line length fix

README.md

@@ -11,7 +11,8 @@ Markdown](https://github.com/uab-cgds-worthey/DITTO/actions/workflows/linting.ym
 > Gitlab](https://gitlab.rc.uab.edu/center-for-computational-genomics-and-data-science/sciops/ditto). It was migrated to
 > Github in April 2023, and the Gitlab version has been archived.
 
-We aim to develop a pipeline for accurate and rapid interpretation of genetic variants for pathogenicity using patient’s genotype (VCF) information.
+We aim to develop a pipeline for accurate and rapid interpretation of genetic variants for pathogenicity using patient’s
+ genotype (VCF) information.
 
 ## Usage
 
@@ -26,7 +27,8 @@ in this [GitHub repo](https://github.com/uab-cgds-worthey/DITTO-API).
 
 ### Setting up to use locally
 
-> ***NOTE:*** This setup will allow one to annotate a VCF sample and make DITTO predictions. Currently tested only in Cheaha (UAB HPC). Docker versions may need to be explored later to make it
+> ***NOTE:*** This setup will allow one to annotate a VCF sample and make DITTO predictions. Currently tested only in
+> Cheaha (UAB HPC). Docker versions may need to be explored later to make it
 > useable in Mac and Windows.
 
 #### System Requirements

docs/build_DITTO.md

@@ -77,11 +77,13 @@ oc run clinvar.vcf.gz -l hg38 -t csv --package mypackage -d path/to/output/direc
 
 ## Preprocessing
 
-By default, OpenCravat annotates all transcript level annotations for each variant in a single row. DITTO makes transcript level
-predictions for each variant. To parse out each transcript level annotations to different rows, use the below command
+By default, OpenCravat annotates all transcript level annotations for each variant in a single row. DITTO makes
+transcript level predictions for each variant. To parse out each transcript level annotations to different rows, use
+the below command
 
 ```sh
-python src/annotation_parsing/parse_single_sample.py -i clinvar.vcf.gz.variant.csv -e parse -o clinvar.vcf.gz.variant.csv_parsed.csv.gz -c configs/opencravat_train_config.json
+python src/annotation_parsing/parse_single_sample.py -i clinvar.vcf.gz.variant.csv -e parse \
+-o clinvar.vcf.gz.variant.csv_parsed.csv.gz -c configs/opencravat_train_config.json
 ```
 
 Filter and process the annotations as shown in this [python
@@ -95,7 +97,8 @@ uses the testing data to calculate accuracy, roc, and prc metrics along with a S
 to train the model.
 
 ```sh
-python training/NN.py --train_x /data/train_class_data_80.csv.gz --test_x /data/test_class_data_20.csv.gz -c configs/col_config.yaml -o /data/
+python training/NN.py --train_x /data/train_class_data_80.csv.gz \
+--test_x /data/test_class_data_20.csv.gz -c configs/col_config.yaml -o /data/
 ```
 
 This script took 10 CPU cores, 100 GB memory and ~17 hrs to tune and train DITTO.

docs/install_openCravat.md

@@ -32,7 +32,12 @@ Test it by using `oc config md` command. It should output the new modules direct
 ```sh
 oc module install-base
 
-oc module  install aloft cadd cadd_exome cancer_genome_interpreter ccre_screen chasmplus civic clingen clinpred clinvar cosmic cosmic_gene cscape dann dann_coding dbscsnv dbsnp dgi ensembl_regulatory_build ess_gene exac_gene fathmm fathmm_xf_coding funseq2 genehancer gerp ghis gnomad gnomad3 gnomad_gene gtex gwas_catalog linsight loftool lrt mavedb metalr metasvm mutation_assessor mutationtaster mutpred1 mutpred_indel ncbigene ndex ndex_chd ndex_signor omim pangalodb phastcons phdsnpg phi phylop polyphen2 prec provean repeat revel rvis segway sift siphy spliceai uniprot vest cgc cgd varity_r
+oc module  install aloft cadd cadd_exome cancer_genome_interpreter ccre_screen chasmplus civic clingen clinpred clinvar \
+cosmic cosmic_gene cscape dann dann_coding dbscsnv dbsnp dgi ensembl_regulatory_build ess_gene exac_gene fathmm \
+fathmm_xf_coding funseq2 genehancer gerp ghis gnomad gnomad3 gnomad_gene gtex gwas_catalog linsight loftool lrt mavedb \
+metalr metasvm mutation_assessor mutationtaster mutpred1 mutpred_indel ncbigene ndex ndex_chd ndex_signor omim \
+pangalodb phastcons phdsnpg phi phylop polyphen2 prec provean repeat revel rvis segway sift siphy spliceai uniprot \
+vest cgc cgd varity_r
 ```
 
 Please look at the [install logs](../docs/install_openCravat.logfile) for the versions of all the above annotators used to