RNAlib-2.2.0RC0
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Various functions dealing with file formats for RNA sequences, structures, and alignments. More...
Go to the source code of this file.
Functions | |
void | vrna_structure_print_helix_list (const char *db, FILE *file) |
Print a secondary structure as helix list. More... | |
void | vrna_structure_print_ct (const char *seq, const char *db, float energy, const char *identifier, FILE *file) |
Print a secondary structure as connect table. More... | |
void | vrna_structure_print_bpseq (const char *seq, const char *db, FILE *file) |
Print a secondary structure in bpseq format. More... | |
unsigned int | vrna_read_fasta_record (char **header, char **sequence, char ***rest, FILE *file, unsigned int options) |
Get a (fasta) data set from a file or stdin. More... | |
unsigned int | read_record (char **header, char **sequence, char ***rest, unsigned int options) |
Get a data record from stdin. More... | |
Various functions dealing with file formats for RNA sequences, structures, and alignments.
void vrna_structure_print_helix_list | ( | const char * | db, |
FILE * | file | ||
) |
Print a secondary structure as helix list.
db | The structure in dot-bracket format |
file | The file handle used to print to (print defaults to 'stdout' if(file == NULL) ) |
void vrna_structure_print_ct | ( | const char * | seq, |
const char * | db, | ||
float | energy, | ||
const char * | identifier, | ||
FILE * | file | ||
) |
Print a secondary structure as connect table.
seq | The RNA sequence |
db | The structure in dot-bracket format |
energy | The free energy of the structure |
identifier | An optional identifier for the sequence |
file | The file handle used to print to (print defaults to 'stdout' if(file == NULL) ) |
void vrna_structure_print_bpseq | ( | const char * | seq, |
const char * | db, | ||
FILE * | file | ||
) |
Print a secondary structure in bpseq format.
seq | The RNA sequence |
db | The structure in dot-bracket format |
file | The file handle used to print to (print defaults to 'stdout' if(file == NULL) ) |
unsigned int vrna_read_fasta_record | ( | char ** | header, |
char ** | sequence, | ||
char *** | rest, | ||
FILE * | file, | ||
unsigned int | options | ||
) |
Get a (fasta) data set from a file or stdin.
This function may be used to obtain complete datasets from a filehandle or stdin. A dataset is always defined to contain at least a sequence. If data starts with a fasta header, i.e. a line like
>some header info
then vrna_read_fasta_record() will assume that the sequence that follows the header may span over several lines. To disable this behavior and to assign a single line to the argument 'sequence' one can pass VRNA_INPUT_NO_SPAN in the 'options' argument. If no fasta header is read in the beginning of a data block, a sequence must not span over multiple lines!
Unless the options VRNA_INPUT_NOSKIP_COMMENTS or VRNA_INPUT_NOSKIP_BLANK_LINES are passed, a sequence may be interrupted by lines starting with a comment character or empty lines.
A sequence is regarded as completely read if it was either assumed to not span over multiple lines, a secondary structure or structure constraint follows the sequence on the next line, or a new header marks the beginning of a new sequence...
All lines following the sequence (this includes comments) that do not initiate a new dataset according to the above definition are available through the line-array 'rest'. Here one can usually find the structure constraint or other information belonging to the current dataset. Filling of 'rest' may be prevented by passing VRNA_INPUT_NO_REST to the options argument.
The main purpose of this function is to be able to easily parse blocks of data in the header of a loop where all calculations for the appropriate data is done inside the loop. The loop may be then left on certain return values, e.g.:
char *id, *seq, **rest; int i; id = seq = NULL; rest = NULL; while(!(vrna_read_fasta_record(&id, &seq, &rest, NULL, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){ if(id) printf("%s\n", id); printf("%s\n", seq); if(rest) for(i=0;rest[i];i++){ printf("%s\n", rest[i]); free(rest[i]); } free(rest); free(seq); free(id); }
In the example above, the while loop will be terminated when vrna_read_fasta_record() returns either an error, EOF, or a user initiated quit request.
As long as data is read from stdin (we are passing NULL as the file pointer), the id is printed if it is available for the current block of data. The sequence will be printed in any case and if some more lines belong to the current block of data each line will be printed as well.
header | A pointer which will be set such that it points to the header of the record |
sequence | A pointer which will be set such that it points to the sequence of the record |
rest | A pointer which will be set such that it points to an array of lines which also belong to the record |
file | A file handle to read from (if NULL, this function reads from stdin) |
options | Some options which may be passed to alter the behavior of the function, use 0 for no options |
unsigned int read_record | ( | char ** | header, |
char ** | sequence, | ||
char *** | rest, | ||
unsigned int | options | ||
) |
Get a data record from stdin.