Man page - bp_download_query_genbank(1)

Packages contains this manual

Package:  libbio-db-ncbihelper-perl
apt-get install libbio-db-ncbihelper-perl

Manuals in package:
• bp_biofetch_genbank_proxy(1)
• bp_query_entrez_taxa(1)
• bp_download_query_genbank(1)
Documentations in package:
• libbio-db-ncbihelper-perl

Manual

BP_DOWNLOAD_QUERY_GENBANK

NAME
USAGE
Other options
Query options
AUTHOR Jason Stajich

---

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

---