seq_here/
info.rs

1use std::path::PathBuf;
2use bio::io::fasta;
3use bio::io::gff::GffType;
4use crate::utils;
5
6/// Define the trait for the different file types
7/// 2 ways to output the information: by file or by println
8pub trait InfoOutput {
9    fn by_file(paths: Vec<PathBuf>);
10    fn by_println(paths: Vec<PathBuf>);
11}
12
13pub struct InfoFa;
14impl InfoOutput for InfoFa {
15    fn by_file(paths: Vec<PathBuf>) {
16        info_fa(paths);
17    }
18
19    fn by_println(paths: Vec<PathBuf>) {
20        info_fa(paths);
21    }
22}
23
24pub struct InfoFq;
25impl InfoOutput for InfoFq {
26    fn by_file(paths: Vec<PathBuf>) {
27        info_fastq(paths);
28    }
29
30    fn by_println(paths: Vec<PathBuf>) {
31        info_fastq(paths);
32    }
33}
34
35pub struct InfoGff;
36impl InfoOutput for InfoGff {
37    fn by_file(paths: Vec<PathBuf>) {
38        info_gff(paths, GffType::GFF3);
39    }
40
41    fn by_println(paths: Vec<PathBuf>) {
42        info_gff(paths, GffType::GFF3);
43    }
44}
45
46
47fn info_fa(paths: Vec<PathBuf>) -> String {
48    for path in paths {
49        let reader = fasta::Reader::from_file(path).unwrap();
50        for record in reader.records() {
51            let record = record.unwrap();
52            println!("Seq Type: {}", utils::try_seq_type_seq(record.seq()).unwrap());
53            println!("ID: {}", record.id());
54            println!("Description: {}", record.desc().unwrap_or("None"));
55            println!("Sequence: {}", String::from_utf8(record.seq().to_vec()).unwrap());
56            println!("Length: {}", record.seq().len());
57            println!("GC content: {:.2}%", bio::seq_analysis::gc::gc_content(&*record.seq()));
58        }
59    }
60
61    "Done".to_string()
62    
63}
64
65
66pub fn info_fastq(paths: Vec<PathBuf>) {
67    for path in paths {
68        let reader = bio::io::fastq::Reader::from_file(path).unwrap();
69        for record in reader.records() {
70            let record = record.unwrap();
71            println!("ID: {}", record.id());
72            println!("Description: {}", record.desc().unwrap());
73            println!("Sequence: {}", String::from_utf8(record.seq().to_vec()).unwrap());
74            println!("Quality: {}", String::from_utf8(record.qual().to_vec()).unwrap());
75        }
76    }
77    
78}
79
80pub fn info_gff(paths: Vec<PathBuf>, gff_type: GffType) {
81    for path in paths {
82        let mut reader = bio::io::gff::Reader::from_file(path, gff_type).unwrap();
83        for record in reader.records() {
84            let record = record.unwrap();
85            // println!("Seqid: {}", record.seqid());
86            println!("Source: {}", record.source());
87            println!("Type: {}", record.feature_type());
88            println!("Start: {}", record.start());
89            println!("End: {}", record.end());
90            // println!("Score: {}", record.score());
91            // println!("Strand: {}", record.strand());
92            // println!("Phase: {}", record.phase());
93            println!("Attributes: {:?}", record.attributes());
94        }
95    }
96    
97}
seq_here/info.rs

seq_here/
info.rs
