[med-svn] [Git][med-team/gasic][master] 6 commits: Remove unnecessary example files

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / gasic


Commits:
a0b828af by Pranav Ballaney at 2020-05-12T17:40:51+05:30
Remove unnecessary example files

- - - - -
de364d47 by Pranav Ballaney at 2020-05-13T01:31:49+05:30
Fix mason_simulator arguments

- - - - -
e611aaf5 by Pranav Ballaney at 2020-05-13T02:38:05+05:30
Add more autopkgtests

- - - - -
c42123d6 by Pranav Ballaney at 2020-05-13T02:39:51+05:30
Remove removed binaries from include-binaries

- - - - -
ac007039 by Pranav Ballaney at 2020-05-13T15:10:46+05:30
Merge branch 'master' of https://salsa.debian.org/med-team/gasic

- - - - -
f2779eb9 by Pranav Ballaney at 2020-05-13T15:18:46+05:30
Update changelog

- - - - -


11 changed files:

- debian/changelog
- debian/patches/use_seqan_mason.patch
- debian/source/include-binaries
- − debian/tests/data/genomes/dwv.fasta-e.gz
- − debian/tests/data/genomes/dwv.fasta.fai.gz
- − debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz
- − debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz
- − debian/tests/data/genomes/vdv1.fasta.fai.gz
- + debian/tests/data/names
- − debian/tests/data/names.gz
- debian/tests/run-unit-test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+gasic (0.0.r19-7) UNRELEASED; urgency=medium
+
+  * Remove unnecessary example files
+  * Fix mason_simulator arguments
+  * Add more autopkgtests
+  * Remove removed binaries from include-binaries
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Wed, 13 May 2020 15:13:02 +0530
+
 gasic (0.0.r19-6) unstable; urgency=medium
 
   * Team upload


=====================================
debian/patches/use_seqan_mason.patch
=====================================
@@ -18,7 +18,7 @@ Description: since there is a name conflict with mason and the Debian package
 +    reportbug gasic
 +to propose enhancements.
 +""" % (out,ref))
-+    command = "/usr/lib/seqan/bin/mason_simulator illumina --illumina-read-length 10000 -o %s %s"%(out,ref)
++    command = "/usr/lib/seqan/bin/mason_simulator --seq-technology illumina -n 10000 --illumina-read-length 72 -o %s -ir %s"%(out,ref)
      print("Executing:",command)
      os.system(command)
      # remove the needless SAM file


=====================================
debian/source/include-binaries
=====================================
@@ -1,11 +1,4 @@
-debian/tests/data/names.gz
-debian/tests/data/genomes/vdv1.fasta.fai.gz
+debian/tests/data/genomes/dwv.fasta.gz
 debian/tests/data/genomes/vdv1.fasta.gz
 debian/tests/data/genomes/vdv1dwv9.fasta.gz
 debian/tests/data/genomes/vdv1dwv5.fasta.gz
-debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz
-debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz
-debian/tests/data/genomes/dwv.fasta-e.gz
-debian/tests/data/genomes/dwv.fasta.fai.gz
-debian/tests/data/genomes/dwv.fasta.gz
-debian/tests/data/reads/SRR059298_subset.fastq.gz


=====================================
debian/tests/data/genomes/dwv.fasta-e.gz deleted
=====================================
Binary files a/debian/tests/data/genomes/dwv.fasta-e.gz and /dev/null differ


=====================================
debian/tests/data/genomes/dwv.fasta.fai.gz deleted
=====================================
Binary files a/debian/tests/data/genomes/dwv.fasta.fai.gz and /dev/null differ


=====================================
debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz deleted
=====================================
Binary files a/debian/tests/data/genomes/vdv-1-dwv-5.fasta.fai.gz and /dev/null differ


=====================================
debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz deleted
=====================================
Binary files a/debian/tests/data/genomes/vdv-1-dwv-9.fasta.fai.gz and /dev/null differ


=====================================
debian/tests/data/genomes/vdv1.fasta.fai.gz deleted
=====================================
Binary files a/debian/tests/data/genomes/vdv1.fasta.fai.gz and /dev/null differ


=====================================
debian/tests/data/names
=====================================
@@ -0,0 +1,4 @@
+dwv
+vdv1
+vdv1dwv5
+vdv1dwv9


=====================================
debian/tests/data/names.gz deleted
=====================================
Binary files a/debian/tests/data/names.gz and /dev/null differ


=====================================
debian/tests/run-unit-test
=====================================
@@ -15,13 +15,33 @@ cd "${AUTOPKGTEST_TMP}"
 
 gunzip -r *
 
+echo -e "\e[93m\e[1mTest 0: Create Genome Indices\e[0m"
 cd genomes
+bwa index dwv.fasta
+bwa index vdv1.fasta            
+bwa index vdv1dwv9.fasta
+bwa index vdv1dwv5.fasta
+cd ..
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
 
-bowtie-build dwv.fasta dwv.fasta
-bowtie-build vdv1.fasta vdv1.fasta             
-bowtie-build vdv1dwv9.fasta vdv1dwv9.fasta
-bowtie-build vdv1dwv5.fasta vdv1dwv5.fasta
+echo -e "\e[93m\e[1mTest 1: run_mappers\e[0m"
+run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bwa
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
 
-cd ..
+echo -e "\e[93m\e[1mTest 2: create_matrix\e[0m"
+create_matrix names -s mason_illumina -m bwa -r genomes/%s.fasta -i genomes/%s.fasta -t ./SAM
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 3: correct_abundances\e[0m"
+correct_abundances names -s ./SAM/mapped_%s.sam -m similarity_matrix.npy -o results.txt
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
+
+echo -e "\e[93m\e[1mTest 4: quality_check\e[0m"
+quality_check ./SAM/mapped_vdv1.sam
+echo -e "\e[92m\e[1mPassed\e[0m"
+echo
 
-run_mappers names reads/SRR059298_subset.fastq -i ./genomes/%s.fasta -o ./SAM/mapped_%s.sam -m bowtie



View it on GitLab: https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9

-- 
View it on GitLab: https://salsa.debian.org/med-team/gasic/-/compare/0c51555761bd86d7ad4110ae12820383c0707064...f2779eb9678c3d88f643a61755f330dcd35aefd9
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