main ()
{
t_text cmds; /* Unix shell commands file */
t_text fof; /* file of file names file */
FILE *fopen (); /* file open function */
int index;
char name [ MAX_LINE ]; /* list file name */
char name2 [ MAX_LINE ]; /* file name suffix */
printf ( "This is the Script program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &fof, "What is the name of the list of file names?" );
d_strcpy ( cmds.name, "cmds" );
cmds.data = fopen ( "cmds", "w" );
/* Process the names. */
while ( fof.eof != TRUE )
{
d_strcpy ( name, fof.line );
if ( name [ d_stridx ( name, "\n" ) ] == '\n' )
name [ d_stridx ( name, "\n" ) ] = '\0';
fprintf ( cmds.data, "gb2fasta %s > %s.fasta\n", name, name );
/* Get the next name. */
get_line ( &fof );
} /* while */
fclose ( cmds.data );
fclose ( fof.data );
} /* main */
main ()
{
long end; /* end of DNA sequence segment */
char header [ MAX_LINE ]; /* FASTA file format header line */
t_text in; /* input DNA sequence file */
int index; /* commands files index */
t_text library; /* library of DNA sequences */
t_text names; /* file of sequence names file */
t_seq seq; /* DNA sequence */
long start; /* start of DNA sequence segment */
int version; /* DNA segment number */
char version_str [ MAX_LINE ]; /* ascii version number */
FILE *fopen (); /* file open function */
printf ( "This is the Sequence files --> Fasta format program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &names, "What is the list of sequences file name?" );
/* Open the DNA library output file. */
d_strcpy ( library.name, names.name );
library.name [ d_stridx ( library.name, "\n" ) ] = '\0';
library.name [ d_stridx ( library.name, "." ) ] = '\0';
d_strcat ( library.name, ".Library" );
library.data = fopen ( library.name, "w" );
/* Process the sequences. */
while ( names.eof != TRUE )
{
/* Open the sequence output file. */
d_strcpy ( in.name, names.line );
in.name [ d_stridx ( in.name, "\n" ) ] = '\0';
/* Open the DNA sequence file for reading. */
open_text_file ( &in );
/* Read in the DNA sequence. */
read_DNA_seq ( &in, &seq );
fclose ( in.data );
/* Set up the name of the DNA sequence file. */
names.line [ d_stridx ( names.line, "\n" ) ] = '\0';
d_strcpy ( seq.name, names.line );
seq.name [ d_stridx ( seq.name, "." ) ] = '\0';
/* Write out the library name line. */
write_fasta_name ( &library, seq.name, 1, seq.total, seq.total );
/* Write out the library DNA sequence. */
write_DNA_seq ( &seq, 0, seq.total - 1, &library );
/* Get the next name. */
get_line ( &names );
} /* while */
fclose ( library.data );
printf ( "\nEnd of DNA Sequences -> Fasta format program.\n" );
} /* main */
main ()
{
t_text fof; /* file of filenames */
t_text in; /* input DNA sequence file */
t_text repeat; /* repeat list for FATAL: errors */
t_text results; /* Summary of Blast results */
t_text trace; /* trace report */
FILE *fopen (); /* file open function */
printf ( "This is the Blast e-mail response output parsing program.\n\n" );
/* Open the commands file. */
results.data = fopen ( "results", "w" );
/* Open the repeat list for FATAL: errors. */
repeat.data = fopen ( "repeat", "w" );
/* Open debug trace file. */
trace.data = fopen ( "trace", "w" );
/* Prompt for the input file name. */
prompt_file ( &fof, "What is the list of sequences file name?" );
/* Process the sequences. */
while ( fof.eof != TRUE )
{
/* Open the sequence output file. */
strcpy ( in.name, fof.line );
in.name [ stridx ( in.name, "\n" ) ] = '\0';
/* Open the DNA sequence file for reading. */
open_text_file ( &in );
/* Process the BLAST results file. */
if ( fof.eof != TRUE )
process_blast ( &in, &results, &repeat, &trace );
/* Get the next file name. */
get_line ( &fof );
/* Close the BLAST results file. */
fclose ( in.data );
} /* while */
/* Close the commands file. */
fclose ( fof.data );
fclose ( results.data );
fclose ( repeat.data );
fclose ( trace.data );
printf ( "\nEnd of program.\n" );
} /* main */
main ()
{
t_text retrieve; /* NCBI retrieve mail file */
t_text sequence; /* retrieved sequence */
FILE *fopen (); /* file open function */
printf ( "This is the SWISS SPLIT program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &retrieve, "What is the retrieve file name?" );
/* Process the retrieved sequences. */
while ( retrieve.eof != TRUE )
{
/* Find the document line. */
while ( ( retrieve.line [ 0 ] != '>' ) &&
( retrieve.eof != TRUE ) )
get_line ( &retrieve );
/* Get the first line of the document. */
get_line ( &retrieve );
/* Get the LOCUS name. */
get_token ( &retrieve );
/* Open the sequence output file. */
strcpy ( sequence.name, retrieve.token );
sequence.data = fopen ( sequence.name, "w" );
if ( retrieve.eof != TRUE )
printf ( "Writing '%s'\n", sequence.name );
/* Copy the sequence file. */
while ( ( sequence.data != NULL ) &&
( retrieve.eof != TRUE ) &&
( retrieve.line [ 0 ] != '>' ) )
{
fprintf ( sequence.data, "%s", retrieve.line );
get_line ( &retrieve );
} /* while */
fclose ( sequence.data );
} /* while */
printf ( "\nEnd of SWISS SPLIT program.\n" );
} /* main */
bool MenuInstanceData::Open() {
Close();
// Open up the main data file
unique_ptr<File> menu_file(new File(create_menu_filename("mnu")));
if (!menu_file->Open(File::modeBinary | File::modeReadOnly, File::shareDenyNone)) {
// Unable to open menu
MenuSysopLog("Unable to open Menu");
return false;
}
// Read the header (control) record into memory
menu_file->Seek(0L, File::seekBegin);
menu_file->Read(&header, sizeof(MenuHeader));
// Version numbers can be checked here.
if (!CreateMenuMap(menu_file.get())) {
MenuSysopLog("Unable to create menu index.");
return false;
}
if (!CheckMenuSecurity(&header, true)) {
MenuSysopLog("< Menu Sec");
return false;
}
// Open/Rease/Close Prompt file. We use binary mode since we want the
// \r to remain on windows (and linux).
TextFile prompt_file(create_menu_filename("pro"), "rb");
if (prompt_file.IsOpen()) {
string tmp = prompt_file.ReadFileIntoString();
string::size_type end = tmp.find(".end.");
if (end != string::npos) {
prompt = tmp.substr(0, end);
} else {
prompt = tmp;
}
}
// Execute command to use on entering the menu (if any).
if (header.szScript[0]) {
InterpretCommand(this, header.szScript);
}
return true;
}
main ()
{
t_text cmds; /* Unix shell commands file */
t_text fof; /* file of file names file */
FILE *fopen (); /* file open function */
int index;
char name [ MAX_LINE ]; /* list file name */
char name2 [ MAX_LINE ]; /* file name suffix */
printf ( "This is the Script program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &fof, "What is the name of the list of file names?" );
d_strcpy ( cmds.name, "cmds" );
cmds.data = fopen ( "cmds", "w" );
fprintf ( cmds.data, "mkdir fsts\n" );
fprintf ( cmds.data, "echo Making directory fsts for results\n" );
/* Process the names. */
while ( fof.eof != TRUE )
{
d_strcpy ( name, fof.line );
if ( name [ d_stridx ( name, "\n" ) ] == '\n' )
name [ d_stridx ( name, "\n" ) ] = '\0';
fprintf ( cmds.data, "dc_template_rt -priority 9 -query %s -template ", name );
fprintf ( cmds.data, "fst_aa_na -mach hermes > fsts/%s.fst\n", name );
/* Get the next name. */
get_line ( &fof );
} /* while */
fclose ( cmds.data );
fclose ( fof.data );
} /* main */
main ()
{
t_text cmds; /* Unix shell commands file */
t_text fof; /* file of file names file */
FILE *fopen (); /* file open function */
int index;
char name [ MAX_LINE ]; /* list file name */
char name2 [ MAX_LINE ]; /* file name suffix */
printf ( "This is the GENSCAN mail Script program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &fof, "What is the name of the list of file names?" );
strcpy ( cmds.name, "cmds" );
cmds.data = fopen ( "cmds", "w" );
/* Process the names. */
while ( fof.eof != TRUE )
{
strcpy ( name, fof.line );
name [ stridx ( name, "\n" ) ] = '\0';
if ( ( fof.eof != TRUE ) && ( cmds.data != NULL ) )
{
fprintf ( cmds.data, "mail [email protected] < %s\n", name );
fprintf ( cmds.data, "echo Sending %s\n", name );
fprintf ( cmds.data, "sleep 300\n" );
fprintf ( cmds.data, "\n" );
} /* if */
/* Get the next name. */
get_line ( &fof );
} /* while */
fclose ( cmds.data );
} /* main */
main ()
{
long end; /* end of DNA sequence segment */
t_text in; /* input DNA sequence file */
long index; /* line index */
t_text trapped; /* trapped exons sequence file */
t_seq seq; /* DNA sequence */
t_text sequence; /* trapped exon sequence */
long start; /* start of DNA sequence segment */
int version; /* DNA segment number */
char version_str [ MAX_LINE ]; /* ascii version number */
FILE *fopen (); /* file open function */
printf ( "This is the Sequence files --> DNA sequence program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &trapped, "What is the list of sequences file name?" );
/* Process the sequences. */
while ( trapped.eof != TRUE )
{
/* Open the sequence output file. */
strcpy ( in.name, trapped.line );
in.name [ stridx ( in.name, "\n" ) ] = '\0';
/* Open the DNA sequence file for reading. */
open_text_file ( &in );
/* Read in the DNA sequence. */
read_DNA_seq ( &in, &seq );
fclose ( in.data );
/* printf ( "DNA length = %d\n", seq.total ); */
version = 0;
start = 0;
end = 999;
trapped.line [ stridx ( trapped.line, "\n" ) ] = '\0';
/* Segment the DNA sequence in blocks of 1000 bp. */
while ( start + MIN_SEQ < seq.total )
{
/* Truncate source name at first period. */
strcpy ( sequence.name, trapped.line );
sequence.name [ stridx ( sequence.name, "." ) ] = '\0';
strcat ( sequence.name, "." );
itoa ( version, version_str );
strcat ( sequence.name, version_str );
sequence.data = fopen ( sequence.name, "w" );
if ( ( trapped.eof != TRUE ) && ( sequence.data != NULL ) )
{
/* Check for end of sequence. */
if ( end > seq.total ) end = seq.total;
/* Write out the DNA sequence. */
write_DNA_seq ( &seq, start, end, &sequence );
fclose ( sequence.data );
version++;
start += 1000;
end += 1000;
} /* if */
} /* while */
/* Get the trapped exon name and sequence. */
get_line ( &trapped );
} /* while */
} /* main */
main ()
{
int count; /* bases printed */
long index; /* line index */
t_text trapped; /* trapped exons sequence file */
t_text sequence; /* trapped exon sequence */
FILE *fopen (); /* file open function */
printf ( "This is the Trapped_Exons->files program.\n\n" );
/* Prompt for the input file name. */
prompt_file ( &trapped, "What is the Trapped Exons file name?" );
/* Process the sequences. */
while ( trapped.eof != TRUE )
{
/* Open the sequence output file. */
strcpy ( sequence.name, trapped.token );
if ( strlen ( sequence.name ) < 2 )
sequence.data = NULL;
else
sequence.data = fopen ( sequence.name, "w" );
if ( ( trapped.eof != TRUE ) && ( sequence.data != NULL ) )
{
printf ( "%s\n", sequence.name );
/* Check for newline separator. */
if ( strlen ( trapped.line ) <= 10 )
get_line ( &trapped );
get_line ( &trapped );
/* Copy the sequence file. */
count = 0;
for ( index = 0; (index < MAX_LINE) &&
(trapped.line [ index ] != '\0'); index++ )
{
if ( ( trapped.line [ index ] != '\t' ) &&
( trapped.line [ index ] != ' ' ) )
{
fprintf ( sequence.data, "%c", trapped.line [ index ] );
count++;
} /* if */
if ( ( ( count % 50 ) == 0 ) && ( count > 1 ) )
{
fprintf ( sequence.data, "\n" );
count = 0;
} /* if */
} /* for */
fprintf ( sequence.data, "\n" );
fclose ( sequence.data );
} /* if */
/* Get the trapped exon name and sequence. */
get_line ( &trapped );
} /* while */
printf ( "\nEnd of Trapped Exons->files program.\n" );
} /* main */
