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Add PSSM computation #193

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@diegozea
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@diegozea diegozea commented Dec 18, 2025

Summary

  • add a PSSMResult container and pssm API to compute log-odds PSSMs from MSAs
  • validate background distributions, gap handling, and zero-handling policies while using MIToS probability estimators
  • cover the new functionality with targeted tests for shapes, correctness, zero policies, and all-gap columns

Testing

  • julia --project -e 'using Test; using MIToS; using MIToS.MSA; using MIToS.Information; include("test/Information/PSSM.jl")'

Codex Task

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codecov bot commented Dec 18, 2025 •
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Codecov Report

❌ Patch coverage is 88.26291% with 25 lines in your changes missing coverage. Please review.
✅ Project coverage is 96.60%. Comparing base (2cdce44) to head (f2ddaac).

Files with missing lines Patch % Lines
src/Information/PSSM.jl 88.20% 25 Missing ⚠️
Additional details and impacted files 
@@            Coverage Diff             @@
##           master     #193      +/-   ##
==========================================
- Coverage   96.97%   96.60%   -0.37%     
==========================================
  Files          64       65       +1     
  Lines        4861     5073     +212     
==========================================
+ Hits         4714     4901     +187     
- Misses        147      172      +25

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github-actions bot commented Dec 18, 2025 •
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Benchmark Results (Julia v1)

Time benchmarks
master f2ddaac... master / f2ddaac...
Information/CorrectedMutualInformation/buslje09/msa 0.891 ± 0.0078 s 0.89 ± 0.0085 s 1 ± 0.013
Information/CorrectedMutualInformation/buslje09/msa_large 0.0378 ± 0.0011 s 0.0377 ± 0.0011 s 1 ± 0.041
Information/CorrectedMutualInformation/buslje09/msa_wide 0.805 ± 0.0066 s 0.798 ± 0.0089 s 1.01 ± 0.014
Information/MIp/PF09645 9.94 ± 0.37 ms 9.82 ± 0.34 ms 1.01 ± 0.051
Information/frequencies!/1 0.29 ± 0.039 μs 0.29 ± 0.04 μs 1 ± 0.19
Information/frequencies!/2 1.56 ± 0.06 μs 1.56 ± 0.05 μs 1 ± 0.05
Information/highlevel/BLMI 0.0629 ± 0.0012 s 0.0644 ± 0.00099 s 0.976 ± 0.024
Information/highlevel/buslje09 12.3 ± 0.27 ms 11.9 ± 0.29 ms 1.03 ± 0.034
Information/shannon_entropy/PF09645 23.1 ± 1.5 μs 22 ± 2 μs 1.05 ± 0.12
MSA/Annotations/filtercolumns/boolean mask 12.6 ± 1.1 μs 12.5 ± 0.82 μs 1 ± 0.11
MSA/Annotations/filtercolumns/index array 4.73 ± 0.98 μs 5.05 ± 0.49 μs 0.936 ± 0.21
MSA/Base.vcat/annotated 7.58 ± 3.4 μs 8.33 ± 1.3 μs 0.911 ± 0.43
MSA/Base.vcat/unannotated 3.04 ± 0.84 μs 2.88 ± 0.69 μs 1.06 ± 0.39
MSA/Residue conversions/char2res 0.506 ± 0.078 ms 0.504 ± 0.92 ms 1 ± 1.8
MSA/Residue conversions/int2res 0.424 ± 0.1 ms 0.413 ± 0.13 ms 1.02 ± 0.41
MSA/Residue conversions/res2char 0.304 ± 0.032 ms 0.298 ± 0.044 ms 1.02 ± 0.18
MSA/Residue conversions/res2int 0.492 ± 0.19 ms 0.461 ± 0.22 ms 1.07 ± 0.65
MSA/hobohmI/pid20 1.19 ± 0.61 μs 1.27 ± 0.55 μs 0.937 ± 0.63
MSA/hobohmI/pid62 1.14 ± 0.72 μs 1.32 ± 0.51 μs 0.864 ± 0.64
MSA/hobohmI/pid80 1.06 ± 0.62 μs 1.43 ± 0.57 μs 0.738 ± 0.52
MSA/hobohmI/pid99 1.52 ± 0.57 μs 1.49 ± 0.65 μs 1.02 ± 0.59
MSA/identity/matrix_Float64 22 ± 4.4 μs 22.3 ± 2 μs 0.983 ± 0.22
MSA/identity/mean 0.127 ± 0.013 ms 0.14 ± 0.012 ms 0.907 ± 0.12
MSA/read/Clustal 0.0365 ± 0.0069 ms 0.0344 ± 0.0066 ms 1.06 ± 0.29
MSA/read/Clustal_num 0.0362 ± 0.0066 ms 0.036 ± 0.0068 ms 1.01 ± 0.26
MSA/read/FASTA 0.0577 ± 0.0099 ms 0.0588 ± 0.0096 ms 0.98 ± 0.23
MSA/read/FASTA.gz 0.057 ± 0.0072 ms 0.0573 ± 0.0075 ms 0.995 ± 0.18
MSA/read/FASTA.gz_annotated 0.0664 ± 0.0076 ms 0.0656 ± 0.007 ms 1.01 ± 0.16
MSA/read/FASTA_deletefullgaps 7.64 ± 2.8 ms 7.27 ± 3.2 ms 1.05 ± 0.6
MSA/read/FASTA_deletefullgaps_mapping 0.107 ± 0.016 s 0.105 ± 0.012 s 1.01 ± 0.19
MSA/read/Stockholm 0.0431 ± 0.009 ms 0.0425 ± 0.0091 ms 1.01 ± 0.3
MSA/read/Stockholm.gz 0.0721 ± 0.011 ms 0.0712 ± 0.011 ms 1.01 ± 0.22
MSA/read/Stockholm_annotated 0.0567 ± 0.012 ms 0.0585 ± 0.011 ms 0.969 ± 0.28
MSA/read/Stockholm_mapping 0.215 ± 0.047 ms 0.216 ± 0.044 ms 0.996 ± 0.3
MSA/read/Stockholm_mapping_coords 0.137 ± 0.034 ms 0.136 ± 0.033 ms 1.01 ± 0.35
MSA/write/FASTA 0.248 ± 0.045 ms 0.234 ± 0.043 ms 1.06 ± 0.27
PDB/_generate_interaction_keys/defaults 0.0528 ± 0.015 ms 0.0532 ± 0.017 ms 0.992 ± 0.42
PDB/_get_matched_Cαs/hemoglobin 0.0455 ± 0.011 ms 0.0505 ± 0.0088 ms 0.901 ± 0.27
PDB/_pdbresidues_to_mmcifdict/2vqc 0.668 ± 0.071 ms 0.709 ± 0.081 ms 0.943 ± 0.15
PDB/contact/1CBN_20_30_CB 0.401 ± 0.21 μs 0.451 ± 0.17 μs 0.889 ± 0.57
PDB/contact/1CBN_20_30_heavy 0.511 ± 0.19 μs 0.531 ± 0.19 μs 0.962 ± 0.5
PDB/count_alanine/1CBN 0.341 ± 0.069 μs 0.341 ± 0.01 μs 1 ± 0.2
PDB/distance/1CBN_20_30 0.14 ± 0.01 μs 0.14 ± 0.02 μs 1 ± 0.16
PDB/read/MMCIFFile 3.25 ± 0.26 ms 3.27 ± 0.23 ms 0.995 ± 0.11
PDB/squared_distance/1CBN_20_30_CB 0.391 ± 0.26 μs 0.511 ± 0.17 μs 0.765 ± 0.57
PDB/squared_distance/1CBN_20_30_heavy 0.381 ± 0.18 μs 0.521 ± 0.21 μs 0.731 ± 0.46
Pfam/accession mapping/acc2seqnames 0.218 ± 0.02 ms 0.213 ± 0.018 ms 1.02 ± 0.13
SIFTS/ResidueDetails/_get_details 2.94 ± 1.9 μs 2.23 ± 0.7 μs 1.32 ± 0.96
SIFTS/ResidueDetails/_is_missing 2.54 ± 0.97 μs 2.71 ± 1.2 μs 0.934 ± 0.54
SIFTS/SIFTSResidue/18gs 0.12 ± 0.15 μs 0.111 ± 0.15 μs 1.08 ± 2
SIFTS/siftsmapping/2vqc 2.57 ± 0.14 ms 2.51 ± 0.12 ms 1.02 ± 0.076
Utils/get_n_words/ascii 0.141 ± 0.1 μs 0.3 ± 0.18 μs 0.47 ± 0.44
Utils/get_n_words/utf8 0.131 ± 0.12 μs 0.241 ± 0.17 μs 0.544 ± 0.63
Utils/hascoordinates/invalid 0.09 ± 0.01 μs 0.081 ± 0.01 μs 1.11 ± 0.18
Utils/hascoordinates/valid 0.13 ± 0.01 μs 0.131 ± 0.01 μs 0.992 ± 0.11
Utils/list2matrix/upper 0.341 ± 0.044 ms 0.293 ± 0.16 ms 1.17 ± 0.65
Utils/list2matrix/upper_diagonal 0.512 ± 0.13 ms 0.482 ± 0.19 ms 1.06 ± 0.49
Utils/matrix2list/upper 0.145 ± 0.081 ms 0.14 ± 0.066 ms 1.04 ± 0.76
Utils/matrix2list/upper_diagonal 0.162 ± 0.065 ms 0.151 ± 0.071 ms 1.07 ± 0.66
time_to_load 0.953 ± 0.015 s 0.934 ± 0.01 s 1.02 ± 0.019
Memory benchmarks
master f2ddaac... master / f2ddaac...
Information/CorrectedMutualInformation/buslje09/msa 0.766 M allocs: 0.032 GB 0.766 M allocs: 0.032 GB 1
Information/CorrectedMutualInformation/buslje09/msa_large 0.0901 M allocs: 5.03 MB 0.0901 M allocs: 5.03 MB 1
Information/CorrectedMutualInformation/buslje09/msa_wide 0.742 M allocs: 30.3 MB 0.742 M allocs: 30.3 MB 1
Information/MIp/PF09645 20.3 k allocs: 0.819 MB 20.3 k allocs: 0.819 MB 1
Information/frequencies!/1 0 allocs: 0 B 0 allocs: 0 B
Information/frequencies!/2 0 allocs: 0 B 0 allocs: 0 B
Information/highlevel/BLMI 19.9 k allocs: 1.19 MB 19.9 k allocs: 1.19 MB 1
Information/highlevel/buslje09 0.0377 M allocs: 2.3 MB 0.0377 M allocs: 2.3 MB 1
Information/shannon_entropy/PF09645 0.047 k allocs: 12.2 kB 0.047 k allocs: 12.2 kB 1
MSA/Annotations/filtercolumns/boolean mask 18 allocs: 5.22 kB 18 allocs: 5.22 kB 1
MSA/Annotations/filtercolumns/index array 16 allocs: 1.62 kB 16 allocs: 1.62 kB 1
MSA/Base.vcat/annotated 0.143 k allocs: 6.58 kB 0.143 k allocs: 6.58 kB 1
MSA/Base.vcat/unannotated 0.064 k allocs: 2.7 kB 0.064 k allocs: 2.7 kB 1
MSA/Residue conversions/char2res 3 allocs: 4.1 MB 3 allocs: 4.1 MB 1
MSA/Residue conversions/int2res 3 allocs: 4.1 MB 3 allocs: 4.1 MB 1
MSA/Residue conversions/res2char 3 allocs: 2.05 MB 3 allocs: 2.05 MB 1
MSA/Residue conversions/res2int 3 allocs: 4.1 MB 3 allocs: 4.1 MB 1
MSA/hobohmI/pid20 31 allocs: 1.77 kB 31 allocs: 1.77 kB 1
MSA/hobohmI/pid62 31 allocs: 1.77 kB 31 allocs: 1.77 kB 1
MSA/hobohmI/pid80 31 allocs: 1.77 kB 31 allocs: 1.77 kB 1
MSA/hobohmI/pid99 31 allocs: 1.77 kB 31 allocs: 1.77 kB 1
MSA/identity/matrix_Float64 0.249 k allocs: 11.8 kB 0.249 k allocs: 11.8 kB 1
MSA/identity/mean 1.23 k allocs: 0.0517 MB 1.23 k allocs: 0.0517 MB 1
MSA/read/Clustal 0.394 k allocs: 24.3 kB 0.394 k allocs: 24.3 kB 1
MSA/read/Clustal_num 0.394 k allocs: 24.3 kB 0.394 k allocs: 24.3 kB 1
MSA/read/FASTA 0.406 k allocs: 0.044 MB 0.406 k allocs: 0.044 MB 1
MSA/read/FASTA.gz 0.443 k allocs: 0.0752 MB 0.443 k allocs: 0.0752 MB 1
MSA/read/FASTA.gz_annotated 0.533 k allocs: 0.0794 MB 0.533 k allocs: 0.0793 MB 1
MSA/read/FASTA_deletefullgaps 13.6 k allocs: 17.4 MB 13.6 k allocs: 17.4 MB 1
MSA/read/FASTA_deletefullgaps_mapping 1.64 M allocs: 0.0795 GB 1.64 M allocs: 0.0795 GB 1
MSA/read/Stockholm 0.402 k allocs: 0.033 MB 0.402 k allocs: 0.033 MB 1
MSA/read/Stockholm.gz 0.479 k allocs: 0.0754 MB 0.479 k allocs: 0.0754 MB 1
MSA/read/Stockholm_annotated 0.559 k allocs: 0.0413 MB 0.559 k allocs: 0.0413 MB 1
MSA/read/Stockholm_mapping 2.08 k allocs: 0.104 MB 2.08 k allocs: 0.104 MB 1
MSA/read/Stockholm_mapping_coords 1.64 k allocs: 0.0812 MB 1.64 k allocs: 0.0812 MB 1
MSA/write/FASTA 0.303 k allocs: 14.1 kB 0.303 k allocs: 14.1 kB 1
PDB/_generate_interaction_keys/defaults 0.497 k allocs: 0.0581 MB 0.497 k allocs: 0.0581 MB 1
PDB/_get_matched_Cαs/hemoglobin 0.584 k allocs: 0.0438 MB 0.584 k allocs: 0.0438 MB 1
PDB/_pdbresidues_to_mmcifdict/2vqc 8.56 k allocs: 1.12 MB 8.56 k allocs: 1.12 MB 1
PDB/contact/1CBN_20_30_CB 4 allocs: 0.281 kB 4 allocs: 0.281 kB 1
PDB/contact/1CBN_20_30_heavy 4 allocs: 0.281 kB 4 allocs: 0.281 kB 1
PDB/count_alanine/1CBN 0 allocs: 0 B 0 allocs: 0 B
PDB/distance/1CBN_20_30 0 allocs: 0 B 0 allocs: 0 B
PDB/read/MMCIFFile 0.039 M allocs: 2.9 MB 0.039 M allocs: 2.9 MB 1
PDB/squared_distance/1CBN_20_30_CB 4 allocs: 0.281 kB 4 allocs: 0.281 kB 1
PDB/squared_distance/1CBN_20_30_heavy 4 allocs: 0.281 kB 4 allocs: 0.281 kB 1
Pfam/accession mapping/acc2seqnames 4.32 k allocs: 0.319 MB 4.32 k allocs: 0.319 MB 1
SIFTS/ResidueDetails/_get_details 25 allocs: 1.45 kB 25 allocs: 1.45 kB 1
SIFTS/ResidueDetails/_is_missing 25 allocs: 1.45 kB 25 allocs: 1.45 kB 1
SIFTS/SIFTSResidue/18gs 4 allocs: 0.125 kB 4 allocs: 0.125 kB 1
SIFTS/siftsmapping/2vqc 5.94 k allocs: 0.88 MB 5.94 k allocs: 0.88 MB 1
Utils/get_n_words/ascii 5 allocs: 0.203 kB 5 allocs: 0.203 kB 1
Utils/get_n_words/utf8 5 allocs: 0.219 kB 5 allocs: 0.219 kB 1
Utils/hascoordinates/invalid 0 allocs: 0 B 0 allocs: 0 B
Utils/hascoordinates/valid 0 allocs: 0 B 0 allocs: 0 B
Utils/list2matrix/upper 3 allocs: 1.91 MB 3 allocs: 1.91 MB 1
Utils/list2matrix/upper_diagonal 6 allocs: 2.86 MB 6 allocs: 2.86 MB 1
Utils/matrix2list/upper 3 allocs: 0.952 MB 3 allocs: 0.952 MB 1
Utils/matrix2list/upper_diagonal 3 allocs: 0.956 MB 3 allocs: 0.956 MB 1
time_to_load 0.149 k allocs: 11.1 kB 0.149 k allocs: 11.1 kB 1

@coveralls
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coveralls commented Dec 18, 2025 •
edited
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Coverage Status

coverage: 96.759% (-0.4%) from 97.156%
when pulling 4892fb5 on codex/implement-pssm-function-for-msa
into 2cdce44 on master.

@diegozea
Improve the PSSM implementation
bc5369b
@diegozea
PSSM: cover background validation branches
0db6f58
@diegozea
Refactor PSSM error handling, improve tests, remove dims
63a59d4
@diegozea
Rename PSSM function and references to position_specific_scoring_matr…
2637023 
…ix for clarity
@diegozea
Refactor PSSM base handling to support multiple types for base and im…
ce6fa7a 
…prove conversion logic
@diegozea
Refactor PSSM structure and tests to use PositionSpecificScoreMatrix …
c4a9c8e 
…and NamedArray
@diegozea
Remove background field from PositionSpecificScoreMatrix and update r…
e7549ef 
…elated tests
@diegozea
Rename AbstractColumnScores to AbstractPositionSpecificMatrix and upd…
ad6e44c 
…ate related structures and methods
@diegozea
Add PositionFrequencyMatrix and PositionSpecificProbabilityMatrix typ…
4618518 
…es with associated functions
@diegozea
Refactor PSSM tests to improve readability and simplify comparison logic
dc9918b
@diegozea
Add getindex method for AbstractPositionSpecificMatrix to improve ind…
4892fb5 
…exing functionality
@diegozea
WIP
f2ddaac
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@diegozea @coveralls