135 lines
3.7 KiB
Plaintext
135 lines
3.7 KiB
Plaintext
/* Stdfiles
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generate standard files to test readseq
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*/
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C
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#include <stdio.h>
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/* no sequence formats use chars > #126, ignore these */
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main(void)
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{
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int c;
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puts("> alphabet['!'..'~']");
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for (c = '!'; c <= '~'; c++) putc(c,stdout);
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putc('\n', stdout);
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}
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link -w -t MPST -c 'MPS ' c.o <20>
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"{Libraries}"Interface.o "{Libraries}"ToolLibs.o <20>
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"{Libraries}"Runtime.o "{CLibraries}"StdClib.o
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link.out > alphabet.orig
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C
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#include <stdio.h>
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main(void)
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{
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/* note: symbols "*" and "/" removed as terminators for various formats */
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const char *aminos = "ABCDEFGHIKLMNPQRSTVWXYZ";
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const char *primenuc = "ACGTU";
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const char *allsymbols = "_.-?<>{}[]()!@#$%^&=+;:'|`~\"\\";
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char *c, all[256];
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int count;
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strcpy(all, aminos);
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strcat(all, primenuc);
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strcat(all, allsymbols);
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puts("> nucleic/amino test");
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for (count=0; count<4; count++) {
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for (c = all; *c!=0; c++) putc(*c, stdout);
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putc('\n', stdout);
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}
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}
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link -w -t MPST -c 'MPS ' c.o <20>
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"{Libraries}"Interface.o "{Libraries}"ToolLibs.o <20>
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"{Libraries}"Runtime.o "{CLibraries}"StdClib.o
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link.out > nucleic.std
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#--------------------------
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#standards (ship w/ readseq)
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#note: not all alphabet.orig chars are expected to be passed by
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# readseq. Numbers are dropped.
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readseq -p alphabet.orig > alphabet.std
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readseq -p -C alphabet.std > upper.std
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cat alphabet.orig
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> alphabet['!'..'~']
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!"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~
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cat alphabet.std
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>alphabet['!'..'~'], 83 bases, 9429 checksum.
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!"#$%&'()*+-./:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]
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^_`abcdefghijklmnopqrstuvwxyz{|}~
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cat upper.std
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>alphabet['!'..'~'], 83 bases, 9429 checksum.
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!"#$%&'()*+-./:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]
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^_`ABCDEFGHIJKLMNOPQRSTUVWXYZ{|}~
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cat nucleic.std
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> nucleic/amino test
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ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}[]()!@#$%^&=+;:'|`~"\
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ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}[]()!@#$%^&=+;:'|`~"\
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ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}[]()!@#$%^&=+;:'|`~"\
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ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}[]()!@#$%^&=+;:'|`~"\
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readseq -p nucleic.std
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>nucleic/amino test, 228 bases, 5952 checksum.
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ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}[]()!@#$%^&=+;
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:'|`~"\ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}[]()!@#
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$%^&=+;:'|`~"\ABCDEFGHIKLMNPQRSTVWXYZACGTU_.-?<>{}
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[]()!@#$%^&=+;:'|`~"\ABCDEFGHIKLMNPQRSTVWXYZACGTU_
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.-?<>{}[]()!@#$%^&=+;:'|`~"\
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#----------------------------------
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#test for general read/write of all chars:
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readseq -p alphabet.std -otest.alpha
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diff test.alpha alphabet.std
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#test for valid toupper, general read/write:
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readseq -p -C alphabet.std -otest.upper
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diff test.upper upper.std
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#for vms, use "-C" to preserve case
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# readseq -p "-C" alphabet.std -otest.upper
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#test for multiple sequence file conversions
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# leave out gcg, raw;
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# test of long seq conversion ?
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# test of mail-header seq conversion ?
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#test for valid format conversions
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readseq -v -p -f1 nucleic.std -otest.f1
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readseq -v -p -f2 test.f1 -otest.f2
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readseq -v -p -f3 test.f2 -otest.f3
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readseq -v -p -f4 test.f3 -otest.f4
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readseq -v -p -f5 test.f4 -otest.f5
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readseq -v -p -f6 test.f5 -otest.f6
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readseq -v -p -f7 test.f6 -otest.f7
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readseq -v -p -f8 test.f7 -otest.f8
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readseq -v -p -f1 test.f8 -otest.f1b
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diff test.f1 test.f1b
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compare test.f1 test.f1b
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readseq -v -p -f13 test.f8 -otest.f13 # raw, drops name
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readseq -v -p -f9 test.f8 -otest.f9 # zuker, little used
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#readseq -v -p -f10 test.f9 -otest.f10 # olsen, input only (output=raw)
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readseq -v -p -f11 test.f8 -otest.f11 # phylip 3.2, output only
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readseq -v -p -f12 test.f8 -otest.f12 # phylip 3.3, output only
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readseq -v -p -f14 test.f8 -otest.f14 # phylip 3.4, output only
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#clean up
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rm test.<2E>
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#-----------------------------
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# some general tests
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readseq -h
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readseq
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