readFASTA             package:Biostrings             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _r_e_a_d _F_A_S_T_A _f_o_r_m_a_t_t_e_d _f_i_l_e_s

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

     FASTA is a simple file format for biological sequence data. A file
     may contain one or more sequences, for each sequence there is a
     description  line which begins with a '>'.

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

     readFASTA(file, checkComments = TRUE)

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

    file: The name of the file to be read from.

checkComments: Whether or not comments, lines beginning with a
          semi-colon should be found and removed. 

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

     FASTA is a widely used format in biology. It is a relatively
     simple markup. I am not aware of a standard. It might be nice to
     check to see if the  data that were parsed are sequences of some
     appropriate type, but without a standard that does not seem
     possible.

     There are many other packages that provide similar, but different 
     capabilities.  The one in the package seqinr seems most similar
     but they separate the biological sequence into single character
     strings, which is too inefficient for large problems.

_V_a_l_u_e:

     A list with one element for each sequence in the file. The
     elements  are in two parts, one the description and the second a
     character string of the biological sequence.

_A_u_t_h_o_r(_s):

     R. Gentleman

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

     'read.table', 'scan'

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

     f1 = system.file("Exfiles/fastaEx", package="Biostrings")
     ff = readFASTA(f1)

