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-rw-r--r--sys/libbio/test.c283
1 files changed, 0 insertions, 283 deletions
diff --git a/sys/libbio/test.c b/sys/libbio/test.c
deleted file mode 100644
index 9926764..0000000
--- a/sys/libbio/test.c
+++ /dev/null
@@ -1,283 +0,0 @@
-#include <u.h>
-#include <libn.h>
-#include <libbio.h>
-
-#include <time.h>
-
-// -----------------------------------------------------------------------
-// Global data
-
-static byte *SEQ[] = {
-"GGCGGCTTCGGTGCGCTGTGTGCATTGCCGCAAAAATATCGTGAACCCGTGCTGGTTTCCGGCACTGACGGCGTAGGTAC"
-"CAAGCTGCGTCTGGCAATGGACTTAAAACGTCACGACACCATTGGTATTGATCTGGTCGCCATGTGCGTTAATGACCTGG"
-"TGGTGCAAGGTGCGGAACCGCTGTTTTTCCTCGACTATTACGCAACCGGAAAACTGGATGTTGATACCGCTTCAGCGGTG"
-"ATCAGCGGCATTGCGGAAGGTTGTCTGCAATCGGGCTGTTCTCTGGTGGGTGGCGAAACGGCAGAAATGCCGGGGATGTA"
-"TCACGGTGAAGATTACGATGTCGCGGGTTTCTGCGTGGGCGTGGTAGAAAAATCAGAAATCATCGACGGCTCTAAAGTCA"
-"GCGACGGCGATGTGCTGATTGCACTCGGTTCCAGCGGTCCGCACTCGAACGGTTATTCGCTGGTGCGCAAAATTCTTGAA"
-"GTCAGCGGTTGTGATCCGCAAACCACCGAACTTGATGGTAAGCCATTAGCCGATCATCTGCTGGCACCGACCCGCATTTA"
-"CGTGAAGTCAGTGCTGGAGTTGATTGAAAAGGTCGATGTGCATGCCATTGCGCACCTGACCGGCGGCGGCTTCTGGGAAA"
-"ACATTCCGCGCGTATTGCCAGATAATACCCAGGCAGTGATTGATGAATCTTCCTGGCAGTGGCCGGAAGTGTTCAACTGG"
-"CTGCAAACGGCAGGTAACGTTGAGCGCCATGAAATGTATCGCACCTTCAACTGCGGCGTCGGGATGATTATCGCCCTGCC"
-"TGCTCCGGAAGTGGACAAAGCCCTCGCCCTGCTCAATGCCAACGGTGAAAACGCGTGGAAAATCGGTATCATCAAAGCCT"
-"CTGATTCCGAACAACGCGTGGTTATCGAATAATGAATATTGTGGTGCTTATTTCCGGCAACGGAAGTAATTTACAGGCAA"
-"TTATTGACGCCTGTAAAACCAACAAAATTAAAGGCACCGTACGGGCAGTTTTCAGCAATAAGGCCGACGCGTTCGGCCTT"
-"GAACGCGCCCGCCAGGCGGGTATTGCAACGCATACGCTCATCGCCAGCGCGTTTGACAGTCGTGAAGCCTATGACCGGGA"
-"GTTGATTCATGAAATCGACATGTACGCACCCGATGTGGTCGTGCTGGCTGGTTTTATGCGCATTCTCAGCCCGGCGTTTG"
-"TCTCCCACTATGCCGGGCGTTTGCTGAACATTCACCCTTCTCTGCTGCCGAAATATCCCGGATTACACACCCATCGTCAA"
-"GCGCTGGAAAATGGCGATGAAGAGCACGGTACATCGGTGCATTTCGTCACCGATGAACTGGACGGTGGCCCGGTTATTTT"
-"ACAGGCGAAAGTCCCGGTATTTGCTGGTGATACGGAAGATGACGTCACCGCCCGCGTGCAAACCCAGGAACACGCCATTT"
-"ATCCACTGGTGATTAGCTGGTTTGCCGATGGTCGTCTGAAAATGCACGAAAACGCCGCGTGGCTGGATGGTCAACGTCTG"
-"CCGCCGCAGGGCTACGCTGCCGACGAGTAATGCCCCCGTAGTTAAAGCGCCAGCTCTGCCGCTGGCGTTTTTCAATTCAC"
-"CTGTAAATCGCAAGCTCCAGCAGTTTTTTTCCCCCTTTTCTGGCATAGTTGGACATCTGCCAATATTGCTCGCCATAATA"
-"TCCAGGCAGTGTCCCGTGAATAAAACGGAGTAAAAGTGGTAATGGGTCAGGAAAAGCTATACATCGAAAAAGAGCTCAGT"
-"TGGTTATCGTTCAATGAACGCGTGCTTCAGGAAGCGGCGGACAAATCTAACCCGCTGATTGAAAGGATGCGTTTCCTGGG"
-"GATCTATTCCAATAACCTTGATGAGTTCTATAAAGTCCGCTTCGCTGAACTGAAGCGACGCATCATTATTAGCGAAGAAC"
-"AAGGCTCCAACTCTCATTCCCGCCATTTACTGGGCAAAATTCAGTCCCGGGTGCTGAAAGCCGATCAGGAATTCGACGGC"
-"CTCTACAACGAGCTATTGCTGGAGATGGCGCGCAACCAGATCTTCCTGATTAATGAACGCCAGCTCTCCGTCAATCAACA"
-"AAACTGGCTGCGTCATTATTTTAAGCAGTATCTGCGTCAGCACATTACGCCGATTTTAATCAATCCTGACACTGACTTAG"
-"TGCAGTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTTCTGGAG"
-"ATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGA"
-"TAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGA"
-"TGACCCGCGATGCCGAATACGATTTAGTGCATGAGATGGAAGCCAGCCTGATGGAGTTGATGTCTTCCAGTCTCAAGCAG"
-"CGTTTAACTGCTGAGCCGGTGCGTTTTGTTTATCAGCGCGATATGCCCAATGCGCTGGTTGAAGTTTTACGCGAAAAACT",
-
-"GGCGGCTTCGGTGCGCTGTGTGCATTGCCGCAAAAATATCGTGAACCCGTGCTGGTTTCCGGCACTGACGGCGTAAATAC"
-"CAAGCTGCGTCTGGCAATGGACTTAAAACGTCACGACACCATTGGTATTGATCTGGTCGCCATGTGCGTTAATGACCTGG"
-"TGGTGCAAGGTGCGGAACCGCTGTTTTTCCTCGACTATTACGCACCGGAAAACTGGATGTTGATACCGCTTCAGCGGTG"
-"ATCAGCGGCATTGCGGAAGGTTGTCTGCAATCGGGCTGTTCTCTGGTGGGTGGCGAAACGGCAGAAATGCCGGGGATGTA"
-"TCACGGTGAAGATTACGATGTCGCGGGTTTCTGCGTGGGCGTGGTAGAAAAATCAGAAATCATCGACGGCAAAGTCA"
-"GCGACGGCGATGTGCTGATTGCACTCGGTTCCAGCGGTCCGCACTCGAACGGTTATTCGCTGGTGCGCAAAATTCTTGAA"
-"GTCAGCGGTTGTGATCCGCAAACCACCGAACTTGATGGTAAGCCATTAGCCGATCATCTGCTGGCACCGACCCGCATTTA"
-"ACATTCCGCGCGTATTGCCAGATAATACCCAGGCAGTGATTGATGAATCTTCCTGGCAGTGGCCGGAAGTGTTCAACTGG"
-"CTGCAAACGGCAGGTAACGTTGAGCGCCATGAAATGTATCGCACCTTCAACTGCGGCGTCGGGATGATTATCCCCTGCC"
-"TGCTCCGGAAGTGGACAAAGCCCTCGCCCTGCTCAATGCCAACGGTGAAAACGCGTGGAAAATCGGTATCATCAAAGCCT"
-"CTGATTCCGAACAACGCGTGGTTATCGAATAATGAATATTGTGTGCTTATTTCCGGCAACGGAAGTAATTTACAGGCAA"
-"TTATTGACGCCTGTAAAACCAACAAAATTAAAGGCACCGTACGGGCAGTTTTCAGCAATAAGGCCGACGCGCGGCCTT"
-"GAACGCGCCCGCCAGGCGGGTATTGCAACGCATACGCTCATCGCCAGCGCGTTTGACAGTCGTGAAGCCTATGACCGGGA"
-"GTTGATTCATGAAATCGACATGTACGCACCCGATGTGGTCGTGCTGGCTGGTTTTATGCGCATTCTCAGCCCGGCGTTTG"
-"TCTCCCACTATGCCGGGCGTTTGCTGAACATTCACCCTTCTCTGCTGCCGAAATATCCCGGATTACACACCCATCGTCAA"
-"GCGCTGGAAAATGGCGATGAAGAGCACGGTACATCGGGCATTTCGTCACCGATGAACTGGACGGTGGCCCGGTTATTTT"
-"ACAGTCGAAAGTCCCGGTATTTGCTGGTGATACGGAAGATGACGTCACCGCCCGCGTGCAAACCCAGGAACACGCCATTT"
-"ATCCTCTGGTGATTAGCTGGTTTGCCGATGGTCGTCTGAAAATGCACGAAAACGCCGCGTGGCTGGATGGTCAACGTCTG"
-"CCGCTGCAGGGCTACGCTGCCGACGAGTAATGCCCCCGTAGTTAAAGCGCCAGCTCTGCCGCTGGCGTTTTTCAATTCAC"
-"CTGTTAATCGCAAGCTCCAGCAGCCCCCCCCCCCCTTTTCTGCATAGTTGGACATCTGCCAATATTGCTCGCCATAATA"
-"TCCATGCAGTGTCCCGTGAATAAAACGGAGTAAAAGTGGTAATGGGTCAGGAAAAGCTATACATAAAAAGAGCTCAGT"
-"TGGTTATCGTTCAATGAACGCGTGCTTCAGGAAGCGGCGGACAAATCTAACCCGCTGATTGAAAGGATGCGTTTCCTGGG"
-"GATCTATTCCAATAACCTTGATGAGTTCTATAAAGTCCGCTTCGCTGAACTGAAGCGACGCATTATTAGCGAAGAAC"
-"AAGGTTCCAACTCTCATTCCCGCCATTTACTGGGAAAATTCAGTCCCGGGTGCTGAAAGCCGATCAGGAATTCGACGGC"
-"CTCTTCAACGAGCTATTGCTGGAGATGGCGCGCAACCAGATCTTCCTGATTAATGAACGCCAGCTCTCCGTCAATCAACA"
-"AAACTGGCTGCGTCATTATTTTAAGCAGTATCTGCGTCAGCACATTACGCCGATTTTAATCAATCCTGACACTGACTTAG"
-"TGCATTTCCTGAAAGATGATTACACCTATCTGGCGGTGGAAATTATCCGTGGCGATACCATCCGTTACGCGCTTCTGGAG"
-"ATCCCATCAGATAAAGTGCCGCGCTTTGTGAATTTACCGCAGAAGCGCCGCGTCGACGCAAGCCGATGATTCTTCTGGA"
-"TAACATTCTGCGTTACTGCCTTGATGATATTTTCAAAGGCTTCTTTGATTATGACGCGCTGAATGCCTATTCAATGAAGA"
-"TGACCCGCGATGCCGAATACGATTTAGTGCATGAGATGGAAGCCAGCCTGATGGAGTTGATGTCTTCCAGTCTCAAGCAG"
-"CGTTTAACTGCTGAGCCGGTGCGTTTTGTTTATCGCGCGATATGCCCAATGCGCTGGTTGAAGTTTTACGCGAAAAACT",
-};
-
-
-static
-int
-my_read(Stream *s, void *buf, int n)
-{
- return io·read(s, 1, n, buf);
-}
-
-// -----------------------------------------------------------------------
-// Point of entry for testing
-
-error
-test·newick()
-{
- error err;
- bio·Tree t;
- mem·Arena *heap;
- Stream *fd[2];
-
- io·Peeker rdr;
- io·Putter wtr;
-
- bio·Node **end, **it, **list;
-
- heap = mem·makearena(mem·sys, nil);
- rdr = (io·Peeker){.get = (byte (*)(void *))io·getbyte, .unget = (error (*)(void *, byte))io·ungetbyte};
- wtr = (io·Putter){.put = (error (*)(void *, byte))io·putbyte, .putstr = (int (*)(void *, string))io·putstring};
-
- fd[0] = io·open("/home/nolln/root/data/test/zika.nwk", "r");
- fd[1] = io·open("/home/nolln/root/data/test/zika.proc.nwk", "w");
-
- t.h = heap;
- t.heap = (mem·Allocator){ .alloc = (void *(*)(void *, uint, ulong))mem·arenaalloc, .free = nil, };
-
- if (err = bio·readnewick(rdr, fd[0], &t), err) {
- errorf("failed to read newick");
- return 1;
- }
- printf("number of children: %d\n", t.root->nchild);
-
- phylo·ladderize(t.root);
-
- list = mem·arenaalloc(heap, t.nleaf, sizeof(**list));
- phylo·getleafs(t, list);
- for (it = list, end = list + t.nleaf; it != end; ++it) {
- printf("Leaf '%s'\n", (*it)->name);
- }
-
- bio·Node *path[100];
- // phylo·diameter(t, path);
-
- printf("Loaded tree with %d leafs and %d nodes\n", t.nleaf, t.root->nnode);
- err = bio·writenewick(t, wtr, fd[1]);
-
- io·flush(fd[1]);
-
- io·close(fd[0]);
- io·close(fd[1]);
-
- mem·freearena(heap);
- return 0;
-}
-
-error
-test·fasta()
-{
- error err;
- Stream *fd;
-
- bio·Seq seq;
- bio·FastaReader *rdr;
-
- clock_t t;
-
- fd = io·open("/home/nolln/root/data/test/zika.fa", "r");
-
- /* Benchmark against Heng */
-#if 0
- int n, slen;
- kseq_t *kseq;
-
- t = clock();
- kseq = kseq_init(fd);
- while (kseq_read(kseq) >= 0) {
- ++n, slen += kseq->seq.l;
- }
- t = clock() - t;
- printf("heng's code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
-
- kseq_destroy(kseq);
-
- io·seek(fd, 0, seek·set);
-#endif
-
- rdr = bio·openfasta((io·Reader){.read = (int (*)(void *, int, int, void *))io·read}, fd, mem·sys, nil);
-
- t = clock();
- err = 0;
- while (!err) {
- err = bio·readfasta(rdr, &seq);
- }
- t = clock() - t;
- printf("nick's code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
- bio·closefasta(rdr);
-
-
- io·close(fd);
- return err <= 0 ? 0 : 1;
-}
-
-#define asrdr(x) (int (*)(void *, int, int, void *))(x)
-error
-test·fastq()
-{
- error err;
- Stream *fd;
-
- bio·Seq seq;
- bio·FastqReader *rdr;
-
- clock_t t;
-
- fd = io·open("/home/nolln/root/data/test/eg.fq", "r");
-
- rdr = bio·openfastq((io·Reader){.read = asrdr(io·read)}, fd, mem·sys, nil);
-
- t = clock();
- err = 0;
- while (!err) {
- err = bio·readfastq(rdr, &seq);
- }
- t = clock() - t;
- printf("nick's fastq code took %f ms to execute\n", 1000.*t/CLOCKS_PER_SEC);
- bio·closefastq(rdr);
-
-
- io·close(fd);
- return err <= 0 ? 0 : 1;
-}
-
-error
-test·align()
-{
- double f;
- error err;
- int i, l, n;
-
- uint64 mem[aln·N][arrlen(SEQ)][aln·L];
- uint64 *phi[aln·N];
- int loc[aln·N][arrlen(SEQ)][aln·L];
- int *pos[aln·N];
-
- for (i = 0; i < arrlen(SEQ); i++) {
- for (n = 0; n < aln·N; n++) {
- phi[n] = mem[n][i];
- pos[n] = loc[n][i];
- }
-
- err = aln·sketch(SEQ[i], aln·L, phi, pos);
- }
-
- f = 0;
- for (n = 0; n < aln·N; n++) {
- aln·sort(arrlen(SEQ), aln·L, (uint64*)mem[n]);
-
- if (!memcmp(mem[n][0], mem[n][1], sizeof(uint64)*aln·L)) {
- f += 1.;
- printf("True : ");
- } else {
- printf("False: ");
- }
- for (i = 0; i < arrlen(SEQ); i++) {
- printf("[");
- for (l = 0; l < aln·L; l++) {
- printf("%lu,", mem[n][i][l]);
- }
- printf("]");
- if (i == 0) printf(" ~ ");
- }
- printf("\n");
- }
-
- printf("Fraction hits %f\n", f/aln·N);
- return err;
-
-}
-
-error
-main()
-{
- error err;
-
- if (err = test·newick(), err) {
- errorf("test fail: newick");
- }
-
-#if 0
- if (err = test·fasta(), err) {
- errorf("test fail: fasta");
- }
-
- if (err = test·fastq(), err) {
- errorf("test fail: fastq");
- }
-#endif
-}
-
generated by cgit v1.2.1 (git 2.18.0) at 2024-06-29 11:13:46 +0000