ncbi_search - visually comparing bacterial, plasmid, chloroplast,
or mitochondrial sequences
- ncbi_search -q STRING -o FILE -d STRING -r
STRING [Options]
- Uses NCBI's eSearch to download collections of sequences.
-q, --query [STRING]
- Raw query text.
-o, --output [FILE]
- Output file to create. If the split option is given, this should be a
directory, where the returned records will be written. If the directory
does not exist it will be created.
-d, --database [STRING]
- Name of the NCBI database to search, such as 'nucleotide', 'protein', or
'gene'.
-r, --return_type [STRING]
- The type of information requested. For sequences 'fasta' is often used.
The accepted formats vary depending on the database being queried.
-s, --split
- Return each record as a separate file where the file name will will be the
accesssion id of the record. This option only works if the return_type is
'gb' or 'gbwithparts'.
-m, --max_records [INTEGER]
- The maximum number of records to return (default is to return all matches
satisfying the query).
-v, --verbose
- Provide progress messages.
-h, --help
- Show this message.
- ncbi_search -q 'dysphagia AND homo sapiens[ORGN]' \
-o results.txt -d pubmed -r uilist
-m 100
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.