readFasta-methods         package:pairseqsim         R Documentation

_r_e_a_d_e_r _f_o_r _d_a_t_a_b_a_s_e_s _i_n _F_a_s_t_a _f_i_l_e _f_o_r_m_a_t.

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

     Reads file in FASTA format. An sequence entry in the fasta dabase
     consists of a header line starting with the \">\" sign which
     contains the id of the sequence. It is followed by several lines
     of the protein sequence. Because the header line may vary the user
     can specify a function which will extract (grep) the id. '
     infogrep <- function(x) { return(sub("^>([a-zA-Z0-9]+)
     .+","\1",x,perl=TRUE)) } '

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

  object: either 'AASequence' or 'AASequenceList'

    file: Path to the file

grepinfo: Function which extracts the id from the fasta description
          line.

 grepseq: Function to pre-process the sequence.

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

     Returns an object of class 'AASequenceList'.

_M_e_t_h_o_d_s:

     _o_b_j_e_c_t = "_A_A_S_e_q_u_e_n_c_e_L_i_s_t" Read sequence database in FASTA format.

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

     Witold E. Wolski witek96@users.sourceforge.net

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

     'AASequenceList-class'

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

     mySequlist <- new("AASequenceList",info="my sequence list")
     #mySequlist<-readFasta(mySequlist,"ex.fasta",grepinfo=infogrep,grepseq=seqgrep)

