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Cargo.toml

@@ -0,0 +1,14 @@
+[package]
+name = "genome-rs"
+version = "0.1.0"
+edition = "2021"
+
+# See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
+
+[dependencies]
+csv="*"
+serde_derive="*"
+serde="*"
+reqwest = {version = "*", features = ["blocking"]}
+scraper = "*"
+zip = "*"

readme.md

@@ -0,0 +1,25 @@
+# Parsing Human Protein Atlas Files - Currently a POC
+
+grabbing the tsv files from https://www.proteinatlas.org/about/download and parsing them into structs for rust. Also able to zip the files into a single json/csv output file as a graph of the App to be deserialized later. 
+
+to download the data files pass an arg
+`cargo run -- download`
+to export the loaded data as json  
+`cargo run -- json my_output.json`
+to export the loaded data as csv
+`cargo run -- csv my_output.csv`
+
+`cargo run` will read and parse the files into an app struct - see main.rs/main
+
+```rust
+    pub struct App
+        tissues: Vec::<Gene>,
+        pathogens: Vec::<Pathogen>,
+        rna_immune_cell_schmiedel: Vec<RNAImmuneCellSchmiedel>,
+        rna_celline_cancer: Vec<RNACellLineCancer>,
+        rna_immune_cell: Vec<RNAImmuneCell>,
+        rna_immune_cell_monaco: Vec<RNAImmuneCellMonaco>,
+        rna_mouse_brain_hpa: Vec<RNAMouseBrainHPA>,
+        rna_mouse_brain_allen: Vec<RNAMouseBrainAllen>,
+        pig_brain: Vec<AnimalSample>,
+        mouse_brain: Vec<AnimalSample>

src/data.rs

@@ -0,0 +1,345 @@
+use serde_derive::Deserialize;
+use serde_derive::Serialize;
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNAMouseBrainHPA {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Brain region")]
+    pub brain_region: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+    #[serde(rename = "pTPM")]
+    pub p_tpm: String,
+    #[serde(rename = "nTPM")]
+    pub n_tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct Pathogen {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Cancer")]
+    pub cancer: String,
+    #[serde(rename = "High")]
+    pub high: String,
+    #[serde(rename = "Medium")]
+    pub medium: String,
+    #[serde(rename = "Low")]
+    pub low: String,
+    #[serde(rename = "Not detected")]
+    pub not_detected: String,
+    #[serde(rename = "prognostic - favorable")]
+    pub prognostic_favorable: String,
+    #[serde(rename = "unprognostic - favorable")]
+    pub unprognostic_favorable: String,
+    #[serde(rename = "prognostic - unfavorable")]
+    pub prognostic_unfavorable: String,
+    #[serde(rename = "unprognostic - unfavorable")]
+    pub unprognostic_unfavorable: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNACellLineCancer {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Cancer")]
+    pub cancer: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+    #[serde(rename = "pTPM")]
+    pub p_tpm: String,
+    #[serde(rename = "nTPM")]
+    pub n_tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNAImmuneCellSchmiedel {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Immune cell")]
+    pub immune_cell: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNAImmuneCellMonaco {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Immune cell")]
+    pub immune_cell: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+    #[serde(rename = "pTPM")]
+    pub p_tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNAImmuneCellSample {
+    #[serde(rename = "Sample ID")]
+    pub sample_id: String,
+    #[serde(rename = "Donor")]
+    pub donor: String,
+    #[serde(rename = "Immune cell")]
+    pub immune_cell: String,
+    #[serde(rename = "ENSG ID")]
+    pub ensg_id: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+    #[serde(rename = "pTPM")]
+    pub p_tpm: String,
+    #[serde(rename = "nTPM")]
+    pub n_tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNAMouseBrainAllen {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Brain region")]
+    pub brain_region: String,
+    #[serde(rename = "Expression energy")]
+    pub expression_energy: String,
+}
+
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct RNAImmuneCell {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene name")]
+    pub gene_name: String,
+    #[serde(rename = "Immune cell")]
+    pub immune_cell: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+    #[serde(rename = "pTPM")]
+    pub p_tpm: String,
+    #[serde(rename = "nTPM")]
+    pub n_tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct AnimalSample {
+    #[serde(rename = "ENSMUSG_ID")]
+    pub ensmusg_id: String,
+    #[serde(rename = "Main_region")]
+    pub main_region: String,
+    #[serde(rename = "Subregion")]
+    pub subregion: String,
+    #[serde(rename = "Animal")]
+    pub animal: String,
+    #[serde(rename = "TPM")]
+    pub tpm: String,
+    #[serde(rename = "pTPM")]
+    pub p_tpm: String,
+    #[serde(rename = "nTPM")]
+    pub n_tpm: String,
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+#[serde(rename_all = "camelCase")]
+pub struct Gene {
+    #[serde(rename = "Gene")]
+    pub gene: String,
+    #[serde(rename = "Gene synonym")]
+    pub gene_synonym: Option<String>,
+    #[serde(rename = "Ensembl")]
+    pub ensembl: Option<String>,
+    #[serde(rename = "Gene description")]
+    pub gene_description: Option<String>,
+    #[serde(rename = "Uniprot")]
+    pub uniprot: Option<String>,
+    #[serde(rename = "Chromosome")]
+    pub chromosome: Option<String>,
+    #[serde(rename = "Position")]
+    pub position: Option<String>,
+    #[serde(rename = "Protein class")]
+    pub protein_class: Option<String>,
+    #[serde(rename = "Biological process")]
+    pub biological_process: Option<String>,
+    #[serde(rename = "Molecular function")]
+    pub molecular_function: Option<String>,
+    #[serde(rename = "Disease involvement")]
+    pub disease_involvement: Option<String>,
+    #[serde(rename = "Evidence")]
+    pub evidence: Option<String>,
+    #[serde(rename = "HPA evidence")]
+    pub hpa_evidence: Option<String>,
+    #[serde(rename = "UniProt evidence")]
+    pub uni_prot_evidence: Option<String>,
+    #[serde(rename = "NeXtProt evidence")]
+    pub ne_xt_prot_evidence: Option<String>,
+    #[serde(rename = "RNA tissue specificity")]
+    pub rna_tissue_specificity: Option<String>,
+    #[serde(rename = "RNA tissue distribution")]
+    pub rna_tissue_distribution: Option<String>,
+    #[serde(rename = "RNA tissue specificity score")]
+    pub rna_tissue_specificity_score: Option<String>,
+    #[serde(rename = "RNA tissue specific nTPM")]
+    pub rna_tissue_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA single cell type specificity")]
+    pub rna_single_cell_type_specificity: Option<String>,
+    #[serde(rename = "RNA single cell type distribution")]
+    pub rna_single_cell_type_distribution: Option<String>,
+    #[serde(rename = "RNA single cell type specificity score")]
+    pub rna_single_cell_type_specificity_score: Option<String>,
+    #[serde(rename = "RNA single cell type specific nTPM")]
+    pub rna_single_cell_type_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA cancer specificity")]
+    pub rna_cancer_specificity: Option<String>,
+    #[serde(rename = "RNA cancer distribution")]
+    pub rna_cancer_distribution: Option<String>,
+    #[serde(rename = "RNA cancer specificity score")]
+    pub rna_cancer_specificity_score: Option<String>,
+    #[serde(rename = "RNA cancer specific FPKM")]
+    pub rna_cancer_specific_fpkm: Option<String>,
+    #[serde(rename = "RNA brain regional specificity")]
+    pub rna_brain_regional_specificity: Option<String>,
+    #[serde(rename = "RNA brain regional distribution")]
+    pub rna_brain_regional_distribution: Option<String>,
+    #[serde(rename = "RNA brain regional specificity score")]
+    pub rna_brain_regional_specificity_score: Option<String>,
+    #[serde(rename = "RNA brain regional specific nTPM")]
+    pub rna_brain_regional_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA blood cell specificity")]
+    pub rna_blood_cell_specificity: Option<String>,
+    #[serde(rename = "RNA blood cell distribution")]
+    pub rna_blood_cell_distribution: Option<String>,
+    #[serde(rename = "RNA blood cell specificity score")]
+    pub rna_blood_cell_specificity_score: Option<String>,
+    #[serde(rename = "RNA blood cell specific nTPM")]
+    pub rna_blood_cell_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA blood lineage specificity")]
+    pub rna_blood_lineage_specificity: Option<String>,
+    #[serde(rename = "RNA blood lineage distribution")]
+    pub rna_blood_lineage_distribution: Option<String>,
+    #[serde(rename = "RNA blood lineage specificity score")]
+    pub rna_blood_lineage_specificity_score: Option<String>,
+    #[serde(rename = "RNA blood lineage specific nTPM")]
+    pub rna_blood_lineage_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA cell line specificity")]
+    pub rna_cell_line_specificity: Option<String>,
+    #[serde(rename = "RNA cell line distribution")]
+    pub rna_cell_line_distribution: Option<String>,
+    #[serde(rename = "RNA cell line specificity score")]
+    pub rna_cell_line_specificity_score: Option<String>,
+    #[serde(rename = "RNA cell line specific nTPM")]
+    pub rna_cell_line_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA tissue cell type enrichment")]
+    pub rna_tissue_cell_type_enrichment: Option<String>,
+    #[serde(rename = "RNA mouse brain regional specificity")]
+    pub rna_mouse_brain_regional_specificity: Option<String>,
+    #[serde(rename = "RNA mouse brain regional distribution")]
+    pub rna_mouse_brain_regional_distribution: Option<String>,
+    #[serde(rename = "RNA mouse brain regional specificity score")]
+    pub rna_mouse_brain_regional_specificity_score: Option<String>,
+    #[serde(rename = "RNA mouse brain regional specific nTPM")]
+    pub rna_mouse_brain_regional_specific_n_tpm: Option<String>,
+    #[serde(rename = "RNA pig brain regional specificity")]
+    pub rna_pig_brain_regional_specificity: Option<String>,
+    #[serde(rename = "RNA pig brain regional distribution")]
+    pub rna_pig_brain_regional_distribution: Option<String>,
+    #[serde(rename = "RNA pig brain regional specificity score")]
+    pub rna_pig_brain_regional_specificity_score: Option<String>,
+    #[serde(rename = "RNA pig brain regional specific nTPM")]
+    pub rna_pig_brain_regional_specific_n_tpm: Option<String>,
+    #[serde(rename = "Antibody")]
+    pub antibody: Option<String>,
+    #[serde(rename = "Reliability (IH)")]
+    pub reliability_ih: Option<String>,
+    #[serde(rename = "Reliability (Mouse Brain)")]
+    pub reliability_mouse_brain: Option<String>,
+    #[serde(rename = "Reliability (IF)")]
+    pub reliability_if: Option<String>,
+    #[serde(rename = "Subcellular location")]
+    pub subcellular_location: Option<String>,
+    #[serde(rename = "Secretome location")]
+    pub secretome_location: Option<String>,
+    #[serde(rename = "Secretome function")]
+    pub secretome_function: Option<String>,
+    #[serde(rename = "CCD Protein")]
+    pub ccd_protein: Option<String>,
+    #[serde(rename = "CCD Transcript")]
+    pub ccd_transcript: Option<String>,
+    #[serde(rename = "Blood concentration - Conc. blood IM [pg/L]")]
+    pub blood_concentration_conc_blood_im_pg_l: Option<String>,
+    #[serde(rename = "Blood concentration - Conc. blood MS [pg/L]")]
+    pub blood_concentration_conc_blood_ms_pg_l: Option<String>,
+    #[serde(rename = "Blood expression cluster")]
+    pub blood_expression_cluster: Option<String>,
+    #[serde(rename = "Tissue expression cluster")]
+    pub tissue_expression_cluster: Option<String>,
+    #[serde(rename = "Brain expression cluster")]
+    pub brain_expression_cluster: Option<String>,
+    #[serde(rename = "Cell line expression cluster")]
+    pub cell_line_expression_cluster: Option<String>,
+    #[serde(rename = "Single cell expression cluster")]
+    pub single_cell_expression_cluster: Option<String>,
+    #[serde(rename = "Interactions")]
+    pub interactions: Option<String>,
+    #[serde(rename = "Subcellular main location")]
+    pub subcellular_main_location: Option<String>,
+    #[serde(rename = "Subcellular additional location")]
+    pub subcellular_additional_location: Option<String>,
+    #[serde(rename = "Antibody RRID")]
+    pub antibody_rrid: Option<String>,
+    #[serde(rename = "Pathology prognostics - Breast cancer")]
+    pub pathology_prognostics_breast_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Cervical cancer")]
+    pub pathology_prognostics_cervical_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Colorectal cancer")]
+    pub pathology_prognostics_colorectal_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Endometrial cancer")]
+    pub pathology_prognostics_endometrial_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Glioma")]
+    pub pathology_prognostics_glioma: Option<String>,
+    #[serde(rename = "Pathology prognostics - Head and neck cancer")]
+    pub pathology_prognostics_head_and_neck_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Liver cancer")]
+    pub pathology_prognostics_liver_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Lung cancer")]
+    pub pathology_prognostics_lung_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Melanoma")]
+    pub pathology_prognostics_melanoma: Option<String>,
+    #[serde(rename = "Pathology prognostics - Ovarian cancer")]
+    pub pathology_prognostics_ovarian_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Pancreatic cancer")]
+    pub pathology_prognostics_pancreatic_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Prostate cancer")]
+    pub pathology_prognostics_prostate_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Renal cancer")]
+    pub pathology_prognostics_renal_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Stomach cancer")]
+    pub pathology_prognostics_stomach_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Testis cancer")]
+    pub pathology_prognostics_testis_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Thyroid cancer")]
+    pub pathology_prognostics_thyroid_cancer: Option<String>,
+    #[serde(rename = "Pathology prognostics - Urothelial cancer")]
+    pub pathology_prognostics_urothelial_cancer: Option<String>,
+}

src/main.rs

@@ -0,0 +1,224 @@
+mod data;
+
+use std::{env, fs};
+
+use data::{
+    AnimalSample, Pathogen, RNACellLineCancer, RNAImmuneCell, RNAImmuneCellMonaco,
+    RNAImmuneCellSample, RNAImmuneCellSchmiedel, RNAMouseBrainAllen, RNAMouseBrainHPA,
+};
+use serde_derive::{Deserialize, Serialize};
+
+use crate::data::Gene;
+
+fn get_records() -> Vec<Gene> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/normal_tissue.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: Gene = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+fn get_pathogens() -> Vec<Pathogen> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/pathology.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: Pathogen = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn get_rna_immune_cell_monaco() -> Vec<RNAImmuneCellMonaco> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_immune_cell_monaco.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNAImmuneCellMonaco = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_mouse_brain_hpa() -> Vec<RNAMouseBrainHPA> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_mouse_brain_hpa.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNAMouseBrainHPA = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_mouse_brain_allen() -> Vec<RNAMouseBrainAllen> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_mouse_brain_allen.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNAMouseBrainAllen = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_immune_cell_sample() -> Vec<RNAImmuneCellSample> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_immune_cell_sample.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNAImmuneCellSample = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_immune_cell() -> Vec<RNAImmuneCell> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_immune_cell.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNAImmuneCell = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_celline_cancer() -> Vec<RNACellLineCancer> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_celline_cancer.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNACellLineCancer = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn get_rna_immune_cell_schmiedel() -> Vec<RNAImmuneCellSchmiedel> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_immune_cell_schmiedel.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: RNAImmuneCellSchmiedel = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_mouse_brain_sample_hpa() -> Vec<AnimalSample> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_mouse_brain_sample_hpa.tsv/rna_mouse_brain_sample_hpa.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: AnimalSample = result.expect("get");
+        records.push(record);
+    }
+    records
+}
+
+fn rna_pig_brain_sample_hpa() -> Vec<AnimalSample> {
+    let mut rdr = csv::ReaderBuilder::new()
+        .delimiter(b'\t')
+        .from_path("data/rna_pig_brain_sample_hpa.tsv/rna_pig_brain_sample_hpa.tsv")
+        .expect("read TSV");
+    let mut records = vec![];
+    for result in rdr.deserialize() {
+        let record: AnimalSample = result.expect("Get record");
+        records.push(record);
+    }
+    records
+}
+
+#[derive(Default, Debug, Clone, PartialEq, Serialize, Deserialize)]
+pub struct App {
+    tissues: Vec<Gene>,
+    pathogens: Vec<Pathogen>,
+    rna_immune_cell_schmiedel: Vec<RNAImmuneCellSchmiedel>,
+    rna_celline_cancer: Vec<RNACellLineCancer>,
+    rna_immune_cell: Vec<RNAImmuneCell>,
+    rna_immune_cell_sample: Vec<RNAImmuneCellSample>,
+    rna_immune_cell_monaco: Vec<RNAImmuneCellMonaco>,
+    rna_mouse_brain_hpa: Vec<RNAMouseBrainHPA>,
+    rna_mouse_brain_allen: Vec<RNAMouseBrainAllen>,
+
+    pig_brain: Vec<AnimalSample>,
+    mouse_brain: Vec<AnimalSample>,
+}
+
+#[cfg(test)]
+mod tests {
+    #[test]
+    fn it_works() {
+        let app = crate::App {
+            tissues: crate::get_records(),
+            pathogens: crate::get_pathogens(),
+            rna_celline_cancer: crate::rna_celline_cancer(),
+            rna_immune_cell: crate::rna_immune_cell(),
+            rna_immune_cell_sample: crate::rna_immune_cell_sample(),
+            rna_immune_cell_schmiedel: crate::get_rna_immune_cell_schmiedel(),
+            rna_immune_cell_monaco: crate::get_rna_immune_cell_monaco(),
+            rna_mouse_brain_allen: crate::rna_mouse_brain_allen(),
+            rna_mouse_brain_hpa: crate::rna_mouse_brain_hpa(),
+
+            mouse_brain: crate::rna_pig_brain_sample_hpa(),
+            pig_brain: crate::rna_mouse_brain_sample_hpa(),
+        };
+        for pb in app.pig_brain {
+            print!("{} - {}", pb.animal, pb.tpm);
+        }
+    }
+}
+fn main() {
+    let args: Vec<String> = env::args().collect();
+    let arg = &args[1];
+    println!("{}", arg);
+    if arg == "download" {
+        let response = reqwest::blocking::get("https://www.proteinatlas.org/about/download")
+            .unwrap()
+            .text()
+            .unwrap();
+        let document = scraper::Html::parse_document(&response);
+        let url_selector = scraper::Selector::parse("a").unwrap();
+        let zipped_to_download:Vec<String> = document.select(&url_selector)
+            .map(|x| x.value().attr("href").expect("get href").to_string())
+            .filter(|href| href.contains("/download/"))
+            .collect();
+        for z in zipped_to_download {
+            let path = z.clone();
+            let splitpath = path.split("/");
+            let fname = splitpath.last().expect("name");
+            let mut file = std::fs::File::create(format!("data/{}", fname)).expect("Create file handler");
+            let response = reqwest::blocking::get(format!("https://www.proteinatlas.org{}", path))
+                .unwrap()
+                .copy_to(&mut file)
+                .expect("Write out to file");
+            println!("{} {} bytes", path, response);
+            
+        }
+        return;
+    }
+
+}