github.com/biogo/biogo@v1.0.4/seq/linear/seq_example_test.go (about)

     1  // Copyright ©2011-2012 The bíogo Authors. All rights reserved.
     2  // Use of this source code is governed by a BSD-style
     3  // license that can be found in the LICENSE file.
     4  
     5  package linear
     6  
     7  import (
     8  	"fmt"
     9  	"strings"
    10  
    11  	"github.com/biogo/biogo/alphabet"
    12  	"github.com/biogo/biogo/feat"
    13  	"github.com/biogo/biogo/seq"
    14  	"github.com/biogo/biogo/seq/sequtils"
    15  )
    16  
    17  func ExampleNewSeq() {
    18  	d := NewSeq("example DNA", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA)
    19  	fmt.Printf("%-s %v\n", d, d.Moltype())
    20  	// Output:
    21  	// ACGCTGACTTGGTGCACGT DNA
    22  }
    23  
    24  func ExampleSeq_Validate() {
    25  	r := NewSeq("example RNA", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.RNA)
    26  	fmt.Printf("%-s %v\n", r, r.Moltype())
    27  	if ok, pos := r.Validate(); ok {
    28  		fmt.Println("valid RNA")
    29  	} else {
    30  		fmt.Println(strings.Repeat(" ", pos-1), "^ first invalid RNA position")
    31  	}
    32  	// Output:
    33  	// ACGCTGACTTGGTGCACGT RNA
    34  	//     ^ first invalid RNA position
    35  }
    36  
    37  func ExampleSeq_truncate_a() {
    38  	s := NewSeq("example DNA", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA)
    39  	fmt.Printf("%-s\n", s)
    40  	if err := sequtils.Truncate(s, s, 5, 12); err == nil {
    41  		fmt.Printf("%-s\n", s)
    42  	}
    43  	// Output:
    44  	// ACGCTGACTTGGTGCACGT
    45  	// GACTTGG
    46  }
    47  
    48  func ExampleSeq_truncate_b() {
    49  	var s *Seq
    50  
    51  	s = NewSeq("example DNA", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA)
    52  	s.Conform = feat.Circular
    53  	fmt.Printf("%-s Conformation = %v\n", s, s.Conformation())
    54  	if err := sequtils.Truncate(s, s, 12, 5); err == nil {
    55  		fmt.Printf("%-s Conformation = %v\n", s, s.Conformation())
    56  	} else {
    57  		fmt.Println("Error:", err)
    58  	}
    59  
    60  	s = NewSeq("example DNA", []alphabet.Letter("ACGCTGACTTGGTGCACGT"), alphabet.DNA)
    61  	fmt.Printf("%-s Conformation = %v\n", s, s.Conformation())
    62  	if err := sequtils.Truncate(s, s, 12, 5); err == nil {
    63  		fmt.Printf("%-s Conformation = %v\n", s, s.Conformation())
    64  	} else {
    65  		fmt.Println("Error:", err)
    66  	}
    67  	// Output:
    68  	// ACGCTGACTTGGTGCACGT Conformation = circular
    69  	// TGCACGTACGCT Conformation = linear
    70  	// ACGCTGACTTGGTGCACGT Conformation = linear
    71  	// Error: sequtils: start position greater than end position for linear sequence
    72  }
    73  
    74  func ExampleSeq_RevComp() {
    75  	s := NewSeq("example DNA", []alphabet.Letter("ATGCtGACTTGGTGCACGT"), alphabet.DNA)
    76  	fmt.Printf("%-s\n", s)
    77  	s.RevComp()
    78  	fmt.Printf("%-s\n", s)
    79  	// Output:
    80  	// ATGCtGACTTGGTGCACGT
    81  	// ACGTGCACCAAGTCaGCAT
    82  }
    83  
    84  func ExampleSeq_join() {
    85  	var s1, s2 *Seq
    86  
    87  	s1 = NewSeq("a", []alphabet.Letter("agctgtgctga"), alphabet.DNA)
    88  	s2 = NewSeq("b", []alphabet.Letter("CGTGCAGTCATGAGTGA"), alphabet.DNA)
    89  	fmt.Printf("%-s %-s\n", s1, s2)
    90  	if err := sequtils.Join(s1, s2, seq.Start); err == nil {
    91  		fmt.Printf("%-s\n", s1)
    92  	}
    93  
    94  	s1 = NewSeq("a", []alphabet.Letter("agctgtgctga"), alphabet.DNA)
    95  	s2 = NewSeq("b", []alphabet.Letter("CGTGCAGTCATGAGTGA"), alphabet.DNA)
    96  	if err := sequtils.Join(s1, s2, seq.End); err == nil {
    97  		fmt.Printf("%-s\n", s1)
    98  	}
    99  	// Output:
   100  	// agctgtgctga CGTGCAGTCATGAGTGA
   101  	// CGTGCAGTCATGAGTGAagctgtgctga
   102  	// agctgtgctgaCGTGCAGTCATGAGTGA
   103  }
   104  
   105  type fe struct {
   106  	s, e int
   107  	st   seq.Strand
   108  	feat.Feature
   109  }
   110  
   111  func (f fe) Start() int                    { return f.s }
   112  func (f fe) End() int                      { return f.e }
   113  func (f fe) Len() int                      { return f.e - f.s }
   114  func (f fe) Orientation() feat.Orientation { return feat.Orientation(f.st) }
   115  
   116  type fs []feat.Feature
   117  
   118  func (f fs) Features() []feat.Feature { return []feat.Feature(f) }
   119  
   120  func ExampleSeq_stitch() {
   121  	s := NewSeq("example DNA", []alphabet.Letter("aAGTATAAgtcagtgcagtgtctggcagTGCTCGTGCgtagtgaagtagGGTTAGTTTa"), alphabet.DNA)
   122  	f := fs{
   123  		fe{s: 1, e: 8},
   124  		fe{s: 28, e: 37},
   125  		fe{s: 49, e: s.Len() - 1},
   126  	}
   127  	fmt.Printf("%-s\n", s)
   128  	if err := sequtils.Stitch(s, s, f); err == nil {
   129  		fmt.Printf("%-s\n", s)
   130  	}
   131  	// Output:
   132  	// aAGTATAAgtcagtgcagtgtctggcagTGCTCGTGCgtagtgaagtagGGTTAGTTTa
   133  	// AGTATAATGCTCGTGCGGTTAGTTT
   134  }
   135  
   136  func ExampleSeq_compose() {
   137  	s := NewSeq("example DNA", []alphabet.Letter("aAGTATAAgtcagtgcagtgtctggcag<TS>gtagtgaagtagggttagttta"), alphabet.DNA)
   138  	f := fs{
   139  		fe{s: 0, e: 32},
   140  		fe{s: 1, e: 8, st: -1},
   141  		fe{s: 28, e: s.Len() - 1},
   142  	}
   143  	fmt.Printf("%-s\n", s)
   144  	if err := sequtils.Compose(s, s, f); err == nil {
   145  		fmt.Printf("%-s\n", s)
   146  	}
   147  	// Output:
   148  	// aAGTATAAgtcagtgcagtgtctggcag<TS>gtagtgaagtagggttagttta
   149  	// aAGTATAAgtcagtgcagtgtctggcag<TS>TTATACT<TS>gtagtgaagtagggttagttt
   150  }