'run_tests.sh' broken with new(?) default output name from 'methylartist segmeth'

[SBurnard]

Minor recommended change for 'run_tests.sh'.

I'm using the newest methylartist release 1.5.2, and just cloned this 'methylartist-test' github.

1.)
In this release of methylartist (not sure about previous), the default output from 'methylartist segmeth -d MCF7.example.data.txt -i MCF7.example.segments.bed -p 8' now seems to include the cananonical and base thresholds so the output is: MCF7.example.segments.MCF7.example.data.mt0.8.ct0.8.segmeth.tsv

segmeth...

2025-07-22 11:33:40,610 starting methylartist with command: /apps/methylartist/1.5.2-python3.10/bin/methylartist segmeth -d MCF7.example.data.txt -i MCF7.example.segments.bed -p 8

2025-07-22 11:33:40,639 using mods: m
2025-07-22 11:33:40,639 methylated base threshold: 0.8
2025-07-22 11:33:40,639 canonical base threshold: 0.8
2025-07-22 11:33:40,641 MCF7.example.segments.bed has 2000 intervals
2025-07-22 11:33:40,676 segmeth output filename: MCF7.example.segments.MCF7.example.data.mt0.8.ct0.8.segmeth.tsv
2025-07-22 11:33:40,719 parse intervals from data/MCF7_ATCC.sample.haplotag.bam phase None
100%|██████████| 2000/2000 [00:00<00:00, 27070.24it/s]
2025-07-22 11:33:40,804 parse intervals from data/MCF7_ECACC.sample.haplotag.bam phase None
100%|██████████| 2000/2000 [00:00<00:00, 81370.91it/s]
2025-07-22 11:33:40,829 building results table
100%|██████████| 4000/4000 [00:46<00:00, 85.91it/s]

real 0m48.947s
user 3m45.647s
sys 0m17.175s

Therefore, these lines

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

Needs to be
echo -e "\nsegplot...\n"
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.mt0.8.ct0.8.segmeth.tsv -c LOW,MED1,MED2,HIGH -v --palette magma
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.mt0.8.ct0.8.segmeth.tsvv -c LOW,MED1,MED2,HIGH -v --palette magma -a
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.mt0.8.ct0.8.segmeth.tsv -c LOW,MED1,MED2,HIGH -g --palette magma
time methylartist segplot -s MCF7.example.segments.MCF7.example.data.mt0.8.ct0.8.segmeth.tsv -c LOW,MED1,MED2,HIGH -g --palette magma -a

2.)
Line 50 seems to refer to a personal miniconda library (also on the github rmd)

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.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 --show_transcripts --smoothed_csv test.csv --exonheight 0.6 --panelratios 2,5,1,3,3

This worked after I change it back to:

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 --show_transcripts --smoothed_csv test.csv --exonheight 0.6 --panelratios 2,5,1,3,3

3.)
Lines 79-81

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

in ./data 'data/NA12878.EMSEQ.GAPDH.db' is already provided so it hangs/exit after that line (line 80) as it seems to infer it as an error.

'sub_data.txt' then needs to point to the files in subdir ./data/

cat sub_test.data.txt
./data/NA12878.EMSEQ.GAPDH.bam ./data/NA12878.EMSEQ.GAPDH.db

After I made these changes I was able to replicate similar plots to what I could see on the test github.

Lastly, thanks for developing this package. Looking forward to testing and using it with my own data!

[adamewing]

Thanks, will do!