github.com/biogo/biogo@v1.0.4/seq/alignment/qalignment_example_test.go

// Copyright ©2011-2012 The bíogo Authors. All rights reserved.
// Use of this source code is governed by a BSD-style
// license that can be found in the LICENSE file.

package alignment

import (
	"fmt"

	"github.com/biogo/biogo/alphabet"
	"github.com/biogo/biogo/seq"
	"github.com/biogo/biogo/seq/linear"
	"github.com/biogo/biogo/seq/sequtils"
)

var qm, qn *QSeq

func init() {
	var err error
	qm, err = NewQSeq("example alignment",
		[]string{"seq 1", "seq 2", "seq 3"},
		[][]alphabet.QLetter{
			{{'A', 40}, {'A', 40}, {'A', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'C', 40}, {'G', 40}, {'A', 40}},
			{{'T', 40}, {'T', 40}, {'T', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'A', 40}, {'A', 40}, {'A', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'T', 40}, {'C', 40}, {'G', 40}},
			{{'T', 40}, {'T', 40}, {'T', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'T', 40}, {'C', 40}, {'C', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'A', 40}, {'G', 40}, {'T', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'G', 40}, {'A', 40}, {'A', 40}},
			{{'T', 40}, {'T', 40}, {'T', 40}},
		},
		alphabet.DNA,
		alphabet.Sanger,
		seq.DefaultQConsensus)

	if err != nil {
		panic(err)
	}
}

func ExampleNewQSeq() {
	qm, err := NewQSeq("example alignment",
		[]string{"seq 1", "seq 2", "seq 3"},
		[][]alphabet.QLetter{
			{{'A', 40}, {'A', 40}, {'A', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'C', 40}, {'G', 40}, {'A', 40}},
			{{'T', 40}, {'T', 40}, {'T', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'A', 40}, {'A', 40}, {'A', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'T', 40}, {'C', 40}, {'G', 40}},
			{{'T', 40}, {'T', 40}, {'T', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'T', 40}, {'C', 40}, {'C', 40}},
			{{'G', 40}, {'G', 40}, {'G', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'A', 40}, {'G', 40}, {'T', 40}},
			{{'C', 40}, {'C', 40}, {'C', 40}},
			{{'G', 40}, {'A', 40}, {'A', 40}},
			{{'T', 40}, {'T', 40}, {'T', 40}},
		},
		alphabet.DNA,
		alphabet.Sanger,
		seq.DefaultQConsensus)
	if err == nil {
		fmt.Printf("%-s\n\n%-s\n", qm, qm.Consensus(false))
	}

	// Output:
	// ACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCAT
	// ACGATGACGTGGCGCTCAT
	//
	// acgntgacntggcgcncat
}

func ExampleQSeq_Add() {
	fmt.Printf("%v %-s\n", qm.Rows(), qm.Consensus(false))
	qm.Add(linear.NewQSeq("example DNA",
		[]alphabet.QLetter{{'a', 40}, {'c', 39}, {'g', 40}, {'C', 38}, {'t', 35}, {'g', 20}},
		alphabet.DNA, alphabet.Sanger))
	fmt.Printf("%v %-s\n", qm.Rows(), qm.Consensus(false))
	// Output:
	// 3 acgntgacntggcgcncat
	// 4 acgctgacntggcgcncat
}

func ExampleQSeq_Clone() {
	qn = qm.Clone().(*QSeq)
	qn.Row(2).Set(3, alphabet.QLetter{L: 't', Q: 40})
	fmt.Printf("%-s\n\n%-s\n\n", qm, qm.Consensus(false))
	fmt.Printf("%-s\n\n%-s\n", qn, qn.Consensus(false))
	// Output:
	// ACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCAT
	// ACGATGACGTGGCGCTCAT
	// acgCtg-------------
	//
	// acgctgacntggcgcncat
	//
	// ACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCAT
	// ACGtTGACGTGGCGCTCAT
	// acgCtg-------------
	//
	// acgctgacntggcgcncat
}

func ExampleQSeq_Rows() {
	fmt.Println(qm.Rows())
	// Output:
	// 4
}

func ExampleQSeq_join() {
	fmt.Printf("%-s\n\n%-s\n", qn, qn.Consensus(false))
	err := sequtils.Join(qn, qm, seq.End)
	if err == nil {
		fmt.Printf("\n%-s\n\n%-s\n", qn, qn.Consensus(false))
	}
	// Output:
	// ACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCAT
	// ACGtTGACGTGGCGCTCAT
	// acgCtg-------------
	//
	// acgctgacntggcgcncat
	//
	// ACGCTGACTTGGTGCACGTACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCATACGGTGACCTGGCGCGCAT
	// ACGtTGACGTGGCGCTCATACGATGACGTGGCGCTCAT
	// acgCtg-------------acgCtg-------------
	//
	// acgctgacntggcgcncatacgctgacntggcgcncat
}

func ExampleQSeq_Len() {
	fmt.Println(qm.Len())
	// Output:
	// 19
}

func ExampleQSeq_RevComp() {
	fmt.Printf("%-s\n\n%-s\n\n", qm, qm.Consensus(false))
	qm.RevComp()
	fmt.Printf("%-s\n\n%-s\n", qm, qm.Consensus(false))
	// Output:
	// ACGCTGACTTGGTGCACGT
	// ACGGTGACCTGGCGCGCAT
	// ACGATGACGTGGCGCTCAT
	// acgCtg-------------
	//
	// acgctgacntggcgcncat
	//
	// ACGTGCACCAAGTCAGCGT
	// ATGCGCGCCAGGTCACCGT
	// ATGAGCGCCACGTCATCGT
	// -------------caGcgt
	//
	// atgngcgccangtcagcgt
}

func ExampleQSeq_stitch() {
	f := fs{
		&fe{s: -1, e: 4},
		&fe{s: 30, e: 38},
	}
	fmt.Printf("%-s\n\n%-s\n", qn, qn.Consensus(false))
	if err := sequtils.Stitch(qn, qn, f); err == nil {
		fmt.Printf("\n%-s\n\n%-s\n", qn, qn.Consensus(false))
	} else {
		fmt.Println(err)
	}
	// Output:
	// ACGCTGACTTGGTGCACGTACGTGCACCAAGTCAGCGT
	// ACGGTGACCTGGCGCGCATATGCGCGCCAGGTCACCGT
	// ACGtTGACGTGGCGCTCATATGAGCGCCACGTCATCGT
	// acgCtg--------------------------caGcgt
	//
	// acgctgacntggcgcncatatgngcgccangtcagcgt
	//
	// ACGCGTCAGCGT
	// ACGGGTCACCGT
	// ACGtGTCATCGT
	// acgC--caGcgt
	//
	// acgcgtcagcgt
}

func ExampleQSeq_truncate() {
	fmt.Printf("%-s\n\n%-s\n", qm, qm.Consensus(false))
	err := sequtils.Truncate(qm, qm, 4, 12)
	if err == nil {
		fmt.Printf("\n%-s\n\n%-s\n", qm, qm.Consensus(false))
	}
	// Output:
	// ACGTGCACCAAGTCAGCGT
	// ATGCGCGCCAGGTCACCGT
	// ATGAGCGCCACGTCATCGT
	// -------------caGcgt
	//
	// atgngcgccangtcagcgt
	//
	// GCACCAAG
	// GCGCCAGG
	// GCGCCACG
	// --------
	//
	// gcgccang
}