XStringSet-io           package:Biostrings           R Documentation

_R_e_a_d/_w_r_i_t_e _a_n _X_S_t_r_i_n_g_S_e_t _o_r _X_S_t_r_i_n_g_V_i_e_w_s _o_b_j_e_c_t _f_r_o_m/_t_o _a _f_i_l_e

_D_e_s_c_r_i_p_t_i_o_n:

     Functions to read/write an XStringSet or XStringViews object
     from/to a file.

_U_s_a_g_e:

       ## XStringSet object
       read.BStringSet(file, format)
       read.DNAStringSet(file, format)
       read.RNAStringSet(file, format)
       read.AAStringSet(file, format)
       write.XStringSet(x, file="", format, width=80)

       ## XStringViews object
       read.XStringViews(file, format, subjectClass, collapse="")
       write.XStringViews(x, file="", format, width=80)

       ## Some related helper functions
       FASTArecordsToCharacter(FASTArecs, use.names=TRUE)
       CharacterToFASTArecords(x)
       FASTArecordsToXStringViews(FASTArecs, subjectClass, collapse="")
       XStringSetToFASTArecords(x)

_A_r_g_u_m_e_n_t_s:

    file: Either a character string naming a file or a connection open
          for reading or writing. If '""' (the default for
          'write.XStringSet' and 'write.XStringViews'), then the
          functions write to the standard output connection (the
          console) unless redirected by 'sink'. 

  format: Only '"fasta"' is supported for now. 

       x: For 'write.XStringSet' and 'write.XStringViews', the object
          to write to 'file'. For 'CharacterToFASTArecords', the
          (possibly named) character vector to be converted to a list
          of FASTA records as one returned by 'readFASTA'. For
          'XStringSetToFASTArecords', the XStringSet object to be
          converted to a list of FASTA records as one returned by
          'readFASTA'. 

   width: Only relevant if 'format' is '"fasta"'. The maximum number of
          letters per line of sequence. 

subjectClass: The class to be given to the subject of the XStringViews
          object created and returned by the function. Must be the name
          of one of the direct XString subtypes i.e. '"BString"',
          '"DNAString"', '"RNAString"' or '"AAString"'. 

collapse: An optional character string to be inserted between the views
          of the XStringViews object created and returned by the
          function. 

FASTArecs: A list of FASTA records as one returned by 'readFASTA'. 

use.names: Whether or not the description line preceding each FASTA
          records should be used to set the names of the returned
          vector. 

_D_e_t_a_i_l_s:

     Only FASTA files are supported for now.

     Reading functions 'read.BStringSet', 'read.DNAStringSet',
     'read.RNAStringSet', 'read.AAStringSet' and 'read.XStringViews'
     load sequences from a file into an XStringSet or XStringViews
     object.

     Writing functions 'write.XStringSet' and 'write.XStringViews'
     write an XStringSet or XStringViews object to a file or
     connection.

     'FASTArecordsToCharacter', 'CharacterToFASTArecords',
     'FASTArecordsToXStringViews' and 'XStringSetToFASTArecords' are
     helper functions used internally by 'write.XStringSet' and
     'read.XStringViews' for switching between different
     representations of the same object.

_S_e_e _A_l_s_o:

     'readFASTA', 'writeFASTA', XStringSet-class, XStringViews-class,
     BString-class, DNAString-class, RNAString-class, AAString-class

_E_x_a_m_p_l_e_s:

       file <- system.file("extdata", "someORF.fa", package="Biostrings")
       x <- read.DNAStringSet(file, "fasta")
       x
       write.XStringSet(x, format="fasta") # writes to the console

       ## Converting 'x'...
       ## ... to a list of FASTA records (as one returned by the "readFASTA" function)
       x1 <- XStringSetToFASTArecords(x)
       ## ... to a named character vector
       x2 <- FASTArecordsToCharacter(x1) # same as 'as.character(x)'

