JPRED-2 Add sources of all binaries (except alscript) to Git

[jpred.git] / sources / readseq / Stdfiles

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