RNAlib-2.3.1
Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments

Functions dealing with file formats for RNA sequences, structures, and alignments. More...

+ Collaboration diagram for Functions to Read/Write several File Formats for RNA Sequences, Structures, and Alignments:

Files

file  commands.h
 Parse and apply different commands that alter the behavior of secondary structure prediction and evaluation.
 
file  file_formats.h
 Read and write different file formats for RNA sequences, structures.
 
file  file_formats_msa.h
 Functions dealing with file formats for Multiple Sequence Alignments (MSA)
 
file  file_utils.h
 Several utilities for file handling.
 
file  ribo.h
 Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments.
 

Macros

#define VRNA_FILE_FORMAT_MSA_CLUSTAL   1U
 Option flag indicating ClustalW formatted files. More...
 
#define VRNA_FILE_FORMAT_MSA_STOCKHOLM   2U
 Option flag indicating Stockholm 1.0 formatted files. More...
 
#define VRNA_FILE_FORMAT_MSA_FASTA   4U
 Option flag indicating FASTA (Pearson) formatted files. More...
 
#define VRNA_FILE_FORMAT_MSA_MAF   8U
 Option flag indicating MAF formatted files. More...
 
#define VRNA_FILE_FORMAT_MSA_DEFAULT
 Option flag indicating the set of default file formats. More...
 
#define VRNA_FILE_FORMAT_MSA_NOCHECK   4096U
 Option flag to disable validation of the alignment. More...
 
#define VRNA_FILE_FORMAT_MSA_UNKNOWN   8192U
 Return flag of vrna_file_msa_detect_format() to indicate unknown or malformatted alignment. More...
 

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. More...
 
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. More...
 
unsigned int vrna_file_msa_detect_format (const char *filename, unsigned int options)
 Detect the format of a multiple sequence alignment file. More...
 
void vrna_file_copy (FILE *from, FILE *to)
 Inefficient `cp'.
 
char * vrna_read_line (FILE *fp)
 Read a line of arbitrary length from a stream. More...
 
int vrna_mkdir_p (const char *path)
 Recursivly create a directory tree.
 
char * vrna_basename (const char *path)
 Extract the filename from a file path.
 
char * vrna_dirname (const char *path)
 Extract the directory part of a file path.
 
typedef struct vrna_command_s vrna_cmd_t
 Typename for the command repesenting data structure vrna_command_s.
 
void vrna_file_helixlist (const char *seq, const char *db, float energy, FILE *file)
 Print a secondary structure as helix list. More...
 

Detailed Description

Functions dealing with file formats for RNA sequences, structures, and alignments.

Macro Definition Documentation

#define VRNA_FILE_FORMAT_MSA_CLUSTAL   1U

#include <ViennaRNA/file_formats_msa.h>

Option flag indicating ClustalW formatted files.

See also
vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()
#define VRNA_FILE_FORMAT_MSA_STOCKHOLM   2U

#include <ViennaRNA/file_formats_msa.h>

Option flag indicating Stockholm 1.0 formatted files.

See also
vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()
#define VRNA_FILE_FORMAT_MSA_FASTA   4U

#include <ViennaRNA/file_formats_msa.h>

Option flag indicating FASTA (Pearson) formatted files.

See also
vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()
#define VRNA_FILE_FORMAT_MSA_MAF   8U

#include <ViennaRNA/file_formats_msa.h>

Option flag indicating MAF formatted files.

See also
vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()
#define VRNA_FILE_FORMAT_MSA_DEFAULT

#include <ViennaRNA/file_formats_msa.h>

Value:
( \
VRNA_FILE_FORMAT_MSA_CLUSTAL \
)
#define VRNA_FILE_FORMAT_MSA_MAF
Option flag indicating MAF formatted files.
Definition: file_formats_msa.h:38
#define VRNA_FILE_FORMAT_MSA_FASTA
Option flag indicating FASTA (Pearson) formatted files.
Definition: file_formats_msa.h:32
#define VRNA_FILE_FORMAT_MSA_STOCKHOLM
Option flag indicating Stockholm 1.0 formatted files.
Definition: file_formats_msa.h:26

Option flag indicating the set of default file formats.

See also
vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()
#define VRNA_FILE_FORMAT_MSA_NOCHECK   4096U

#include <ViennaRNA/file_formats_msa.h>

Option flag to disable validation of the alignment.

See also
vrna_file_msa_read(), vrna_file_msa_read_record()
#define VRNA_FILE_FORMAT_MSA_UNKNOWN   8192U

#include <ViennaRNA/file_formats_msa.h>

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

See also
vrna_file_msa_detect_format()

Function Documentation

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

#include <ViennaRNA/file_formats.h>

Print a secondary structure as helix list.

Parameters
seqThe RNA sequence
dbThe structure in dot-bracket format
energyFree energy of the structure in kcal/mol
fileThe file handle used to print to (print defaults to 'stdout' if(file == NULL) )
int vrna_file_msa_read ( const char *  filename,
char ***  names,
char ***  aln,
char **  id,
char **  structure,
unsigned int  options 
)

#include <ViennaRNA/file_formats_msa.h>

Read a multiple sequence alignment from file.

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:

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.
See also
vrna_file_msa_read_record(), VRNA_FILE_FORMAT_MSA_CLUSTAL, VRNA_FILE_FORMAT_MSA_STOCKHOLM, VRNA_FILE_FORMAT_MSA_FASTA, VRNA_FILE_FORMAT_MSA_MAF, VRNA_FILE_FORMAT_MSA_DEFAULT, VRNA_FILE_FORMAT_MSA_NOCHECK
Parameters
filenameThe name of input file that contains the alignment
namesAn address to the pointer where sequence identifiers should be written to
alnAn address to the pointer where aligned sequences should be written to
idAn address to the pointer where the alignment ID should be written to (Maybe NULL)
structureAn address to the pointer where consensus structure information should be written to (Maybe NULL)
optionsOptions 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 
)

#include <ViennaRNA/file_formats_msa.h>

Read a multiple sequence alignment from file handle.

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:

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.
See also
vrna_file_msa_read(), vrna_file_msa_detect_format(), VRNA_FILE_FORMAT_MSA_CLUSTAL, VRNA_FILE_FORMAT_MSA_STOCKHOLM, VRNA_FILE_FORMAT_MSA_FASTA, VRNA_FILE_FORMAT_MSA_MAF, VRNA_FILE_FORMAT_MSA_DEFAULT, VRNA_FILE_FORMAT_MSA_NOCHECK
Parameters
fpThe file pointer the data will be retrieved from
namesAn address to the pointer where sequence identifiers should be written to
alnAn address to the pointer where aligned sequences should be written to
idAn address to the pointer where the alignment ID should be written to (Maybe NULL)
structureAn address to the pointer where consensus structure information should be written to (Maybe NULL)
optionsOptions 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 
)

#include <ViennaRNA/file_formats_msa.h>

Detect the format of a multiple sequence alignment file.

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.

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!
See also
vrna_file_msa_read(), vrna_file_stockholm_read_record(), vrna_file_clustal_read_record(), vrna_file_fasta_read_record()
Parameters
filenameThe name of input file that contains the alignment
optionsOptions to manipulate the behavior of this function
Returns
The MSA file format, or VRNA_FILE_FORMAT_MSA_UNKNOWN
char* vrna_read_line ( FILE *  fp)

#include <ViennaRNA/file_utils.h>

Read a line of arbitrary length from a stream.

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
fpA file pointer to the stream where the function should read from
Returns
A pointer to the resulting string