Develop a codebase to address the the following regarding calcification gene activity in corals:

Gene expression of calcification genes is more variable in Acropora and Pocillopora than Porites

To assess variability, examine  expression across samples and time, considering both gene level expression as well as exon expression variation.


Data neccessary to test the hypotheses 

Expression matrices of calicification genes across timepoints and treatments for each species.

https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/M-multi-species/output/33-biomin-pathway-counts/apul_biomin_counts.csv

https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/M-multi-species/output/33-biomin-pathway-counts/peve_biomin_counts.csv

https://raw.githubusercontent.com/urol-e5/timeseries-molecular-calcification/refs/heads/main/M-multi-species/output/33-biomin-pathway-counts/ptua_biomin_counts.csv


Annotation file
M-multi-species/output/12-ortho-annot/ortholog_groups_annotated.csv



Exon-Level Expression Data 

Located at: M-multi-species/output/40-exon-count-matrix/

Raw exon count matrices:
- apul-exon_gene_count_matrix.csv
- peve-exon_gene_count_matrix.csv  
- ptua-exon_gene_count_matrix.csv

Exon summary files with ortholog group mappings:
- apul-exon_summary_by_ortholog.csv
- peve-exon_summary_by_ortholog.csv
- ptua-exon_summary_by_ortholog.csv


IMPORTANT: Gene ID Format Differences

The gene IDs in the exon count matrices have DIFFERENT formats than the biomin count matrices:

| Species | Exon Count Matrix gene_id | Biomin Counts gene_id |
|---------|---------------------------|----------------------|
| Apul | FUN_000001 | FUN_002435 | ✓ Same format - direct matching works |
| Peve | gene-Peve_00000001 | Peve_00000077 | Need to remove "gene-" prefix |
| Ptua | gene-Pocillopora_meandrina_HIv1___RNAseq.10273_t | Pocillopora_meandrina_HIv1___TS.g25680.t1b | Completely different gene annotation formats! |

SOLUTION: Use ortholog group IDs (group_id) for matching instead of gene_id

Both the biomin counts and the exon summary files contain a `group_id` column with ortholog group identifiers (e.g., OG_08948). These are consistent across datasets and should be used for joining exon variability data with expression and methylation data.

Steps for proper matching:
1. Load exon summary files (*-exon_summary_by_ortholog.csv) to get gene_id → group_id mapping
2. Add group_id to the raw exon count data using this mapping
3. Join exon variability results with biomin/methylation data using group_id (not gene_id)