The tests/ folder contain a series of Perl scripts to test the correct functioning of each SeqCode command:
>ls tests/
inputs
outputs
test_buildChIPprofile.pl
test_combineChIPprofiles.pl
test_combineTSSplots.pl
test_findPeaks.pl
test_genomeDistribution.pl
test_matchpeaksgenes.pl
test_matchpeaks.pl
test_produceGENEmaps.pl
test_produceGENEplots.pl
test_producePEAKmaps.pl
test_producePEAKplots.pl
test_produceTSSmaps.pl
test_produceTSSplots.pl
test_recoverChIPlevels.pl
Each test can be executed with the option -v to see the messages of basic information:
./tests/test_produceTSSmaps.pl -v
%%%% Starting SeqCode test for the produceTSSmaps tool by Enrique Blanco (Wed Jun 23 16:50:35 CEST 2021)
%%%% Stage 0. Reading options [DONE]
%%%% Stage 1. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (default plot)
%%%% bin/produceTSSmaps -d tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_1 5000 [DONE]
%%%% Stage 2. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (lower resolution)
%%%% bin/produceTSSmaps -d -w 1000 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_2 5000 [DONE]
%%%% Stage 3. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (one gene, default plot)
%%%% bin/produceTSSmaps -d tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/onegene.txt test_3 5000 [DONE]
%%%% Stage 4. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (another color scheme)
%%%% bin/produceTSSmaps -d -b black -B black -H black -f darkgoldenrod1 -F darkgoldenrod1 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_4 5000 [DONE]
%%%% Stage 5. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (noise reduction plot)
%%%% bin/produceTSSmaps -d -t 0 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_5 5000 [DONE]
%%%% Stage 6. Running the test for H3K4me3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (noise reduction plot 2)
%%%% bin/produceTSSmaps -d -t 2 tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3K4me3_sample.bam tests/inputs/genes_sample.txt test_6 5000 [DONE]
%%%% Stage 7. Running the test for H3 --chr10:5,774,999-6,225,000 (mm9)-- in mESC (default plot)
%%%% bin/produceTSSmaps -d tests/inputs/ChromInfo.txt tests/inputs/refGene_sample.txt tests/inputs/H3_sample.bam tests/inputs/genes_sample.txt test_7 5000 [DONE]
%%%% R CMD BATCH tests/inputs/Rscript_produceTSSmaps.txt [DONE]
%%%% Stage 8. Finishing the test (produceTSSmaps)
%%%% Checking output file 1: tests/outputs/produceTSSmaps/test_1_TSSmap_5000/PlotHEATmap_test_1_5000.pdf [OK]
%%%% Checking output file 2: tests/outputs/produceTSSmaps/test_2_TSSmap_5000/PlotHEATmap_test_2_5000.pdf [OK]
%%%% Checking output file 3: tests/outputs/produceTSSmaps/test_3_TSSmap_5000/PlotHEATmap_test_3_5000.pdf [OK]
%%%% Checking output file 4: tests/outputs/produceTSSmaps/test_4_TSSmap_5000/PlotHEATmap_test_4_5000.pdf [OK]
%%%% Checking output file 5: tests/outputs/produceTSSmaps/test_5_TSSmap_5000/PlotHEATmap_test_5_5000.pdf [OK]
%%%% Checking output file 6: tests/outputs/produceTSSmaps/test_6_TSSmap_5000/PlotHEATmap_test_6_5000.pdf [OK]
%%%% Checking output file 7: tests/outputs/produceTSSmaps/test_7_TSSmap_5000/PlotHEATmap_test_7_5000.pdf [OK]
%%%% Checking output file 7 (2): tests/outputs/produceTSSmaps/produceTSS2maps.pdf [DONE]
%%%% Total running time (hours): 0.001 hours
%%%% Total running time (minutes): 0.1 mins
%%%% Total running time (seconds): 6 secs
%%%% Successful termination: [DONE]
To see the full verbose information of each SeqCode command, please use the option -w.
The input folder contains the original files employed throughout the test routines:
> ls tests/inputs
ChromInfo.txt
genes_sample.txt
H3K27me3_chr10.bed
H3K27me3_mESC_sample.bed
H3K4me3_chr10.bed
H3K4me3_mESC_sample.bed
H3K4me3_sample.bam
H3_sample.bam
onegene.txt
onepeak.bed
refGene_sample.txt
Rscript_combineTSSplots.txt
Rscript_produceGENEmaps.txt
Rscript_produceGENEplots.txt
Rscript_producePEAKmaps.txt
Rscript_producePEAKplots.txt
Rscript_produceTSSmaps.txt
Rscript_produceTSSplots.txt
Rscript_recoverChIPlevels.txt
The output folder will contain the resulting output files generated during the tests by the user (one subfolder
per program). Such results can be afterwards compared with the original resulting plots delivered in the finaloutputs
folder, which is not ever rewritten by the execution of the abovementioned tests:
> ls tests/finaloutputs
buildChIPprofile
combineChIPprofiles
combineTSSplots
findPeaks
genomeDistribution
matchpeaks
matchpeaksgenes
produceGENEmaps
produceGENEplots
producePEAKmaps
producePEAKplots
produceTSSmaps
produceTSSplots
recoverChIPlevels
For each SeqCode command, users can check the resulting output of the tests performed on their computer:
> ls tests/outputs/produceTSSmaps
produceTSS2maps.pdf
test_1_TSSmap_5000
test_2_TSSmap_5000
test_3_TSSmap_5000
test_4_TSSmap_5000
test_5_TSSmap_5000
test_6_TSSmap_5000
test_7_TSSmap_5000
This is the panel of resulting plots for the test of the produceTSSmaps function:
TEST 1 | TEST 2 | TEST 3 | TEST 4 |
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TEST 5 | TEST 6 | TEST 7 | TEST 7B |
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To generate a compact distribution of SeqCode, tests are performed in one locus
of the genome. To have an idea of the whole picture (from which the test is extracted),
this the panel of resulting plots in whole chromosomes for the test
of the produceTSSmaps function (results not included in the tests/ folder):
TEST 1 | TEST 2 | TEST 3 | TEST 4 |
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TEST 5 | TEST 6 | TEST 7 | TEST 7B |
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