List of queries with getz

[Heikki Lehvaslaiho]

Olivier POIROT wrote:
> 
> Is it possible to use a file containing a list of Ids with getz (SRS
> version 5.1)?


Dear Olivier,

I suppose you mean lists like these:

%  more  my.list
EMBL:AB015259
EMBL:AB015260
EMBL:AB015261
EMBL:AB015262
%

getz needs its input formatted in a slightly different way. Let's
write a script, in icarus of course, that does what you want and can
be extended as needed. 

Create a file named 'list.i', put the follwing lines into it 
and give it execute permissions:
-------------------------cut----------------------------------
#!/bin/env icarus

if:($ArgN<2) {
   $Print:|Usage: list.i srs_entry_name_list [>entries]
   $Exit
}
$infile = $Arg:2

$rules={

  entry:  ~ {$In:[file:text] $Out} 
          	  ln? {$Wrt}
          ~
  printout:  ~ {$In:entry $Out}
            /([^:]+):([^\n]+)/
            {$System:["getz '[$1-id:$2]' -e" out:stdout]}
	  ~
  #other
  ln:     ~ /[^\n]*\n/ ~
}

if:$TestMode {
  $job = $JobNew:[prod:$rules fileName:$infile]
  while:$JobHasInput:$job {
    $JobTokens:[$job name:printout print:0] 
    $JobNext:$job
  }
}
-------------------------cut----------------------------------

Command

%  list.i  my.list > my.seqs

will then put those entries into a file 'my.seqs'


Have fun,

	-Heikki

______ _/      _/_____________________________________________________
      _/      _/                      http://www2.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
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