Christopher Fields > BioPerl > bp_download_query_genbank

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NAME ^

bp_download_query_genbank - script to query Genbank and retrieve records

USAGE ^

 bp_download_query_genbank --query "Neurospora[ORGN]" --db nucest -o Ncrassa_ESTs.fa --format fasta

 bp_download_query_genbank --queryfile 'filewithquery' --db nucest -o Ncrassa_ESTs.fa --format fasta 

Other options

 Provide ONE of:

  -q --query query string OR
  --queryfile profile file with query OR
  --gi --gis --gifile file with list of GIs to download

 Database type:

 -d --db database (nucleotide [default], nucest, protein, )

 -o --out --outfile output file (results are displayed on screen otherwise)
 -f --format sequence file output format (fasta by default)
 -v --verbose debugging output

Query options

 --maxids maximum number of IDs to retrieve in a set (100 at a time by default)
 --reldate 
 --maxdate maxdate for a record
 --mindate minimum date for record
 --datetype edat or mdat (entered or modified)

AUTHOR Jason Stajich ^

Jason Stajich, jason-AT-bioperl.org

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