scopBuilder_DB          package:PAnnBuilder          R Documentation

_B_u_i_l_d _D_a_t_a _P_a_c_k_a_g_e _f_o_r _S_t_r_u_c_t_u_r_a_l _C_l_a_s_s_i_f_i_c_a_t_i_o_n _o_f _P_r_o_t_e_i_n_s

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

     Given the URL to SCOP database, this function creates a
     SQLite-based  annotation data package.

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

     scopBuilder_DB(prefix, pkgPath, version, author)

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

  prefix: the prefix of the name of the data package to be built. (e.g.
           "hsaSP"). The name of builded package is prefix+".db". 

 pkgPath: a character string for the full path of an existing directory
          where the built backage will be stored.

 version: a character string for the version number.

  author: a list with named elements "authors" containing a character
          vector of author names and "maintainer" containing the
          complete character string for the maintainer field, for
          example, "Jane Doe <jdoe@doe.com>".

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

     Build annotation data packages for structural classification of
     proteins.  Data is from SCOP database: <URL:
     http://scop.mrc-lmb.cam.ac.uk/scop> ;

     'writeSCOPData_DB' to parse and write data from SCOP database.

     Data files in the database will be automatically downloaded to the
     tmp directory, so enough space is needed for the data files. After
     downloading, files are parsed by perl, so perl must be installed. 
     It may  take a long time to parse database and build R package.
     Alternatively, we have  produced diverse R packages by
     PAnnBuilder, and you can download appropriate  package via  <URL:
     http://www.biosino.org/PAnnBuilder>.

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

     This function does not return any value.

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

     Hong Li

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

     # Set path, version and author for the package.
     pkgPath <- tempdir()
     version <- "1.0.0"
     author <- list()
     author[["authors"]] <- "Hong Li"
     author[["maintainer"]] <- "Hong Li <sysptm@gmail.com>"

     ## It may take a long time to parse database and build R package.
     if(interactive()){    
         # Build annotation data packages "scop.db" for SCOP database.
         scopBuilder_DB(prefix = "scop", pkgPath, version, author)
     }

