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New sequence version numbers

Tim Cutts timc at chiark.greenend.org.uk
Thu Feb 25 06:10:41 EST 1999


Oh dear, following up to my own post.

Actually, it seems to me that the changes required are not difficult.
I've only done EMBL so far, and would like to know what people think
about whether I'm going about this the right way.

First, the change to embl.is:

*** /tmp/T0a001U5	Thu Feb 25 11:04:12 1999
--- embl.is	Thu Feb 25 10:57:09 1999
***************
*** 17,23 ****
  $fn={
    ID:id      OG:org       KW:key   RN:rn  '//':sep
    AC:acc     OC:org       RP:rp    RT:rt  FH: fh
!   DT:date    OS:org       SQ:sq    RC:rc
    DE:des     CC:cmnt      RL:rl    RA:ra
    NI:nid     DR:link      RX:rx    XX:sep 
  }
--- 17,23 ----
  $fn={
    ID:id      OG:org       KW:key   RN:rn  '//':sep
    AC:acc     OC:org       RP:rp    RT:rt  FH: fh
!   DT:date    OS:org       SQ:sq    RC:rc  SV: sv
    DE:des     CC:cmnt      RL:rl    RA:ra
    NI:nid     DR:link      RX:rx    XX:sep 
  }
***************
*** 77,82 ****
--- 77,83 ----
    mol:       ~ {$In:[fields c:id] $Out:mol} 
		 /ID +/ name  /[]+/ ';' /[]+/  {$Wrt} ~
    acc:       ~ {$In:[fields c:acc] $Out:acc} ('AC' (name {$Wrt} ';')+)+  ~
+   sv:        ~ {$In:[fields c:sv] $Out:sv} 'SV' name '.' num {$Wrt} ~
    nid:       ~ {$In:[fields c:nid] $Out:nid} 'NI' name {$Wrt}  ~
    dates:     ~ { $In:[fields c:date] $Out:date 
		   init $month={JAN:1 FEB:2 MAR:3 APR:4 MAY:5 JUN:6 JUL:7 
***************

Then I added a field definition to srsgen.i:

DF_SeqVersion:$SrsField:[SeqVersion short:sv]

And then added the new field to EMBL_FORMAT in embl.i:

    $field:[@DF_SeqVersion code:sv index:int indexToken:sv
      tableToken:sv  tableFormat:right]

Is anything else required?  Would you advise indexing this a different
way?

Tim.




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