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
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

//! Partition writer module
use std::io::prelude::*;
use std::path::Path;

use anyhow::Result;

use crate::helper::types::{DataType, Partition, PartitionFmt};
use crate::writer::FileWriter;

impl FileWriter for PartWriter<'_> {}

macro_rules! write_partition {
    ($self:ident, $write_type:ident, $partition:ident, $is_codon: expr_2021) => {{
        let mut writer = $self
            .$write_type($self.fpath)
            .expect("Failed creating/appending a partition file");
        $self
            .$partition(&mut writer, $is_codon)
            .expect("Failed writing a partition file");
    }};
}

pub struct PartWriter<'a> {
    fpath: &'a Path,
    partition: &'a [Partition],
    part_fmt: &'a PartitionFmt,
    datatype: &'a DataType,
}

impl<'a> PartWriter<'a> {
    pub fn new(
        fpath: &'a Path,
        partition: &'a [Partition],
        part_fmt: &'a PartitionFmt,
        datatype: &'a DataType,
    ) -> Self {
        Self {
            fpath,
            partition,
            part_fmt,
            datatype,
        }
    }

    pub fn write_partition(&self) {
        match self.part_fmt {
            PartitionFmt::Charset => {
                write_partition!(self, append_output_file, write_part_charset, false);
            }
            PartitionFmt::CharsetCodon => {
                write_partition!(self, append_output_file, write_part_charset, true);
            }
            PartitionFmt::Nexus => {
                write_partition!(self, create_output_file, write_part_nexus, false);
            }
            PartitionFmt::NexusCodon => {
                write_partition!(self, create_output_file, write_part_nexus, true);
            }
            PartitionFmt::Raxml => {
                write_partition!(self, create_output_file, write_part_raxml, false);
            }
            PartitionFmt::RaxmlCodon => {
                write_partition!(self, create_output_file, write_part_raxml, true)
            }
        }
    }

    fn write_part_nexus<W: Write>(&self, writer: &mut W, is_codon: bool) -> Result<()> {
        writeln!(writer, "#nexus")?;
        self.write_part_charset(writer, is_codon)?;
        Ok(())
    }

    fn write_part_raxml<W: Write>(&self, writer: &mut W, is_codon: bool) -> Result<()> {
        let dtype = if DataType::Dna == *self.datatype {
            "DNA, "
        } else {
            ""
        };
        self.partition.iter().for_each(|part| {
            if is_codon {
                self.write_raxml_codon(writer, part, dtype).unwrap();
            } else {
                writeln!(
                    writer,
                    "{}{} = {}-{}",
                    dtype, part.gene, part.start, part.end
                )
                .expect("Failed writing a partition file");
            }
        });
        writer.flush()?;
        Ok(())
    }

    fn write_part_charset<W: Write>(&self, writer: &mut W, is_codon: bool) -> Result<()> {
        writeln!(writer, "begin sets;")?;
        self.partition.iter().for_each(|part| {
            if is_codon {
                self.write_nex_codon(writer, part).unwrap();
            } else {
                writeln!(
                    writer,
                    "charset {} = {}-{};",
                    self.get_gene_name(&part.gene),
                    part.start,
                    part.end
                )
                .unwrap();
            }
        });
        writeln!(writer, "end;")?;
        writer.flush()?;
        Ok(())
    }

    fn get_gene_name(&self, name: &str) -> String {
        if name.contains('-') {
            format!("'{}'", name)
        } else {
            name.to_string()
        }
    }

    fn write_raxml_codon<W: Write>(
        &self,
        writer: &mut W,
        part: &Partition,
        dtype: &str,
    ) -> Result<()> {
        writeln!(
            writer,
            "{}{}_Subset1 = {}-{}\\3",
            dtype, part.gene, part.start, part.end
        )?;
        writeln!(
            writer,
            "{}{}_Subset2 = {}-{}\\3",
            dtype,
            part.gene,
            part.start + 1,
            part.end
        )?;
        writeln!(
            writer,
            "{}{}_Subset3 = {}-{}\\3",
            dtype,
            part.gene,
            part.start + 2,
            part.end
        )?;

        Ok(())
    }

    fn write_nex_codon<W: Write>(&self, writer: &mut W, part: &Partition) -> Result<()> {
        writeln!(
            writer,
            "charset {}_Subset1 = {}-{}\\3;",
            part.gene, part.start, part.end
        )?;
        writeln!(
            writer,
            "charset {}_Subset2 = {}-{}\\3;",
            part.gene,
            part.start + 1,
            part.end
        )?;
        writeln!(
            writer,
            "charset {}_Subset3 = {}-{}\\3;",
            part.gene,
            part.start + 2,
            part.end
        )?;

        Ok(())
    }
}