Files and I/O#

Nucleic Acid Sequences and Structures#

Defines

VRNA_OPTION_MULTILINE#

Tell a function that an input is assumed to span several lines.

#include <ViennaRNA/io/file_formats.h>

If used as input-option a function might also be returning this state telling that it has read data from multiple lines.

VRNA_CONSTRAINT_MULTILINE#

parse multiline constraint

#include <ViennaRNA/io/file_formats.h>

Deprecated:: see vrna_extract_record_rest_structure()

VRNA_INPUT_VERBOSE#

#include <ViennaRNA/io/file_formats.h>

Functions

void vrna_file_helixlist(const char *seq, const char *db, float energy, FILE *file)#

Print a secondary structure as helix list.

#include <ViennaRNA/io/file_formats.h>

Parameters:

seq – The RNA sequence
db – The structure in dot-bracket format
energy – Free energy of the structure in kcal/mol
file – The file handle used to print to (print defaults to ‘stdout’ if(file == NULL) )

void vrna_file_connect(const char *seq, const char *db, float energy, const char *identifier, FILE *file)#

Print a secondary structure as connect table.

#include <ViennaRNA/io/file_formats.h>

Connect table file format looks like this:

* 300  ENERGY = 7.0  example
* 1 G       0    2   22    1
* 2 G       1    3   21    2
*

where the headerline is followed by 6 columns with:

Base number: index n
Base (A, C, G, T, U, X)
Index n-1 (0 if first nucleotide)
Index n+1 (0 if last nucleotide)
Number of the base to which n is paired. No pairing is indicated by 0 (zero).
Natural numbering.

Parameters:

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_file_bpseq(const char *seq, const char *db, FILE *file)#

Print a secondary structure in bpseq format.

#include <ViennaRNA/io/file_formats.h>

Parameters:

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) )

void vrna_file_json(const char *seq, const char *db, double energy, const char *identifier, FILE *file)#

Print a secondary structure in jsonformat.

#include <ViennaRNA/io/file_formats.h>

Parameters:

seq – The RNA sequence
db – The structure in dot-bracket format
energy – The free energy
identifier – An identifier for the sequence
file – The file handle used to print to (print defaults to ‘stdout’ if(file == NULL) )

unsigned int vrna_file_fasta_read_record(char **header, char **sequence, char ***rest, FILE *file, unsigned int options)#

Get a (fasta) data set from a file or stdin.

#include <ViennaRNA/io/file_formats.h>

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_file_fasta_read_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_file_fasta_read_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_file_fasta_read_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.

Note

This function will exit any program with an error message if no sequence could be read!

This function is NOT threadsafe! It uses a global variable to store information about the next data block. Do not forget to free the memory occupied by header, sequence and rest!

Parameters:

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

Returns:

A flag with information about what the function actually did read

char *vrna_extract_record_rest_structure(const char **lines, unsigned int length, unsigned int option)#

Extract a dot-bracket structure string from (multiline)character array.

#include <ViennaRNA/io/file_formats.h>

This function extracts a dot-bracket structure string from the ‘rest’ array as returned by vrna_file_fasta_read_record() and returns it. All occurences of comments within the ‘lines’ array will be skipped as long as they do not break the structure string. If no structure could be read, this function returns NULL.

See also

vrna_file_fasta_read_record()

Parameters:

lines – The (multiline) character array to be parsed
length – The assumed length of the dot-bracket string (passing a value < 1 results in no length limit)
option – Some options which may be passed to alter the behavior of the function, use 0 for no options

Pre:

The argument ‘lines’ has to be a 2-dimensional character array as obtained by vrna_file_fasta_read_record()

Returns:

The dot-bracket string read from lines or NULL

int vrna_file_SHAPE_read(const char *file_name, int length, double default_value, char *sequence, double *values)#

Read data from a given SHAPE reactivity input file.

#include <ViennaRNA/io/file_formats.h>

This function parses the informations from a given file and stores the result in the preallocated string sequence and the double array values.

Parameters:

file_name – Path to the constraints file
length – Length of the sequence (file entries exceeding this limit will cause an error)
default_value – Value for missing indices
sequence – Pointer to an array used for storing the sequence obtained from the SHAPE reactivity file
values – Pointer to an array used for storing the values obtained from the SHAPE reactivity file

double *vrna_file_doubles_read(const char *file_name, unsigned int options, size_t *values_count)#

Read double values separated by newlines from a given input file.

#include <ViennaRNA/io/file_formats.h>

This function parses an input file file_name expecting a double value per line. It then extracts all the double values and returns them as double array.

Parameters:

file_name – Path to the input file
options – Option flags to change the behavior of this function
values_count – The adress of a counter to store the total size of the returned double array

Returns:

An array of double values read from the input file

int vrna_file_connect_read_record(FILE *fp, char **id, char **sequence, char **structure, char **remainder, unsigned int options)#

#include <ViennaRNA/io/file_formats.h>

int vrna_file_RNAstrand_db_read_record(FILE *fp, char **name_p, char **sequence_p, char **structure_p, char **source_p, char **fname_p, char **id_p, unsigned int options)#

#include <ViennaRNA/io/file_formats.h>

void vrna_extract_record_rest_constraint(char **cstruc, const char **lines, unsigned int option)#

Extract a hard constraint encoded as pseudo dot-bracket string.

#include <ViennaRNA/io/file_formats.h>

Deprecated:: Use vrna_extract_record_rest_structure() instead!

Parameters:

cstruc – A pointer to a character array that is used as pseudo dot-bracket output
lines – A 2-dimensional character array with the extension lines from the FASTA input
option – The option flags that define the behavior and recognition pattern of this function

Pre:

The argument ‘lines’ has to be a 2-dimensional character array as obtained by vrna_file_fasta_read_record()

char *extract_record_rest_structure(const char **lines, unsigned int length, unsigned int option)#

#include <ViennaRNA/io/file_formats.h>

unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options)#

Get a data record from stdin.

#include <ViennaRNA/io/file_formats.h>

Deprecated:: This function is deprecated! Use vrna_file_fasta_read_record() as a replacment.

unsigned int get_multi_input_line(char **string, unsigned int options)#

#include <ViennaRNA/io/file_formats.h>

Multiple Sequence Alignments#

Defines

VRNA_FILE_FORMAT_MSA_CLUSTAL#

Option flag indicating ClustalW formatted files.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_STOCKHOLM#

Option flag indicating Stockholm 1.0 formatted files.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_FASTA#

Option flag indicating FASTA (Pearson) formatted files.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_MAF#

Option flag indicating MAF formatted files.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_MIS#

Option flag indicating most informative sequence (MIS) output.

#include <ViennaRNA/io/file_formats_msa.h>

The default reference sequence output for an alignment is simply a consensus sequence. This flag allows to write the most informative equence (MIS) instead.

See also

vrna_file_msa_write()

VRNA_FILE_FORMAT_MSA_DEFAULT#

Option flag indicating the set of default file formats.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_NOCHECK#

Option flag to disable validation of the alignment.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_UNKNOWN#

Return flag of vrna_file_msa_detect_format() to indicate unknown or malformatted alignment.

#include <ViennaRNA/io/file_formats_msa.h>

See also

vrna_file_msa_detect_format()

VRNA_FILE_FORMAT_MSA_APPEND#

Option flag indicating to append data to a multiple sequence alignment file rather than overwriting it.

#include <ViennaRNA/io/file_formats_msa.h>

See also

vrna_file_msa_write()

VRNA_FILE_FORMAT_MSA_QUIET#

Option flag to suppress unnecessary spam messages on stderr.

#include <ViennaRNA/io/file_formats_msa.h>

VRNA_FILE_FORMAT_MSA_SILENT#

Option flag to completely silence any warnings on stderr.

#include <ViennaRNA/io/file_formats_msa.h>

Functions

int vrna_file_msa_read(const char *filename, char ***names, char ***aln, char **id, char **structure, unsigned int options)#

Read a multiple sequence alignment from file.

#include <ViennaRNA/io/file_formats_msa.h>

This function reads the (first) multiple sequence alignment from an input file. The read alignment is split into the sequence id/name part and the actual sequence information and stored in memory as arrays of ids/names and sequences. If the alignment file format allows for additional information, such as an ID of the entire alignment or consensus structure information, this data is retrieved as well and made available. The options parameter allows to specify the set of alignment file formats that should be used to retrieve the data. If 0 is passed as option, the list of alignment file formats defaults to VRNA_FILE_FORMAT_MSA_DEFAULT.

Currently, the list of parsable multiple sequence alignment file formats consists of:

SWIG Wrapper Notes:: In the target scripting language, only the first and last argument, filename and options, are passed to the corresponding function. The other arguments, which serve as output in the C-library, are available as additional return values. This function exists as an overloaded version where the options parameter may be omitted! In that case, the options parameter defaults to VRNA_FILE_FORMAT_MSA_STOCKHOLM. See, e.g. RNA.file_msa_read() in the The RNA Python module and Parsing Alignments in the Python examples.

Note

After successfully reading an alignment, this function performs a validation of the data that includes uniqueness of the sequence identifiers, and equal sequence lengths. This check can be deactivated by passing VRNA_FILE_FORMAT_MSA_NOCHECK in the options

parameter.

It is the users responsibility to free any memory occupied by the output arguments

names, aln, id, and structure after calling this function. The function automatically sets the latter two arguments to NULL in case no corresponding data could be retrieved from the input alignment.

Parameters:

filename – The name of input file that contains the alignment
names – An address to the pointer where sequence identifiers should be written to
aln – An address to the pointer where aligned sequences should be written to
id – An address to the pointer where the alignment ID should be written to (Maybe NULL)
structure – An address to the pointer where consensus structure information should be written to (Maybe NULL)
options – Options to manipulate the behavior of this function

Returns:

The number of sequences in the alignment, or -1 if no alignment record could be found

int vrna_file_msa_read_record(FILE *fp, char ***names, char ***aln, char **id, char **structure, unsigned int options)#

Read a multiple sequence alignment from file handle.

#include <ViennaRNA/io/file_formats_msa.h>

Similar to vrna_file_msa_read(), this function reads a multiple sequence alignment from an input file handle. Since using a file handle, this function is not limited to the first alignment record, but allows for looping over all alignments within the input.

The read alignment is split into the sequence id/name part and the actual sequence information and stored in memory as arrays of ids/names and sequences. If the alignment file format allows for additional information, such as an ID of the entire alignment or consensus structure information, this data is retrieved as well and made available. The options parameter allows to specify the alignment file format used to retrieve the data. A single format must be specified here, see vrna_file_msa_detect_format() for helping to determine the correct MSA file format.

Currently, the list of parsable multiple sequence alignment file formats consists of:

SWIG Wrapper Notes:: In the target scripting language, only the first and last argument, fp and options, are passed to the corresponding function. The other arguments, which serve as output in the C-library, are available as additional return values. This function exists as an overloaded version where the options parameter may be omitted! In that case, the options parameter defaults to VRNA_FILE_FORMAT_MSA_STOCKHOLM. See, e.g. RNA.file_msa_read_record() in the The RNA Python module and Parsing Alignments in the Python examples.

Note

After successfully reading an alignment, this function performs a validation of the data that includes uniqueness of the sequence identifiers, and equal sequence lengths. This check can be deactivated by passing VRNA_FILE_FORMAT_MSA_NOCHECK in the options

parameter.

It is the users responsibility to free any memory occupied by the output arguments

names, aln, id, and structure after calling this function. The function automatically sets the latter two arguments to NULL in case no corresponding data could be retrieved from the input alignment.

Parameters:

fp – The file pointer the data will be retrieved from
names – An address to the pointer where sequence identifiers should be written to
aln – An address to the pointer where aligned sequences should be written to
id – An address to the pointer where the alignment ID should be written to (Maybe NULL)
structure – An address to the pointer where consensus structure information should be written to (Maybe NULL)
options – Options to manipulate the behavior of this function

Returns:

The number of sequences in the alignment, or -1 if no alignment record could be found

unsigned int vrna_file_msa_detect_format(const char *filename, unsigned int options)#

Detect the format of a multiple sequence alignment file.

#include <ViennaRNA/io/file_formats_msa.h>

This function attempts to determine the format of a file that supposedly contains a multiple sequence alignment (MSA). This is useful in cases where a MSA file contains more than a single record and therefore vrna_file_msa_read() can not be applied, since it only retrieves the first. Here, one can try to guess the correct file format using this function and then loop over the file, record by record using one of the low-level record retrieval functions for the corresponding MSA file format.

SWIG Wrapper Notes:: This function exists as an overloaded version where the options parameter may be omitted! In that case, the options parameter defaults to VRNA_FILE_FORMAT_MSA_DEFAULT. See, e.g. RNA.file_msa_detect_format() in the The RNA Python module .

See also

vrna_file_msa_read(), vrna_file_stockholm_read_record(), vrna_file_clustal_read_record(), vrna_file_fasta_read_record()

Note

This function parses the entire first record within the specified file. As a result, it returns VRNA_FILE_FORMAT_MSA_UNKNOWN not only if it can’t detect the file’s format, but also in cases where the file doesn’t contain sequences!

Parameters:

filename – The name of input file that contains the alignment
options – Options to manipulate the behavior of this function

Returns:

The MSA file format, or VRNA_FILE_FORMAT_MSA_UNKNOWN

int vrna_file_msa_write(const char *filename, const char **names, const char **aln, const char *id, const char *structure, const char *source, unsigned int options)#

Write multiple sequence alignment file.

#include <ViennaRNA/io/file_formats_msa.h>

SWIG Wrapper Notes:: In the target scripting language, this function exists as a set of overloaded versions, where the last four parameters may be omitted. If the options parameter is missing the options default to (VRNA_FILE_FORMAT_MSA_STOCKHOLM | VRNA_FILE_FORMAT_MSA_APPEND). See, e.g. RNA.file_msa_write() in the The RNA Python module .

Note

Currently, we only support msa-formats-stockholm output

Parameters:

filename – The output filename
names – The array of sequence names / identifies
aln – The array of aligned sequences
id – An optional ID for the alignment
structure – An optional consensus structure
source – A string describing the source of the alignment
options – Options to manipulate the behavior of this function

Returns:

Non-null upon successfully writing the alignment to file

Command Files#

Functions to parse and interpret the content of usage-io-commands .

Defines

VRNA_CMD_PARSE_HC#

Command parse/apply flag indicating hard constraints.

#include <ViennaRNA/io/commands.h>

VRNA_CMD_PARSE_SC#

Command parse/apply flag indicating soft constraints.

#include <ViennaRNA/io/commands.h>

VRNA_CMD_PARSE_UD#

Command parse/apply flag indicating unstructured domains.

#include <ViennaRNA/io/commands.h>

VRNA_CMD_PARSE_SD#

Command parse/apply flag indicating structured domains.

#include <ViennaRNA/io/commands.h>

VRNA_CMD_PARSE_DEFAULTS#

Command parse/apply flag indicating default set of commands.

#include <ViennaRNA/io/commands.h>

VRNA_CMD_PARSE_SILENT#

#include <ViennaRNA/io/commands.h>

Typedefs

typedef struct vrna_command_s *vrna_cmd_t#

A data structure that contains commands.

#include <ViennaRNA/io/commands.h>

Functions

vrna_cmd_t vrna_file_commands_read(const char *filename, unsigned int options)#

Extract a list of commands from a command file.

#include <ViennaRNA/io/commands.h>

Read a list of commands specified in the input file and return them as list of abstract commands

SWIG Wrapper Notes:: This function is available as global function file_commands_read(). See, e.g. RNA.file_commands_read() in the The RNA Python module .

Parameters:

filename – The filename
options – Options to limit the type of commands read from the file

Returns:

A list of abstract commands

int vrna_file_commands_apply(vrna_fold_compound_t *fc, const char *filename, unsigned int options)#

Apply a list of commands from a command file.

#include <ViennaRNA/io/commands.h>

This function is a shortcut to directly parse a commands file and apply all successfully parsed commands to a vrna_fold_compound_t data structure.

SWIG Wrapper Notes:: This function is attached as method file_commands_apply() to objects of type fold_compound. See, e.g. RNA.fold_compound.file_commands_apply() in the The RNA Python module .

Parameters:

fc – The vrna_fold_compound_t the command list will be applied to
filename – The filename
options – Options to limit the type of commands read from the file

Returns:

The number of commands successfully applied

int vrna_commands_apply(vrna_fold_compound_t *fc, vrna_cmd_t commands, unsigned int options)#

Apply a list of commands to a vrna_fold_compound_t.

#include <ViennaRNA/io/commands.h>

SWIG Wrapper Notes:: This function is attached as method commands_apply() to objects of type fold_compound. See, e.g. RNA.fold_compound.commands_apply() in the The RNA Python module .

Parameters:

fc – The vrna_fold_compound_t the command list will be applied to
commands – The commands to apply
options – Options to limit the type of commands read from the file

Returns:

The number of commands successfully applied

void vrna_commands_free(vrna_cmd_t commands)#

Free memory occupied by a list of commands.

#include <ViennaRNA/io/commands.h>

Release memory occupied by a list of commands

Parameters:

commands – A pointer to a list of commands

Other I/O Utils#

Functions

void vrna_file_copy(FILE *from, FILE *to)#

Inefficient ‘cp’.

#include <ViennaRNA/io/utils.h>

char *vrna_read_line(FILE *fp)#

Read a line of arbitrary length from a stream.

#include <ViennaRNA/io/utils.h>

Returns a pointer to the resulting string. The necessary memory is allocated and should be released using free() when the string is no longer needed.

Parameters:

fp – A file pointer to the stream where the function should read from

Returns:

A pointer to the resulting string

int vrna_mkdir_p(const char *path)#

Recursivly create a directory tree.

#include <ViennaRNA/io/utils.h>

char *vrna_basename(const char *path)#

Extract the filename from a file path.

#include <ViennaRNA/io/utils.h>

char *vrna_dirname(const char *path)#

Extract the directory part of a file path.

#include <ViennaRNA/io/utils.h>

char *vrna_filename_sanitize(const char *name, const char *replacement)#

Sanitize a file name.

#include <ViennaRNA/io/utils.h>

Returns a new file name where all invalid characters are substituted by a replacement character. If no replacement character is supplied, invalid characters are simply removed from the filename. File names may also never exceed a length of 255 characters. Longer file names will undergo a ‘smart’ truncation process, where the filenames’ suffix, i.e. everything after the last dot ‘.’, is attempted to be kept intact. Hence, only the filename part before the suffix is reduced in such a way that the total filename complies to the length restriction of 255 characters. If no suffix is present or the suffix itself already exceeds the maximum length, the filename is simply truncated from the back of the string.

For now we consider the following characters invalid:

backslash ‘’
slash ‘/’
question mark ‘?’
percent sign ‘’
asterisk ‘*’
colon ‘:’
pipe symbol ‘|’
double quote ‘”’
triangular brackets ‘<’ and ‘>’

Furthermore, the (resulting) file name must not be a reserved file name, such as:

’.’
’..’

Note

This function allocates a new block of memory for the sanitized string. It also may return (a) NULL if the input is pointing to NULL, or (b) an empty string if the input only consists of invalid characters which are simply removed!

Parameters:

name – The input file name
replacement – The replacement character, or NULL

Returns:

The sanitized file name, or NULL

int vrna_file_exists(const char *filename)#

Check if a file already exists in the file system.

#include <ViennaRNA/io/utils.h>

Parameters:

filename – The name of (path to) the file to check for existence

Returns:

0 if it doesn’t exists, 1 otherwise

float **readribosum(char *name)#

Read a RiboSum or other user-defined Scoring Matrix and Store into global Memory.

#include <ViennaRNA/params/ribosum.h>