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PertInInt relies on filenames to determine domain names
Line 173 in 6e97c09
This is a hack which only works for the ig domain. Need to investigate pertInInt code and decouple it from filenames, and/or generate the correctly named files before calling pertInInt.
Biopython version
Bio.Alphabet has been removed from biopython>=1.78 as per:
https://biopython.org/wiki/Alphabet
Till dsprint-pipeline is tweaked to work with the latest biopython versions, biopython will be pinned to version 1.77 in `environment.yml'
Ambiguous rule with latest snakemake
With snakemake version 5.27.4, we're getting the following error on running the step for downloading data:
snakemake --cores 1 --use-conda --until download_exac download_exac_coverage download_hg19_2bit download_uniprot_fasta download_uniprot_idmapping download_phastCons download_phyloP download_pertinint_mafs install_pertinint install_hmmer2 install_hmmer3 install_tabix install_twoBitToFa --dryrun
AmbiguousRuleException:
Rules pertinint_compute_jsd and pertinint_verify_exons are ambiguous for the file /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1.jsd.txt.
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
pertinint_compute_jsd: chromosome=1
pertinint_verify_exons: chromosome=1.jsd.txt
Expected input files:
pertinint_compute_jsd: pertinint-internal/config.py /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1 /scratch/gpfs/vineetb/dsprint2/pertinint/ucscgb/hg19alignment/mafs/chr1.maf.gz
pertinint_verify_exons: pertinint-internal/config.py /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/Homo_sapiens.GRCh37.pep.all.withgenelocs.fa.gz /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/dna_smExpected output files:
pertinint_compute_jsd: /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1.jsd.txt
pertinint_verify_exons: /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1.jsd.txt
Till this is resolved, snakemake will be pinned to version 5.19.2 in requirements.txt
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