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New integration tests.

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dbolotin committed Dec 18, 2018
1 parent 211e722 commit e7290f06e185177c649351aeb40218679f01cad7
Showing with 23 additions and 13 deletions.
  1. +1 −1 .travis.yml
  2. +22 −12 itests.sh
@@ -14,7 +14,7 @@ before_install:
- mv .cache ./repseqio/.cache
- cd repseqio && mvn clean install -DskipTests -B && cd ..
- mv ./repseqio/.cache .cache

- ./ensure-test-data.sh

script:
- mvn test -B && ./itests.sh test
@@ -75,6 +75,8 @@ mkdir ${dir}/test_target
cp ${dir}/src/test/resources/sequences/*.fastq ${dir}/test_target/

cd ${dir}/test_target/
ln -s ../src/test/resources/sequences/big/CD4M1_test_R1.fastq.gz ${dir}/test_target/CD4M1_test_R1.fastq.gz
ln -s ../src/test/resources/sequences/big/CD4M1_test_R2.fastq.gz ${dir}/test_target/CD4M1_test_R2.fastq.gz

PATH=${dir}:${PATH}

@@ -86,7 +88,7 @@ function go_assemble {
mixcr assemble -r $1.clns.report $1.vdjca $1.clns
for c in TCR IG TRB TRA TRG TRD IGH IGL IGK ALL
do
mixcr exportClones -c ${c} -s $1.clns $1.clns.${c}.txt
mixcr exportClones -c ${c} $1.clns $1.clns.${c}.txt
done
}

@@ -103,15 +105,23 @@ fi
# UseCase 1

if [[ $run_tests == true ]]; then
echo "Running test case 1"
mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP -OsaveOriginalReads=true test_R1.fastq test_R2.fastq case1.vdjca
mixcr assemble case1.vdjca case1.clns

mixcr exportAlignments -nFeatureImputed VDJRegion -descrsR1 -descrsR2 case1.vdjca case1.alignments.txt

echo "Running test case 2"
mixcr analyze shotgun -f --species hs --contig-assembly --impute-germline-on-export --starting-material rna test_R1.fastq test_R2.fastq case2

echo "Running test case 3"
mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters no-adapters test_R1.fastq test_R2.fastq case3
# echo "Running test case 1"
# mixcr align -s hs -OvParameters.geneFeatureToAlign=VGeneWithP -OsaveOriginalReads=true test_R1.fastq test_R2.fastq case1.vdjca
# mixcr assemble case1.vdjca case1.clns
#
# mixcr exportAlignments -nFeatureImputed VDJRegion -descrsR1 -descrsR2 case1.vdjca case1.alignments.txt
#
# echo "Running test case 2"
# mixcr analyze shotgun -f --species hs --contig-assembly --impute-germline-on-export --starting-material rna test_R1.fastq test_R2.fastq case2
#
# echo "Running test case 3"
# mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters no-adapters test_R1.fastq test_R2.fastq case3

echo "Running test case 4"
mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case4
# Checking skip steps behaviour
mixcr analyze amplicon --receptor-type tra --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case4

echo "Running test case 5"
mixcr analyze amplicon --receptor-type tra --align '-OseparateByC=true' --align '-OseparateByV=true' --align '-OseparateByJ=true' --impute-germline-on-export -s hs --starting-material rna --contig-assembly --5-end v-primers --3-end j-primers --adapters adapters-present CD4M1_test_R1.fastq.gz CD4M1_test_R2.fastq.gz case4
fi

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