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run_tests.sh
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run_tests.sh
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#!/bin/sh
if [ ! -e data/Homo_sapiens_assembly38.fasta.gz ] ; then
echo "Please download the GATK HG38 reference. For example:"
echo "wget -P data https://media.githubusercontent.com/media/broadinstitute/gatk/master/src/test/resources/large/Homo_sapiens_assembly38.fasta.gz"
exit 1
fi
if [ ! -e data/Homo_sapiens_assembly38.fasta.gz.fai ] ; then
echo "indexing reference..."
samtools faidx data/Homo_sapiens_assembly38.fasta.gz
fi
set -e # exit run_tests.sh if anything fails
echo -e "\ndistribution plot...\n"
time methylartist scoredist -n 300000 -d data/MCF7_ATCC.sample.megalodon.db,data/MCF7_ECACC.sample.megalodon.db -m m
echo -e "\nsegmeth...\n"
time methylartist segmeth -d MCF7.example.data.txt -i MCF7.example.segments.bed -p 8
echo -e "\nsegmeth from modbam...\n"
time methylartist segmeth -b data/MCF7_ATCC.modification_tags.bam -i MCF7.example.segments.bed -p 8 --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG
echo -e "\nsegplot...\n"
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -v --palette magma
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -v --palette magma -a
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -g --palette magma
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.segmeth.tsv -c LOW,MED1,MED2,HIGH -g --palette magma -a
echo -e "\nwgmeth...\n"
time methylartist wgmeth -b data/MCF7_ATCC.modification_tags.bam -f data/Homo_sapiens_assembly38.fasta.gz.fai -c chr19 --mod m --motif CG --ref data/Homo_sapiens_assembly38.fasta.gz -s 10000 -p 8 --dss
echo -e "\nwgmeth phased..."
time methylartist wgmeth -b data/MCF7_ATCC.sample.haplotag.bam -d data/MCF7_ATCC.sample.megalodon.db -f data/Homo_sapiens_assembly38.fasta.gz.fai -c chr19 --mod m -s 10000 -p 8 --dss --phased
echo -e "\n~15kbp locus from db...\n"
time methylartist locus -d MCF7.example.data.txt -i chr19:56172382-56187168 --samplepalette crest -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes
echo -e "\n~15kbp locus from db, limit smoothed axis...\n"
time methylartist locus -d MCF7.example.data.txt -i chr19:56172382-56187168 --samplepalette crest -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ymin 0.2 --ymax 0.8
echo -e "\ntest --primary_only option\n"
time methylartist locus -d MCF7.example.data.txt -i chr19:56172382-56187168 --samplepalette crest -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --primary_only
echo -e "\n~15kbp locus from mod bam...\n"
time methylartist locus -b data/MCF7_ATCC.modification_tags.bam,data/MCF7_ECACC.modification_tags.bam -i chr19:56172382-56187168 --samplepalette cubehelix -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG
echo -e "\nas above, with --show_transcripts, --smoothed_csv, and --exonheight ...\n"
methylartist with command: /home/taewing/miniconda3/bin/methylartist locus -b data/MCF7_ATCC.modification_tags.bam,data/MCF7_ECACC.mo
dification_tags.bam -i chr19:56172382-56187168 --samplepalette cubehelix -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembl
y38.fasta.gz --motif CG --show_transcripts --smoothed_csv test.csv --exonheight 0.6 --panelratios 2,5,1,3,3
echo -e "\n~15kbp locus from mod bam custom colour...\n"
time methylartist locus -b data/MCF7_ATCC.modification_tags.bam:#32a852,data/MCF7_ECACC.modification_tags.bam:#9a32a8 -i chr19:56172382-56187168 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG
echo -e "\n~15kbp locus from mod bam custom colour from file...\n"
time methylartist locus -b test_colours.txt -i chr19:56172382-56187168 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG
echo -e "\n~15kbp locus from mod bam, primary_only...\n"
time methylartist locus -b data/MCF7_ATCC.modification_tags.bam,data/MCF7_ECACC.modification_tags.bam -i chr19:56172382-56187168 --samplepalette cubehelix -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG --primary_only
echo -e "\nuse MM/ML instead of Mm/Ml...\n"
methylartist locus -b data/MCF7_ATCC.modification_tags.caps_MM_ML.bam -i chr19:56172382-56187168 --samplepalette cubehelix -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --ref data/Homo_sapiens_assembly38.fasta.gz --motif CG
echo -e "\n~30 kbp phased locus...\n"
time methylartist locus -d MCF7.example.data.txt -i chr19:56810076-56870725 -l 56835376-56840476 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genes PEG3 --samplepalette viridis --phased --maskcutoff 0
echo -e "\n~2 Mbp region...\n"
time methylartist region -d MCF7.example.data.txt -i chr19:55810082-57840726 -n CG -r data/Homo_sapiens_assembly38.fasta.gz -p 8 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genepalette viridis --samplepalette magma
echo -e "\n~2 Mbp region from modbam custom colour...\n"
time methylartist region -b data/MCF7_ATCC.modification_tags.bam:#32a852,data/MCF7_ECACC.modification_tags.bam:#9a32a8 -i chr19:55810082-57840726 -n CG -r data/Homo_sapiens_assembly38.fasta.gz -p 8 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genepalette viridis
echo -e "\n~2 Mbp region from modbam custom colour from file...\n"
time methylartist region -b test_colours.txt -i chr19:55810082-57840726 -n CG -r data/Homo_sapiens_assembly38.fasta.gz -p 8 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genepalette viridis
echo -e "\n~2 Mbp region, limit smoothed y-axis...\n"
time methylartist region -d MCF7.example.data.txt -i chr19:55810082-57840726 -n CG -r data/Homo_sapiens_assembly38.fasta.gz -p 8 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genepalette viridis --samplepalette magma --ymin 0.2 --ymax 0.8
echo -e "\nC/U substitution based methylation data...\n"
methylartist db-sub -b data/NA12878.EMSEQ.GAPDH.bam -d data/NA12878.EMSEQ.GAPDH.db
methylartist locus -d sub_test.data.txt -i chr12:6,517,169-6,555,718 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --labelgenes --panelratios 5,5,1,3,3
echo -e "\nCRAM test...\n"
time methylartist region -b data/MCF7_ATCC.modification_tags.cram -i chr19:55810082-57840726 -n CG -r data/Homo_sapiens_assembly38.fasta.gz -p 8 -g data/Homo_sapiens.GRCh38.97.chr.sorted.gtf.gz --genepalette viridis