[BiO BB] fastacmd - sequence retreival using "string" ?

Cook, Malcolm MEC at Stowers-Institute.org
Wed Jan 31 09:51:48 EST 2007


It is unclear to me exactly what you want to do.  What exactly do you
mean by "string query"?

Does knowing that the following two command return the same result
answer your question?:

> fastacmd -s 15674171,66818355
> fastacmd -s NP_268346.1,XP_642837.1
> fastacmd -s 'gi|15674171|ref|NP_268346.1,gi|66818355|ref|XP_642837.1'

(note: you must quote the query to prevent the shell from trying to
interpret the '|' character as pipe operator).

If this does not help you, then I'm really unsure what you're after...

The options that appear relevant to your need, taken from running
fastacmd with --help as only option, are

  -s  Comma-delimited search string(s).
      GIs, accessions, loci, or fullSeq-id strings may be used,
      e.g. 555, AC147927, 'gnl|dbname|tag' [String]  Optional
  -i  Input file with GIs/accessions/loci for batch
      retrieval [String]  Optional
  -L  Range of sequence to extract (Format: start,stop)
      0 in 'start' refers to the beginning of the sequence
      0 in 'stop' refers to the end of the sequence [String]  Optional
    default = 0,0
If you want to subsequences (ranges) from a bunch of different
sequences, you must make separate calls to fastacmd.  The -L option will
not help you for this.  The -L option only allows you to specify a
single range.  If you use it in conjuntion with multiple comma delimited
search strings, this single range option is applied equally to all of
the resulting sequences.

Malcolm Cook
Database Applications Manager - Bioinformatics
Stowers Institute for Medical Research - Kansas City, Missouri

> -----Original Message-----
> From: 
> bio_bulletin_board-bounces+mec=stowers-institute.org at bioinform
> atics.org 
> [mailto:bio_bulletin_board-bounces+mec=stowers-institute.org at b
> ioinformatics.org] On Behalf Of Shameer Khadar
> Sent: Tuesday, January 30, 2007 9:19 PM
> To: General Forum at Bioinformatics.Org
> Subject: [BiO BB] fastacmd - sequence retreival using "string" ?
> Dear All,
> Is it possible to retreive sequence(s) from a fastacmd nr 
> database based on
> string qureies delimited by commas.
> I know it is possible with the Accession IDs, Is there any 
> way to do it for
> the string query.
> Thanks,
> Shameer
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