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bp_download_query_genbankp - Online in the Cloud

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This is the command bp_download_query_genbankp that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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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