pubseqos.txt

来自「ncbi源码」· 文本 代码 · 共 88 行

Update of PubSeqOS interface from Michael Kimelman at 12/19/2003.


1. id_gi_by_seqid_asn
this call now return sat, sat_key and external features mask for any resolvable
Seqid.

keep in mind that it also recognises constructions like
Seq-id ::= general { db "NCBI" , tag id 2 }'
which is actually a reference to whole blob (sat=4,sat_key=2) rather than specific
sequence in it.


   PUBSEQ_OS.kimelman.|20.1> id_gi_by_seqid_asn 'Seq-id ::= gi 6';
    gi          sat    sat_key     extra_feat
    ----------- ------ ----------- -----------
              6      2     4197975           0

   PUBSEQ_OS.kimelman.|27.1> id_gi_by_seqid_asn 'Seq-id ::= general { db "TRACE" ,
tag id 2 }';
    gi          sat    sat_key     extra_feat
    ----------- ------ ----------- -----------
              0     28           2           0

   PUBSEQ_OS.kimelman.|28.1> id_gi_by_seqid_asn 'Seq-id ::= general { db "ti" , tag
id 2 }';
    gi          sat    sat_key     extra_feat
    ----------- ------ ----------- -----------
              0     28           2           0

   PUBSEQ_OS.kimelman.|37.1> id_gi_by_seqid_asn 'Seq-id ::= general { db "ANNOT:CDD"
, tag id 6 }';
    gi          sat    sat_key     extra_feat
    ----------- ------ ----------- -----------
              6     26           6           0

2. show_annotations
   this call allows you to retrieve the interpretation of extra_feat mask.
   you need to run it once for the life of connection. (or refresh it once in a
while)

   PUBSEQ_OS.kimelman.|29.1> show_annotations ;
    name            annot_bit   sat    internal
    --------------- ----------- ------ -----------
    SNP                       1     26           0

3. id_get_asn
   this new satellite 26 provides annotation in different packaging.
   they are packaged as a regular Seq-entry with seqid like
   Seqid ::= general { db "ANNOT:<annot_name>" , tag id <gi> }

   you can check id_get_asn 6,6,26,0,1,0,0,0,8; as example.
   Seq-entry ::= seq {
     id { general { db "Annot:CDD" , tag id 6 } } ,
     inst {
       repr delta , mol aa , length 342 , topology not-set ,
       ext delta {
         loc int { from 0 , to 341 , id gi 6 } } } ,
     annot { ....
   }}

you also can get new values of zip_type field in first result set of id_get_asn.

PUBSEQ_OS.kimelman.|36.1> id_get_asn 6,6,26,0,0,0,0,0,8;
  sat_key     sat    state confidential suppress override username div class hup_date
zip_type last_touched_m
  ----------- ------ ----- ------------ -------- -------- -------- --- -----
---------------
-------- --------------
            6     26   100            0        0        0 kimelman N/A     0 1/1/1900
2       17823575


the old values was:
0: nothing special : plain asn1 (or smth else according to outfmt (fifth argument of
id_get_asn))
1: nlmzipped SNP annotation.
new values:
2: bit flag - output is gzipped.
      you will get zip_type&2>0 only if you informed pubseq that you can accept
gzipped
      data.  by
      PUBSEQ_OS.kimelman.|35.1> set accept gzip;
4: bit_flag - output contains more than one seq-entry wrapped in
        Seq-entry ::= set { class genbank, set { <set of seqentries> } }
    currently you can get this kind of output only if you request more than one
    external annotation for gi which actually has more than one.