Merge pull request #29 from ZEZE1020/readme-update

Readme update

Author: LCrossman

.gitignore

@@ -18,7 +18,7 @@ Cargo.lock
 #  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
-#.idea/*~
+.idea/*~
 .DS_Store
 env/
 venv/

README.md

@@ -1,264 +1,41 @@
-# microBioRust
+ <img src="docs/assets/MICROBIO B.svg" width=200em alt="logo" /> 
+
+[![Docs](https://img.shields.io/badge/docs-mkdocs-blue.svg)](https://lcrossman.github.io/microBioRust/)
+
+![Crates.io Version](https://img.shields.io/crates/v/microBioRust?style=flat&link=https%3A%2F%2Fcrates.io%2Fcrates%2FmicroBioRust)
+
+
+
 
 ## A Rust bioinformatics crate aimed at Microbial genomics<br>
 
 The aim of this crate is to provide Microbiology friendly Rust functions for bioinformatics.<br>
 
-Very much under construction!<br>
+> Very much under construction!<br>
 
 Some concepts with many thanks to Rust-bio<br>
-Please see the Roadmap for futher details [here](https://github.com/LCrossman/microBioRust/issues/18)
+Please see the Roadmap for futher details [here](ROADMAP.md)
 
 To install Rust - please see here [Rust install](https://www.rust-lang.org/tools/install) or with Conda<br>
 If you would like to contribute please follow the [Rust code of conduct](https://www.rust-lang.org/policies/code-of-conduct)
 
 Questions and comments - please join the Discord server :) [here](https://discord.gg/xP2ngwTttz)
 
-Currently there is functionality for:<br>
-
-# 1. A Genbank to GFF parser
-
-# 2. An Embl to GFF and GBK parser
-
-# 3. Calculate sequence metrics <i>e.g.</i> hydrophobicity, distance measures
-
-# 4. A Heatmap plot with wasm and d3.js
-
-To use a specific workspace (at the moment microSeqIO or heatmap) clone the project, cd into the specific directory required and build the project from there
 
-for more background please see <https://LCrossman.github.io/microBioRust_details>
-
-In microBioRust:
-
-You can parse genbank files and save as a GFF (gff3) format as well as extracting DNA sequences, gene DNA sequences (ffn) and protein fasta sequences (faa)
-Super simple way:
-
-```rust
-pub fn genbank_to_faa() -> Result<(), anyhow::Error> {
-    let args = Arguments::parse();
-    let records = genbank!(&args.filename);
-    for record in records.iter() {
-        for (k, v) in &record.cds.attributes {
-            if let Some(seq) = record.seq_features.get_sequence_faa(k) {
-                println!(">{}|{}\n{}", &record.id, &k, seq);
-            }
-        }
-    }
-    return Ok(());
-}
-
-```
-
-Better for Debugging:
-
-```rust
-pub fn genbank_to_faa() -> Result<(), anyhow::Error> {
-    let args: Vec<String> = env::args().collect();
-    let config = Config::new(&args).unwrap_or_else(|err| {
-        println!("Problem with parsing file arguments: {}", err);
-        process::exit(1);
-    });
-    let file_gbk = fs::File::open(config.filename)?;
-    let mut reader = Reader::new(file_gbk);
-    let mut records = reader.records();
-    let mut cds_counter: u32 = 0;
-    loop {
-        //collect from each record advancing on a next record basis, count cds records
-        match records.next() {
-            Some(Ok(mut record)) => {
-                for (k, v) in &record.cds.attributes {
-                    match record.seq_features.get_sequence_faa(&k) {
-                        Some(value) => {
-                            let seq_faa = value.to_string();
-                            println!(">{}|{}\n{}", &record.id, &k, seq_faa);
-                        }
-                        _ => (),
-                    };
-                }
-                cds_counter += 1;
-            }
-            Some(Err(e)) => {
-                println!("Error encountered - an err {:?}", e);
-            }
-            None => {
-                println!("finished iteration");
-                break;
-            }
-        }
-    }
-    println!("Total records processed: {}", read_counter);
-    return Ok(());
-}
-```
-
-Example to save a provided multi- or single genbank file as a GFF file (by joining any multi-genbank)
-
-```rust
-pub fn genbank_to_gff() -> io::Result<()> {
-    let args: Vec<String> = env::args().collect();
-    let config = Config::new(&args).unwrap_or_else(|err| {
-        println!("Problem with parsing file arguments: {}", err);
-        process::exit(1);
-        });
-    let file_gbk = fs::File::open(&config.filename)?;
-    let prev_start: u32 = 0;
-    let mut prev_end: u32 = 0;
-    let mut reader = Reader::new(file_gbk);
-    let mut records = reader.records();
-    let mut read_counter: u32 = 0;
-    let mut seq_region: BTreeMap<String, (u32,u32)> = BTreeMap::new();
-    let mut record_vec: Vec<Record> = Vec::new();
-    loop {  
-        match records.next() {   
-            Some(Ok(mut record)) => {
-                //println!("next record");
-                //println!("Record id: {:?}", record.id);
-                let source = record.source_map.source_name.clone().expect("issue collecting source name");
-                let beginning = match record.source_map.get_start(&source) {
-                                    Some(value) => value.get_value(),
-                                    _ => 0,
-                                    };
-                let ending = match record.source_map.get_stop(&source) {
-                                    Some(value) => value.get_value(),
-                                    _ => 0,
-                                    };
-                if ending + prev_end < beginning + prev_end {
-                    }
-                seq_region.insert(source, (beginning + prev_end, ending + prev_end));
-                record_vec.push(record);
-                // Add additional fields to print if needed
-                read_counter+=1;
-                prev_end+=ending; // create the joined record if there are multiple
-                },
-            Some(Err(e)) => { println!("theres an err {:?}", e); },
-                None => {
-                println!("finished iteration");
-                        break; },
-            }
-        }
-    let output_file = format!("{}.gff", &config.filename);
-    gff_write(seq_region.clone(), record_vec, &output_file, true);
-    println!("Total records processed: {}", read_counter);
-    return Ok(());
-}
-```
-
-Example to create a completely new record, use of setters or set_ functionality
+Currently there is functionality for:<br>
+````
+ 1. A Genbank to GFF parser
 
-To write into GFF format requires gff_write(seq_region, record_vec, filename, true or false)
+ 2. An Embl to GFF and GBK parser
 
-The seq_region is the region of interest to save with name and DNA coordinates such as `seqregion.entry("source_1".to_string(), (1,897))`
+ 3. Calculate sequence metrics e.g. hydrophobicity, distance measures
 
-This makes it possible to save the whole file or to subset it
+ 4. A Heatmap plot with wasm and d3.js
 
-record_vec is a list of the records.  If there is only one record, include this as a vec using `vec![record]`
+````
 
-The boolean true/false describes whether the DNA sequence should be included in the GFF3 file
+To see more on how to use have a look at usage [here](docs/usage.md)
 
-To write into genbank format requires gbk_write(seq_region, record_vec, filename), no true or false since genbank format will include the DNA sequence
+To use a specific workspace (at the moment microSeqIO or heatmap) clone the project, cd into the specific directory required and build the project from there
 
- ```rust
-pub fn create_new_record() -> Result<(), anyhow::Error> {
-    let filename = format!("new_record.gff");
-    let mut record = Record::new();
-    let mut seq_region: BTreeMap<String, (u32, u32)> = BTreeMap::new();
-    //example from E.coli K12
-    seq_region.insert("source_1".to_string(), (1, 897));
-    //Add the source into SourceAttributes
-    record
-        .source_map
-        .set_counter("source_1".to_string())
-        .set_start(RangeValue::Exact(1))
-        .set_stop(RangeValue::Exact(897))
-        .set_organism("Escherichia coli".to_string())
-        .set_mol_type("DNA".to_string())
-        .set_strain("K-12 substr. MG1655".to_string())
-        .set_type_material("type strain of Escherichia coli K12".to_string())
-        .set_db_xref("PRJNA57779".to_string());
-    //Add the features into FeatureAttributes, here we are setting two features, i.e. coding sequences or genes
-    record
-        .cds
-        .set_counter("b3304".to_string())
-        .set_start(RangeValue::Exact(1))
-        .set_stop(RangeValue::Exact(354))
-        .set_gene("rplR".to_string())
-        .set_product("50S ribosomal subunit protein L18".to_string())
-        .set_codon_start(1)
-        .set_strand(-1);
-    record
-        .cds
-        .set_counter("b3305".to_string())
-        .set_start(RangeValue::Exact(364))
-        .set_stop(RangeValue::Exact(897))
-        .set_gene("rplF".to_string())
-        .set_product("50S ribosomal subunit protein L6".to_string())
-        .set_codon_start(1)
-        .set_strand(-1);
-    //Add the sequences for the coding sequence (CDS) into SequenceAttributes
-    record
-        .seq_features
-        .set_counter("b3304".to_string())
-        .set_start(RangeValue::Exact(1))
-        .set_stop(RangeValue::Exact(354))
-        .set_sequence_ffn(
-            "ATGGATAAGAAATCTGCTCGTATCCGTCGTGCGACCCGCGCACGCCGCAAGCTCCAGGAG
-CTGGGCGCAACTCGCCTGGTGGTACATCGTACCCCGCGTCACATTTACGCACAGGTAATT
-GCACCGAACGGTTCTGAAGTTCTGGTAGCTGCTTCTACTGTAGAAAAAGCTATCGCTGAA
-CAACTGAAGTACACCGGTAACAAAGACGCGGCTGCAGCTGTGGGTAAAGCTGTCGCTGAA
-CGCGCTCTGGAAAAAGGCATCAAAGATGTATCCTTTGACCGTTCCGGGTTCCAATATCAT
-GGTCGTGTCCAGGCACTGGCAGATGCTGCCCGTGAAGCTGGCCTTCAGTTCTAA"
-                .to_string(),
-        )
-        .set_sequence_faa(
-            "MDKKSARIRRATRARRKLQELGATRLVVHRTPRHIYAQVIAPNGSEVLVAASTVEKAIAE
-QLKYTGNKDAAAAVGKAVAERALEKGIKDVSFDRSGFQYHGRVQALADAAREAGLQF"
-                .to_string(),
-        )
-        .set_codon_start(1)
-        .set_strand(-1);
-    record
-        .seq_features
-        .set_counter("bb3305".to_string())
-        .set_start(RangeValue::Exact(364))
-        .set_stop(RangeValue::Exact(897))
-        .set_sequence_ffn(
-            "ATGTCTCGTGTTGCTAAAGCACCGGTCGTTGTTCCTGCCGGCGTTGACGTAAAAATCAAC
-GGTCAGGTTATTACGATCAAAGGTAAAAACGGCGAGCTGACTCGTACTCTCAACGATGCT
-GTTGAAGTTAAACATGCAGATAATACCCTGACCTTCGGTCCGCGTGATGGTTACGCAGAC
-GGTTGGGCACAGGCTGGTACCGCGCGTGCCCTGCTGAACTCAATGGTTATCGGTGTTACC
-GAAGGCTTCACTAAGAAGCTGCAGCTGGTTGGTGTAGGTTACCGTGCAGCGGTTAAAGGC
-AATGTGATTAACCTGTCTCTGGGTTTCTCTCATCCTGTTGACCATCAGCTGCCTGCGGGT
-ATCACTGCTGAATGTCCGACTCAGACTGAAATCGTGCTGAAAGGCGCTGATAAGCAGGTG
-ATCGGCCAGGTTGCAGCGGATCTGCGCGCCTACCGTCGTCCTGAGCCTTATAAAGGCAAG
-GGTGTTCGTTACGCCGACGAAGTCGTGCGTACCAAAGAGGCTAAGAAGAAGTAA"
-                .to_string(),
-        )
-        .set_sequence_faa(
-            "MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNTLTFGPRDGYAD
-GWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVINLSLGFSHPVDHQLPAG
-ITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK"
-                .to_string(),
-        )
-        .set_codon_start(1)
-        .set_strand(-1);
-    //Add the full sequence of the entire record into the record.sequence
-    record.sequence = "TTAGAACTGAAGGCCAGCTTCACGGGCAGCATCTGCCAGTGCCTGGACACGACCATGATA
-TTGGAACCCGGAACGGTCAAAGGATACATCTTTGATGCCTTTTTCCAGAGCGCGTTCAGC
-GACAGCTTTACCCACAGCTGCAGCCGCGTCTTTGTTACCGGTGTACTTCAGTTGTTCAGC
-GATAGCTTTTTCTACAGTAGAAGCAGCTACCAGAACTTCAGAACCGTTCGGTGCAATTAC
-CTGTGCGTAAATGTGACGCGGGGTACGATGTACCACCAGGCGAGTTGCGCCCAGCTCCTG
-GAGCTTGCGGCGTGCGCGGGTCGCACGACGGATACGAGCAGATTTCTTATCCATAGTGTT
-ACCTTACTTCTTCTTAGCCTCTTTGGTACGCACGACTTCGTCGGCGTAACGAACACCCTT
-GCCTTTATAAGGCTCAGGACGACGGTAGGCGCGCAGATCCGCTGCAACCTGGCCGATCAC
-CTGCTTATCAGCGCCTTTCAGCACGATTTCAGTCTGAGTCGGACATTCAGCAGTGATACC
-CGCAGGCAGCTGATGGTCAACAGGATGAGAGAAACCCAGAGACAGGTTAATCACATTGCC
-TTTAACCGCTGCACGGTAACCTACACCAACCAGCTGCAGCTTCTTAGTGAAGCCTTCGGT
-AACACCGATAACCATTGAGTTCAGCAGGGCACGCGCGGTACCAGCCTGTGCCCAACCGTC
-TGCGTAACCATCACGCGGACCGAAGGTCAGGGTATTATCTGCATGTTTAACTTCAACAGC
-ATCGTTGAGAGTACGAGTCAGCTCGCCGTTTTTACCTTTGATCGTAATAACCTGACCGTT
-GATTTTTACGTCAACGCCGGCAGGAACAACGACCGGTGCTTTAGCAACACGAGACAT"
-        .to_string();
-    gff_write(seq_region, vec![record], &filename, true);
-    return Ok(());
-}
-```
+For more background please see <https://LCrossman.github.io/microBioRust_details>