twobit_test.go

// Copyright 2015 Andrew E. Bruno. All rights reserved.
// Use of this source code is governed by a BSD style
// license that can be found in the LICENSE file.

package twobit

import (
	"os"
	"testing"
)

func openTestTwoBit() (*Reader, error) {
	f, err := os.Open("test.2bit")
	if err != nil {
		return nil, err
	}

	tb, err := NewReader(f)
	if err != nil {
		return nil, err
	}

	return tb, nil
}

func TestHeader(t *testing.T) {
	tb, err := openTestTwoBit()
	if err != nil {
		t.Errorf("%s", err)
	}

	if tb.Count() != 1 {
		t.Errorf("Invalid sequence count: %d != %d", tb.Count(), 1)
	}

	names := map[string]bool{
		"ex1": false,
	}

	for name := range tb.index {
		if _, ok := names[name]; !ok {
			t.Errorf("Invalid sequence name: %s", name)
		}
		names[name] = true
	}
	for name, seen := range names {
		if !seen {
			t.Errorf("Sequence name not found in file index: %s", name)
		}
	}
}

func TestNamesLength(t *testing.T) {
	tb, err := openTestTwoBit()
	if err != nil {
		t.Errorf("%s", err)
	}

	names := tb.Names()

	if len(names) != 1 {
		t.Errorf("Invalid length of sequence names: %d != %d", len(names), 1)
	}

	if names[0] != "ex1" {
		t.Errorf("Invalid sequence name: %s != %s", names[0], "ex1")
	}

	sz, err := tb.Length("ex1")
	if err != nil {
		t.Errorf("%s", err)
	}
	if sz != 21 {
		t.Errorf("Invalid length of ex1 sequence: %d != %d", sz, 21)
	}

	sz, err = tb.LengthNoN("ex1")
	if err != nil {
		t.Errorf("%s", err)
	}
	if sz != 15 {
		t.Errorf("Invalid lengthNoN of ex1 sequence: %d != %d", sz, 15)
	}
}

func TestRead(t *testing.T) {
	tb, err := openTestTwoBit()
	if err != nil {
		t.Errorf("%s", err)
	}

	_, err = tb.Read("not-found")
	if err == nil {
		t.Errorf("Found non-existent name")
	}

	regions := map[string][]int{
		"ACTgcctttnnnNantnaCgc": []int{0, 0},
		"ACTgc":                 []int{0, 5},
		"ctttnn":                []int{5, 11},
		"tnaCgc":                []int{15, 21},
		"gc":                    []int{19, 21},
		"c":                     []int{20, 21},
	}

	for good, coords := range regions {
		seq, err := tb.ReadRange("ex1", coords[0], coords[1])
		if err != nil {
			t.Errorf("Failed to read sequence: %s", err)
		}

		if string(seq) != good {
			t.Errorf("Invalid sequence: %s != %s", seq, good)
		}
	}
}