bp_download_query_genbank - script to query Genbank and retrieve records
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
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
--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)
Jason Stajich, jason-AT-bioperl.org
To install Bio::Seq, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::Seq
CPAN shell
perl -MCPAN -e shell install Bio::Seq
For more information on module installation, please visit the detailed CPAN module installation guide.