Couldn't follow the tutorial

[YonkoBigMom]

Hi

I tried to follow your quickstart at https://github.com/KarchinLab/HotMAPS/wiki/Quick-start

I did download 1E96.pdb and 1E96.pdb1 to a local folder, and edited the config file.

Then run
make annotateStructures

python scripts/add_path_info.py -p data/pdb_info.txt -o data/pdb_info.path.txt
There are 119297 missing pdb files
There are 19368 missing non-bioassembly pdb file
NOTE: Several dozen missing PDBs are expected because the PDB database is constantly changing
python scripts/chain_description.py -i data/pdb_info.path.txt -o data/fully_described_pdb_info.txt
python scripts/divide_pdb_info.py
-f data/fully_described_pdb_info.txt
-m data/mutations.txt
--split-dir data/split_pdbs/
119297

make runNormalHotspot OUTPUT_DIR=output/1e96_output (-->show a lot of output but "successful")

make multipleTestCorrect OUTPUT_DIR=output/1e96_output MUPIT_ANNOTATION_DIR=1e96_example/mupit_annotations
python multiple_testing_correction.py
-i output/1e96_output/output_merged.txt
-f min
-m 1e96_example/mupit_annotations
-q .01
-o output/1e96_output/mtc_output_min_.01.txt
-s output/1e96_output/significance_level_.01.txt
skipping HNSC

make findHotregionStruct OUTPUT_DIR=output/1e96_output MUPIT_ANNOTATION_DIR=1e96_example/mupit_annotations

python find_hotspot_regions_struct.py
-i output/1e96_output/output_merged.txt
-a 1e96_example/mupit_annotations
-p data/fully_described_pdb_info.txt
-r 10.0
-o output/1e96_output/hotspot_regions_structure_.01.txt
-s output/1e96_output/significance_level_.01.txt
--log=stdout
Number of non-float pvals = 0
Number of lines with missing info = 0
Finished Successfully!!!

There is no detected hotspot in the output file.

Do you know what might have happened?

Thanks

[ctokheim]

Can you post whats in output/1e96_output/mtc_output_min_.01.txt and output/1e96_output/significance_level_.01.txt?

[NatureGeorge]

This error may have been caused by a failed read of the PDB file, especially an error PDB file name.
Here's what happens when you run the code (scripts/add_path_info.py):
... putative_path2 = os.path.join(pdb_dir, '{0}.pdb.gz'.format(struct_id)) ... pdb_path = os.path.abspath(os.path.join(biounit_dir, '{0}.pdb{1}.gz'.format(struct_id, tmp_bionum))) ...
Noted that the variable struct_id stands for the lowercase pdb_id.
Thus, if the PDB files stored in your local folder with uppercase pdb_id in file name, it wouldn't work.