makeIndex               package:GeneR               R Documentation

_I_n_d_e_x _f_i_l_e _c_r_e_a_t_i_o_n _f_o_r _a _b_a_n_k _f_i_l_e (_i_n_t_e_r_n_a_l _f_u_n_c_t_i_o_n)

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

     Makes an index for a bank file (if there wasn't).

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

     makeIndex(file, type="E", index="ix")

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

    file: string/scalar, file name of bank file

    type: Sequence format ("E" for Embl, "G", for Genebank, "F" for
          Fasta)

   index: Suffix for the index file (usually: ix)

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

     Checks if index file exists and is newer than bank file. If not,
     calls one of indexFasta, indexEmbl, indexGbk functions.

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

       1: Index already exists (and no changes)

       0: Index successfully created

      -1: Error

_N_o_t_e:

     Index files are in the form:


     Accno   deb_feature   deb_sequence   length_sequence

     with one line by sequence. Number of char must be the same for
     each line (it is used to search a specific access number) but size
     used for accno is of 40 char by default. This can be change by
     setting variable  'MAX_LEN_ACCNO' in GeneR_globals.h file and
     recompile the library.

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

     Antoine Lucas

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

     'indexFasta','indexEmbl', 'indexGbk'

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

       seqNcbi("BY608190",file="BY608190.fa")

       # Write index file BY608190.fa.ix ...
       indexFasta("BY608190.fa")

       

