seqSrs                 package:GeneR                 R Documentation

_D_o_w_n_l_o_a_d _a _s_e_q_u_e_n_c_e _i_n _F_a_s_t_a / _G_e_n_b_a_n_k / _E_m_b_l _f_o_r_m_a_t _f_r_o_m _N_c_b_i _o_r _S_r_s

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

     Get a sequence in Fasta / Genbank / Embl format trough web with
     only an accno

     seqUrl will get the sequence through a srs web program. seqNcbi
     will do the same with ncbi web server (I prefer this one).

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

     seqSrs (accno,file="toto.seq",submotif=FALSE,
     srs="http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz",
     bank=c("EMBL","REFSEQ"))
     seqNcbi (accno,file="toto.seq",submotif=FALSE,type="fasta")

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

   accno: Access Number: "dbj|BY608190.1|BY608190" or "BY608190"

    file: file where seqence will be downloaded

submotif: a logical value  indicating whether we look for a subpatern
          of accno 

     srs: a url srs web program

    type: fasta or genbank for seqNcbi (file format of sequence).

    bank: List of banks to search into.

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

     1 if file has been correctly created. A file containing the
     sequence in file format requested

_N_o_t_e:

     SeqNcbi returns sometimes Genbank file in a not very valid format
     (specially with EST sequences). These files will not be computed
     by readseq. (Use Fasta format, then).

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

     Antoine Lucas, Centre de Gntique molculaire, CNRS Gif / Yvette

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

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

     ## Not run: 
     # idem:
     seqSrs("dbj|BY608190.1|BY608190",file="BY608190.embl",submotif=TRUE,type="embl")

     seqSrs("AK129232",type="embl",srs="http://www.infobiogen.fr/srs71bin/cgi-bin/wgetz")
     ## End(Not run)
       

