segul 0.23.2

An ultrafast and memory-efficient tool for phylogenomics
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

//! Contig summary writer
use std::{
    io::{Result, Write},
    path::{Path, PathBuf},
};

use crate::stats::contigs::ContigSummary;

use super::FileWriter;

const OUTPUT_SUFFIX: &str = "contig-summary";
const DEFAULT_EXTENSION: &str = "csv";

pub struct ContigSummaryWriter<'a> {
    summary: &'a [ContigSummary],
    output: &'a Path,
    prefix: Option<&'a str>,
}

impl FileWriter for ContigSummaryWriter<'_> {}

impl<'a> ContigSummaryWriter<'a> {
    pub fn new(summary: &'a [ContigSummary], output: &'a Path, prefix: Option<&'a str>) -> Self {
        Self {
            summary,
            output,
            prefix,
        }
    }

    pub fn write(&self) -> Result<()> {
        let output_path = self.create_final_output_path();
        let mut writer = self
            .create_output_file(&output_path)
            .expect("Failed writing to file");
        self.write_records(&mut writer)?;
        writer.flush()?;
        Ok(())
    }

    fn create_final_output_path(&self) -> PathBuf {
        match self.prefix {
            Some(prefix) => {
                let file_name = format!("{}_{}", prefix, OUTPUT_SUFFIX);
                self.output
                    .join(file_name)
                    .with_extension(DEFAULT_EXTENSION)
            }
            None => self
                .output
                .join(OUTPUT_SUFFIX)
                .with_extension(DEFAULT_EXTENSION),
        }
    }

    fn write_records<W: Write>(&self, writer: &mut W) -> Result<()> {
        writeln!(
            writer,
            "file_path,contig_name,\
            contig_count,base_count,nucleotide,\
            GC_content,AT_content,\
            sum,min,max,mean,median,\
            N50,N75,N90,\
            contig_750,contig_1000,contig_1500,\
            G_Count,C_Count,A_Count,T_Count"
        )?;
        for summary in self.summary {
            writeln!(
                writer,
                "{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{},{}",
                summary.file_path,
                summary.contig_name,
                summary.contig_count,
                summary.base_count,
                summary.nucleotide,
                summary.gc_content,
                summary.at_content,
                summary.stats.sum,
                summary.stats.min,
                summary.stats.max,
                summary.stats.mean,
                summary.stats.median,
                summary.nstats.n50,
                summary.nstats.n75,
                summary.nstats.n90,
                summary.contig750,
                summary.contig1000,
                summary.contig1500,
                summary.g_count,
                summary.c_count,
                summary.a_count,
                summary.t_count,
            )?;
        }

        Ok(())
    }
}