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use clap::{Parser, Subcommand};
#[derive(Debug, Parser)]
#[command(
name = "huget",
version = "1.0",
about = "huget: human genomics conversion
************************************************
Gaurav Sablok
codeprog@icloud.com
************************************************"
)]
pub struct CommandParse {
/// subcommands for the specific actions
#[command(subcommand)]
pub command: Commands,
}
#[derive(Subcommand, Debug)]
pub enum Commands {
MaprsID {
// provide the path to the identified snps in personal genomics
pathfile: String,
// provide the specific snp for the token
rsid: String,
/// threads for the analysis
thread: String,
},
GenerateInfo {
// provide the rsid for the variant
rsid: String,
/// thread for the analysis
thread: String,
},
AnnotateAll {
// provide yes as a comment and it will annotate all variants
annotate: String,
// provide the path to the file
pathfile: String,
/// threads for the analysis
thread: String,
},
/// threaded version of genelength for human
ThreadedLengthHuman {
/// provide yes as argument
generate: String,
/// thread for the analysis
thread: String,
},
/// trhreaded version of genelength for mouse
ThreadedLengthMouse {
/// provide yes as argument
generate: String,
/// thread for the analysis
thread: String,
},
/// threaded version of genelength for human
ThreadedHuman {
/// provide yes as argument
count: String,
/// thread for the analysis
thread: String,
},
/// threaded version of genelength for mouse
ThreadedMouse {
/// provide yes as argument
count: String,
/// thread for the analysis
thread: String,
},
/// Exon search
Exon {
/// path to the file
pathname: String,
/// searched gene
searchgene: String,
/// threads for the analysis
threads: String,
},
/// GOBP fetch
GOBP {
/// path to the GOBP file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// GOCC fetch
GOCC {
/// path to the GOCC file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// GOMF fetch
GOMF {
/// path to the GOMF file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// HP fetch
HP {
/// path to the HP file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// HPA fetch
HPA {
/// path to the HPA file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// React fetch
React {
/// path to the React file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// Pathways fetch
Pathways {
/// path to the Pathways file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// miRNA fetch
MiRNA {
/// path to the Pathways file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// pdB fetch
PDB {
/// path to the Pdb file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// HGNC fetch
HGNC {
/// path to the hgnc file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// RefSeqfetch
RefSeq {
/// path to the RefSeq file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// Swiss fetch
Swiss {
/// path to the Swiss file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// TreMBL fetch
TrEMBL {
/// path to the TrEMBL file
pathname: String,
/// searched ensembl id
ensemblid: String,
},
/// MetaData fetch
MetaData {
/// path to the Pathways file
pathname: String,
/// searched ensembl id
ensemblid: String,
/// Refseq or CCDS
typestring: String,
},
/// Train the Conv1D using the Burn convolution network
NeuralConv1D {
/// path to the classification file
pathname: String,
/// threads
thread: String,
},
}