Man page - ncbi_search(1)
Packages contains this manual
- create_zoomed_maps(1)
- redraw_maps(1)
- build_blast_atlas(1)
- remove_long_seqs(1)
- fetch_refseq_bacterial_genomes_by_name(1)
- convert_vcf_to_features(1)
- remove_short_seqs(1)
- build_blast_atlas_all_vs_all(1)
- fetch_all_refseq_mitochondrial_genomes(1)
- fetch_all_refseq_chloroplast_genomes(1)
- ncbi_search(1)
- fetch_genome_by_accession(1)
- fetch_all_refseq_bacterial_genomes(1)
- cgview_comparison_tool(1)
apt-get install cct
Manual
NCBI_SEARCH
NAMEDESCRIPTION
USAGE:
DESCRIPTION:
REQUIRED ARGUMENTS:
EXAMPLE:
AUTHOR
NAME
ncbi_search - visually comparing bacterial, plasmid, chloroplast, or mitochondrial sequences
DESCRIPTION
USAGE:
ncbi_search -q STRING -o FILE -d STRING -r STRING [Options]
DESCRIPTION:
Uses NCBI’s eSearch to download collections of sequences.
REQUIRED ARGUMENTS:
|
-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.
EXAMPLE:
ncbi_search -q ’dysphagia AND homo sapiens[ORGN]’ \
|
-o results.txt -d pubmed -r uilist -m 100 |
AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.