main_test.go

package main

import (
	"context"
	"fmt"
	"log"
	"testing"

	"github.com/superphy/prairiedog/kmers"
	"github.com/superphy/prairiedog/pangenome"
	"github.com/superphy/prairiedog/utils"
)

func BenchmarkNew(*testing.B) {
	pangenome.NewGraph()
}
func ExampleKmers() {
	km := kmers.New("testdata/172.fa")
	header, _ := km.Next()
	fmt.Println(header)
	// Output: >gi|1062504329|gb|CP014670.1| Escherichia coli strain CFSAN004177, complete genome
}

func ExampleKmersNext() {
	km := kmers.New("testdata/172.fa")
	header, kmer := km.Next()
	fmt.Println(header)
	fmt.Println(kmer)
	header, kmer = km.Next()
	fmt.Println(header)
	fmt.Println(kmer)
	// Output:
	// >gi|1062504329|gb|CP014670.1| Escherichia coli strain CFSAN004177, complete genome
	// TCGCTTTCGTT
	// >gi|1062504329|gb|CP014670.1| Escherichia coli strain CFSAN004177, complete genome
	// CGCTTTCGTTC
}

func ExampleKmersIndex() {
	km := kmers.New("testdata/ECI-2866_lcl.fasta")
	fmt.Println(len(km.Headers))
	fmt.Println(len(km.Sequences))
	fmt.Println(len(km.Sequences) == len(km.Headers))
	// Note: index starts at 0.
	fmt.Println(km.Headers[0])
	fmt.Println(km.Headers[1])
	fmt.Println(km.Sequences[0])
	fmt.Println(km.Sequences[1])
	n := len(km.Sequences[0])
	fmt.Println(n)
	fmt.Println(string(km.Sequences[0][n-1]))
	fmt.Println(string(km.Sequences[0][n-2]))
	fmt.Println(string(km.Sequences[0][n-3]))
	// Output:
	// 297
	// 297
	// true
	// >lcl|ECI-2866|NODE_177_length_532_cov_12.8938_ID_353
	// >lcl|ECI-2866|NODE_222_length_438_cov_0.710611_ID_443
	// AACGCGCACTGACGTGAGGCCAGCGTACAGGCCGGATTATCGACATATTTCTGACAGGTGCCGTTATCTGCGGACTGTGTGACATATTTATCCCGGTATGCCCAGCACGCCTGTGTGATGCTCCAGGGTTTACCTTCCATCACACCTGTTTTCGTCCCCCCCGGCTCTGAACACTCAGTACCTTTCAGCACGCCATCCGCTTTATTAAACGGACAACTCTCCACCCACTCCACCCGTGGAACCCATTCCTTATCACGGACCTTCATCCTGAGTTTCAGCGTAAAGGTGGAAGCACCACTGACAAGCGATTCATAGACCATCCTGTCACCATTCCCGTGCGGGAGGCAATTACCGTTTGCAGTACAGCCACTACCGATCAGAACCTGCCCCTGTGTGACAGAAAACCCGGAGGGCACAGGTATGGTGAAAGTCCCGCTCTGTCCTGTAACCAGTTGCACATTAAAGGCTGTGTTCATAAAGTCGTAACGGGAGTTAAGGAAATATAGCCCTGCATGAGCCGACAGCGAGGCAC
	// ACATCGTGCCGCATTGTTGGCAGAGGGAATTCCTTTTCATTGCTTTTATTATCCCTGTGTTAGTGAAATACTACGTTAGGGTTTGGAACACGTAAGAAAAATGGCGTTGTCAATGGGATTGTTTTTTTTTTATGCCGGTCAGATCTCAAAAACTAGGCCAGAGATCAATTCTACTTGACCTCATGACAGTTTACTGCCGCTGCTGCCGGAATCCAAATCTCGTGGTATCCTAACTCAAGGAGTCGGCATGAAGTCCATCGAAGCATATTTTCTGTTCATCAGGTATTGACTAGTGACTCTGCAAGGACAAATCACCTTACTACATCCTGGTCCATGGTGAAGTCTAGCTTTGATACCTTGAGTTGTCCATTCCCGGAAATGCACCTCCGGGCCAGGGGTGCTCGCTCTGACCTTCGTGTCCCATGGAACTTCAGCCAG
	// 532
	// C
	// A
	// C
}

// ExampleKmersIndexEnd checks end case.
func ExampleKmersIndexEnd() {
	km := kmers.New("testdata/ECI-2866_lcl.fasta")
	var header, kmer string
	h, k := km.Next()
	for ; h != ""; h, k = km.Next() {
		header, kmer = h, k
		// log.Println(header, kmer)
	}
	fmt.Println(header)
	fmt.Println(kmer)
	// Output:
	// >lcl|ECI-2866|NODE_22_length_88582_cov_33.0406_ID_43
	// TACGGATTCTT
}

// ExampleKmersIndexDiff checks last of a contig before switching.
func ExampleKmersIndexDiff() {
	km := kmers.New("testdata/GCA_900015695.1_ED647_contigs_genomic.fna")
	var header, kmer string
	h, k := km.Next()
	header, kmer = h, k
	for ; h == header; h, k = km.Next() {
		header, kmer = h, k
		// log.Println(header, kmer)
	}
	fmt.Println(header)
	fmt.Println(kmer)
	// Output:
	// >FAVS01000269.1 Escherichia coli strain ED647 genome assembly, contig: out_269, whole genome shotgun sequence
	// TACTGCTACTG
}

func ExampleNewNode() {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()

	// Make sure we're using a clean database.
	g.DropAll(contextMain)

	km := kmers.New("testdata/ECI-2523.fsa")
	_, seq := km.Next()
	_, err := g.CreateNode(seq, contextMain)
	fmt.Println(err)
	// Output:
	// <nil>
}

func ExampleGetNode() {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()

	// Make sure we're using a clean database.
	g.DropAll(contextMain)

	km := kmers.New("testdata/ECI-2523.fsa")
	_, seq := km.Next()
	uid, err := g.CreateNode(seq, contextMain)
	fmt.Println(err)
	uidRetrieved, b := g.GetNode(seq, contextMain)
	log.Println(uid)
	log.Println(uidRetrieved)
	fmt.Println(b)
	fmt.Println(uid == uidRetrieved)
	// Output:
	// <nil>
	// true
	// true
}

func ExampleNewNodes() {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()

	// Make sure we're using a clean database.
	g.DropAll(contextMain)

	km := kmers.New("testdata/ECI-2523.fsa")

	_, seq := km.Next()
	uid1, _ := g.CreateNode(seq, contextMain)
	fmt.Println(uid1)
	_, seq = km.Next()
	uid2, _ := g.CreateNode(seq, contextMain)
	fmt.Println(uid2)
	_, seq = km.Next()
	uid3, _ := g.CreateNode(seq, contextMain)
	fmt.Println(uid3)
	// TODO: Not sure why we're starting from 2.
	// Output:
	// 2
	// 3
	// 4
}

func BenchmarkNewNode(b *testing.B) {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()

	// Make sure we're using a clean database.
	g.DropAll(contextMain)

	km := kmers.New("testdata/ECI-2523.fsa")

	b.ResetTimer()
	for i := 0; i < b.N; i++ {
		_, seq := km.Next()
		g.CreateNode(seq, contextMain)
	}
}

func ExampleNewEdge() {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()
	km := kmers.New("testdata/GCA_900015695.1_ED647_contigs_genomic.fna")
	_, seq1 := km.Next()
	_, seq2 := km.Next()
	uid1, err := g.CreateNode(seq1, contextMain)
	fmt.Println(err)
	uid2, err := g.CreateNode(seq2, contextMain)
	fmt.Println(err)
	_, err = g.CreateEdge(uid1, uid2, contextMain)
	fmt.Println(err)
	// Output:
	// <nil>
	// <nil>
	// <nil>
}

func ExampleWalk() {
	_, err := utils.Walk("testdata")
	fmt.Println(err)
	// Output:
	// <nil>
}

func BenchmarkCreateAll(b *testing.B) {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	log.Println("Starting becnhmark.")
	g := pangenome.NewGraph()
	log.Println("Graph created OK.")
	defer g.Close()
	km := kmers.New("testdata/GCA_900015695.1_ED647_contigs_genomic.fna")
	log.Println("Kmers created OK.")
	b.ResetTimer()
	log.Println("Starting Node/Edge creation.")
	g.CreateAll(km, contextMain)
	log.Println("Nodes/Edges created OK.")
}

func ExampleCreateAll() {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()
	km := kmers.New("testdata/GCA_900015695.1_ED647_contigs_genomic_SHORTENED.fna")
	b, _ := g.CreateAll(km, contextMain)
	fmt.Println(b)
	// Output:
	// true
}

func ExampleSetKVInt() {
	g := pangenome.NewGraph()
	defer g.Close()
	b, _ := g.SetKVInt("apple", 1)
	fmt.Println(b)
	v, _ := g.GetKVInt("apple")
	fmt.Println(v)
	// Output:
	// true
	// 1
}

func ExampleSetKVStr() {
	g := pangenome.NewGraph()
	defer g.Close()
	b, _ := g.SetKVStr("apple", "cat")
	fmt.Println(b)
	v, _ := g.GetKVStr("apple")
	fmt.Println(v)
	// Output:
	// true
	// cat
}

func ExampleSetKVSliceUint64() {
	g := pangenome.NewGraph()
	defer g.Close()

	// Create a test slice.
	var sl []uint64
	sl = append(sl, 1)
	sl = append(sl, 2)

	b, _ := g.SetKVSliceUint64("sl", sl)
	fmt.Println(b)
	v, _ := g.GetKVSliceUint64("sl")
	fmt.Println(v)
	// Output:
	// true
	// [1 2]
}

func ExampleSetKVSliceUint64Genome() {
	contextMain, cancel := context.WithCancel(context.Background())
	defer cancel()

	g := pangenome.NewGraph()
	defer g.Close()

	// Make sure we're using a clean database.
	g.DropAll(contextMain)
	log.Println("Dropped all values in Dgraph.")

	km := kmers.New("testdata/GCA_900015695.1_ED647_contigs_genomic_SHORTENED.fna")
	log.Println("Created km OK.")

	b, _ := g.CreateAll(km, contextMain)
	log.Println("Done creating all nodes/edges.")
	fmt.Println(b)

	log.Println("Retrieving slice 1...")
	v1, _ := g.GetKVSliceUint64(">FAVS01000269.1 Escherichia coli strain ED647 genome assembly, contig: out_269, whole genome shotgun sequence")
	log.Println("Retrieving slice 2...")
	v2, _ := g.GetKVSliceUint64(">FAVS01000267.1 Escherichia coli strain ED647 genome assembly, contig: out_267, whole genome shotgun sequence")
	log.Println("Retrieving slice 3...")
	v3, _ := g.GetKVSliceUint64(">FAVS01000266.1 Escherichia coli strain ED647 genome assembly, contig: out_266, whole genome shotgun sequence")
	fmt.Println(v1)
	fmt.Println(v2)
	fmt.Println(v3)
	// Output:
	// true
	// []
	// []
	// []
}