2to3_additions.patch ===================================== debian/tests/README.test_data ===================================== @@ -0,0 +1,12 @@ +File: NC_004830.2.sam +This file was obtained using mason and bowtie as described +in the supplementary data for the following publication: + http://dx.doi.org/10.1093/bioinformatics/btt147 + +A fasta file was downloaded from: + https://www.ncbi.nlm.nih.gov/nuccore/NC_004830 +and the following operations were performed on it: + mason illumina -N 100000 -n 75 -sq -o NC_004830.2.fastq NC_004830.2.fa + bowtie -p 20 -q -k 1 -S NC_004830.2.fa NC_004830.2.fastq NC_004830.2.sam + +-- Pranav Ballaney <[email protected]> \ No newline at end of file ===================================== debian/tests/control ===================================== @@ -0,0 +1,3 @@ +Tests: run-unit-test +Depends: @, python3-matplotlib +Restrictions: allow-stderr ===================================== debian/tests/data/NC_004830.2.sam ===================================== The diff for this file was not included because it is too large. ===================================== debian/tests/run-unit-test ===================================== @@ -0,0 +1,34 @@ +#!/bin/bash +set -e + +pkg=fitgcp + +export LC_ALL=C.UTF-8 +if [ "${AUTOPKGTEST_TMP}" = "" ] ; then + AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) + # Double quote below to expand the temporary directory variable now versus + # later is on purpose. + # shellcheck disable=SC2064 + 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 * + +echo -e "\e[93m\e[1mTest 1: Verbose with a plot\e[0m" +fitgcp -l -p NC_004830.2.sam +test -f "NC_004830.2_zn.png" +test -f "NC_004830.2_zn_log.txt" +test -f "NC_004830.2_zn_results.txt" +rm NC_004830.2_zn.png NC_004830.2_zn_log.txt NC_004830.2_zn_results.txt +echo -e "\e[92m\e[1mPassed\e[0m" +echo + +echo -e "\e[93m\e[1mTest 2: Only ten iterations\e[0m" +fitgcp -i 10 NC_004830.2.sam +test -f NC_004830.2_zn_results.txt +echo -e "\e[92m\e[1mPassed\e[0m" +echo View it on GitLab: https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064 -- View it on GitLab: https://salsa.debian.org/med-team/fitgcp/-/compare/a6997381dbbf1de8f0b897bec247a1440162994d...a1b3c6db184655b706e1df70e2013d0b6b48b064 You're receiving this email because of your account on salsa.debian.org.
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