rustfastq 0.5.0

bare metal fastq parsing
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222

//! Code to demultiplex (based on I1, I2)
//! 

use std::{collections::HashMap, fs::File, io::{BufReader, BufWriter, Write}, path::Path};

use itertools::{izip, Itertools};
use rust_htslib::bgzf::{self, CompressionLevel};

use crate::utils::get_spinner;

#[derive(Debug, Eq, PartialEq, Hash, Clone)]
pub  struct DualIndex(pub String, pub String);

// to denote a single sample by some prefix
#[derive(Debug, Eq, PartialEq, Hash, Clone)]
pub  struct Samplename(pub String);

pub struct Samplesheet {
    sheet: HashMap<DualIndex, Samplename>, 
    empty_sample: Samplename, // a special samplename indicating anything not matchgin the indices
}

impl Samplesheet {

    pub fn new(sheet: HashMap<DualIndex, Samplename>) -> Self {
        Self { 
            sheet , 
            empty_sample: Samplename("Undetermined".to_owned())
        }
    }

    /// Constructs the Samplesheet from a csv table
    /// with three columns i7 index, i5 index, samplename
    pub fn from_csv(file: &Path) -> Self {
        let sheet = samplesheet_to_hashmap_2(file);
        Self::new(sheet)
    }

    /// creates the FastQ writers for the sample sheet,
    /// i.e. each sample has a writer for R1 and R2
    fn create_writers(&self, outdir: &Path, undetermined_prefix: &str) -> HashMap<Samplename, (Box<dyn Write>, Box<dyn Write>)> {
        let prefixes = self.sheet.values().unique().collect_vec();
        let mut writers: HashMap<Samplename, (Box<dyn Write>, Box<dyn Write>)> = HashMap::new();
    
        fn get_encoder(fname: &str) -> BufWriter<rust_htslib::bgzf::Writer> {
            let encoder = BufWriter::new(
                bgzf::Writer::from_path_with_level(fname, CompressionLevel::Fastest).unwrap()
            );
            encoder
        }

        // create a writer for each sample (which can have multiple sample-indices)
        for sname in prefixes {
            let fname_r1 = format!("{}/{}.R1.fq.gz", outdir.to_str().unwrap(), sname.0);
            let fname_r2 = format!("{}/{}.R2.fq.gz", outdir.to_str().unwrap(), sname.0);
            let encoder_r1 = get_encoder(&fname_r1);
            let encoder_r2 = get_encoder(&fname_r2);
            writers.insert(sname.clone(), (Box::new(encoder_r1), Box::new(encoder_r2)));       
        }

        // add the writer for unassigned
        let fname_r1 = format!("{}/{}.R1.fq.gz", outdir.to_str().unwrap(), undetermined_prefix);
        let fname_r2 = format!("{}/{}.R2.fq.gz", outdir.to_str().unwrap(), undetermined_prefix);
        let encoder_r1 = get_encoder(&fname_r1);
        let encoder_r2 = get_encoder(&fname_r2);
        let empty_sample = Samplename("Undetermined".to_owned());
        writers.insert(empty_sample.clone(), (Box::new(encoder_r1), Box::new(encoder_r2)));        
        writers
    }


    pub fn get_samplename_from_index(&self, dual_ix: DualIndex) -> &Samplename {
        let samplename = self.sheet.get(&dual_ix).unwrap_or(&self.empty_sample,);
        samplename
    }

}


pub  fn demux_dual_index_2(samplesheet: Samplesheet, undetermined_prefix: String, i1_list: Vec<String>, i2_list: Vec<String>, r1_list: Vec<String>, r2_list: Vec<String>, outfolder: &Path) {

    // let prefixes = sample_indices_fnames.values().unique().collect_vec();
    // let mut writers: HashMap<Samplename, (Box<dyn Write>, Box<dyn Write>)> = HashMap::new();

    // // create a writer for each sample (which can have multiple sample-indices)
    // for sname in prefixes {
    //     let fname_r1 = format!("{}/{}.R1.fq.gz", outfolder, sname.0);
    //     let fname_r2 = format!("{}/{}.R2.fq.gz", outfolder, sname.0);

    //     let encoder_r1 = BufWriter::new(
    //         bgzf::Writer::from_path_with_level(fname_r1, CompressionLevel::Fastest).unwrap()
    //     );
    //     let encoder_r2 = BufWriter::new(
    //         bgzf::Writer::from_path_with_level(fname_r2, CompressionLevel::Fastest).unwrap()
    //     );
    //     writers.insert(sname.clone(), (Box::new(encoder_r1), Box::new(encoder_r2)));       
    // }
    // // add the writer for unassigned
    // let fname_r1 = format!("{}/{}.R1.fq.gz", outfolder, undetermined_prefix);
    // let fname_r2 = format!("{}/{}.R2.fq.gz", outfolder, undetermined_prefix);
    // let encoder_r1 = BufWriter::new(
    //     bgzf::Writer::from_path_with_level(fname_r1, CompressionLevel::Fastest).unwrap()
    // );
    // let encoder_r2 = BufWriter::new(
    //     bgzf::Writer::from_path_with_level(fname_r2, CompressionLevel::Fastest).unwrap()
    // );    
    // let empty_sample = Samplename("Undetermined".to_owned());

    // writers.insert(empty_sample.clone(), (Box::new(encoder_r1), Box::new(encoder_r2)));

    
    let mut writers = samplesheet.create_writers(outfolder, &undetermined_prefix);

    let i1_iter = crate::io::fastq_list_iter(&i1_list);
    let i2_iter = crate::io::fastq_list_iter(&i2_list);
    let r1_iter = crate::io::fastq_list_iter(&r1_list);
    let r2_iter = crate::io::fastq_list_iter(&r2_list);

    let pbar = get_spinner();
    for (counter, (i1, i2, r1, r2)) in izip!(i1_iter, i2_iter, r1_iter, r2_iter).enumerate() {
        let key: DualIndex = DualIndex(i1.seq, i2.seq);

        // let samplename = sample_indices_fnames.get(&key).unwrap_or(&empty_sample,);
        let samplename = samplesheet.get_samplename_from_index(key);
        let (writer_r1, writer_r2) = writers.get_mut(samplename).unwrap();

        write!(writer_r1, "{}", r1.to_string(), ).unwrap();
        write!(writer_r2, "{}", r2.to_string(), ).unwrap();

        if counter % 1_000_000 == 0{
            pbar.inc(1_000_000);
        }
    }
}

pub  fn demux_dual_index(sample_indices_fnames: HashMap<DualIndex, (String, String)>, undetermined_fname: (String,String), i1_list: Vec<String>, i2_list: Vec<String>, r1_list: Vec<String>, r2_list: Vec<String>) {
    let i1_iter = crate::io::fastq_list_iter(&i1_list);
    let i2_iter = crate::io::fastq_list_iter(&i2_list);
    let r1_iter = crate::io::fastq_list_iter(&r1_list);
    let r2_iter = crate::io::fastq_list_iter(&r2_list);

    let empty_index = DualIndex("".to_string(), "".to_string());

    let mut writers: HashMap<DualIndex, (Box<dyn Write>, Box<dyn Write>)> = HashMap::new();
    for (ix,(fname_r1, fname_r2)) in sample_indices_fnames.iter() {
        let encoder_r1 = BufWriter::new(
            bgzf::Writer::from_path_with_level(fname_r1, CompressionLevel::Fastest).unwrap()
        );
        let encoder_r2 = BufWriter::new(
            bgzf::Writer::from_path_with_level(fname_r2, CompressionLevel::Fastest).unwrap()
        );        
        writers.insert(ix.clone(), (Box::new(encoder_r1), Box::new(encoder_r2)));
    }
    // add the writer for unassigned
    let encoder_r1 = BufWriter::new(
        bgzf::Writer::from_path_with_level(undetermined_fname.0, CompressionLevel::Fastest).unwrap()
    );
    let encoder_r2 = BufWriter::new(
        bgzf::Writer::from_path_with_level(undetermined_fname.1, CompressionLevel::Fastest).unwrap()
    );    
    writers.insert(empty_index.clone(), (Box::new(encoder_r1), Box::new(encoder_r2)));


    let pbar = get_spinner();
    for (counter, (i1, i2, r1, r2)) in izip!(i1_iter, i2_iter, r1_iter, r2_iter).enumerate() {
        let key = DualIndex(i1.seq, i2.seq);

        let (writer_r1, writer_r2) = match writers.get_mut(&key){ // if Index not present, default to the undetermined
            Some(writer) => writer,
            None => writers.get_mut(&empty_index).unwrap()
        };
        
        write!(writer_r1, "{}", r1.to_string(), ).unwrap();
        write!(writer_r2, "{}", r2.to_string(), ).unwrap();

        if counter % 1_000_000 == 0{
            pbar.inc(1_000_000);
        }
    }
}

/// From a csv with i5,i7, R1filename, R2filename
/// 
pub fn samplesheet_to_hashmap(fname: &str) -> HashMap<DualIndex, (String, String)> {
    
    let mut sheet = HashMap::new();
    let mut rdr = csv::Reader::from_reader(BufReader::new(File::open(fname).unwrap()));
    for result in rdr.records() {
        let record = result.expect("a CSV record");

        let i1 = record.get(0).unwrap();
        let i2 = record.get(1).unwrap();
        let f1 = record.get(2).unwrap();
        let f2 = record.get(3).unwrap();

        sheet.insert(
            DualIndex(i1.to_string(), i2.to_string()), 
            (f1.to_string(), f2.to_string())
        );
    };
    sheet
}

/// From a csv with i5,i7, Prefix
pub fn samplesheet_to_hashmap_2(fname: &Path) -> HashMap<DualIndex, Samplename> {
    
    let mut sheet = HashMap::new();
    let mut rdr = csv::Reader::from_reader(BufReader::new(File::open(fname).unwrap()));
    for result in rdr.records() {
        let record = result.expect("a CSV record");

        let i1 = record.get(0).unwrap();
        let i2 = record.get(1).unwrap();
        let prefix = record.get(2).unwrap();

        sheet.insert(
            DualIndex(i1.to_string(), i2.to_string()), 
            Samplename(prefix.to_string())
        );
    };
    sheet
}