Pepstats Workflow¶

The Pepstats workflow runs pepstats on ensembl protein sequences.

Overview¶

The workflow computes essential statistics about protein sequences from Ensembl core databases.

Workflow Components¶

Computes core metrics from the database:

nextflow run main.nf \
  --csvFile databases.csv \
  --run_pepstats \
  --host mysql-server.example.com \
  --port 3306 \
  --user_r ensro \
  --enscode /path/to/ensembl/modules \
  --outdir results

Required Parameters¶

Parameter	Description	Example
`--enscode`	Path to Ensembl API modules	`/nfs/software/ensembl/ENSCODE`
`--host`	Database host server	`mysql-ens-sta-5.ebi.ac.uk`
`--port`	Database port	`4686`
`--user_r`	Read-only user (for generation)	`ensro`
`--user`	Write user (for applying)	`ensadmin`
`--password`	Database password (for applying)	-
`--team`	Team responsible (metakey)	`genebuild`

CSV Input¶

dbname,species_id
homo_sapiens_core_110_38,1
mus_musculus_core_110_39,1
danio_rerio_core_110_11,1

Generated Statistics¶

Pepstats applied to the database¶

Statistic	Description	Example Value
`IsoPoint`	Isoelectric point	10.0024
`Charge`	Charge	-0.5
`MolecularWeight`	Number of residues	100008.72
`AvgResWeight`	Ave. residue weight	100.092
`NumResidues`	Number of residues	100

Output Files¶

Statistics JSON¶

{database}_statistics.json

{
  "database": "homo_sapiens_core_110_38",
  "species_id": 1,
  "generated_date": "2024-01-15T10:30:00",
  "statistics": {
    "coding_cnt": 19950,
    "pseudogene_cnt": 14723,
    "noncoding_cnt_lncRNA": 17910,
    "noncoding_cnt_misc_RNA": 2212,
    "noncoding_cnt_miRNA": 1879,
    "noncoding_cnt_rRNA": 549,
    "noncoding_cnt_snoRNA": 943,
    "noncoding_cnt_snRNA": 1901,
    "gene_cnt": 60670,
    "transcript_cnt": 251769,
    "coding_transcript_cnt": 87521,
    "exon_cnt": 756234,
    "toplevel_seq_cnt": 639,
    "chromosome_cnt": 24
  }
}

Directory Structure¶

results/
└── ensembl_stats/
    ├── homo_sapiens_core_110_38_statistics.json
    ├── mus_musculus_core_110_39_statistics.json
    └── danio_rerio_core_110_11_statistics.json

Database Connection Failed¶

Problem: Cannot connect to database

Solutions:

# Test connection
mysql -h mysql-server.example.com -P 3306 -u ensro -e "SHOW DATABASES;"

# Check credentials
--host mysql-server.example.com \
--port 3306 \
--user_r ensro

Permission Denied¶

Problem: Cannot write to database

Solution: Use user with write permissions:

--user ensadmin \
--password ${DB_PASSWORD}