cdssubmit: Submit a set of queries to NCBI's CD-SEARCH via R.
In vragh/seqvisr: Biological Sequence Visualization and Auxiliary Functions in R
cdssubmit R Documentation
Submit a set of queries to NCBI's CD-SEARCH via R.
Description
Core internal cdsearchr function that prepares and submit queries to the
CD-SEARCH webserver located at a specified URL. Uses httr for POST\'ing to
the server.
Usage
cdssubmit(queries = NA, cdsurl = NULL,
db = c("cdd", "pfam", "smart", "tigrfam", "cog", "kog"),
smode = c("auto", "prec", "live"), evalue = 0.01, useid1 = TRUE, compbasedadj = 1,
biascompfilter = TRUE, tdata = c("hits", "aligns", "feats"), alnfmt = NA,
dmode = c("rep", "std", "full"), qdefl = TRUE, cddefl = TRUE, maxhit = 500,
nseqs = NULL)
Arguments
queries
(character string, mandatory) path to a FASTA file containing the
query protein sequences.
cdsurl
(character string, mandatory) the URL at which the remote CD-SEARCH
server is accessible. Should be inherited from cdsearchr. (Set to
NULL by default.)
db
(character string, optional) controls which databases CD-SEARCH should
search the queries against. Please refer to "database selection" under the URL
https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#BatchRPSBSearchMode
for particulars on the databases. This parameter only has an effect if smode is
set to "live" (see below). (Set to "cdd" by default.)
smode
(character string, optional) controls which search mode CD-SEARCH
should use. "auto" will check the queries first against a set of precalculated
results (by checking query identifiers; really only works if these are sequences
in NCBI already), and if that fails, it performs a "live" search against the
CD-SEARCH database. "prec" would return results only for queries that have a
result in the precalculated database. "live" will search every query anew against
its databases even if precalculated results exist for that query. (Set to "auto"
by default.)
evalue
(numeric, optional) expect value (statistical significance threshold)
used for filtering and reporting annotation matches. (Set to 0.01 by default.)
useid1
(binary, optional) controls whether queries should also be
searched against archived sequence identifiers if the query's identifier (if
it happens to be an NCBI identifier) does not match anything in the current
Entrez Protein database records. (Set to TRUE by default.)
compbasedadj
(integer, optional) should CD-SEARCH use compositionally-
corrected scoring? (0 - correction turned off; 1 - correction turned on.) (Set
to 1 by default.)
biascompfilter
(binary, optional) should compositionally biased regions
of the queries be filtered out? (Set to TRUE by default.)
tdata
(character string, optional) what type of target data should be
returned: "hits" (domain hits), "aligns" (domain alignments), or "feats" (domain
features). Changing from the default might break functionality as of the current
version of seqvisr. (Set to "hits" by default.)
alnfmt
(character string, optional) data format to be used for downloading
alignment data in the event tmode is set to "aligns". This will never be the
case for cdsearchr, and this option exists only for the sake of completeness.
(Set to NA by default.)
dmode
(character string, optional) which data mode must be used for the results.
This dictates what set of domains are returned: the highest scoring hit for each region
of the sequence ("rep"), the best hits from each database available in CD-SEARCH (so
multiple hits per query region are possible; "std"), or all hits ("full"). (Set to
"rep" by default.)
qdefl
(binary, optional) should query titles be included in the results? (Set to
TRUE by default.)
cddefl
(binary, optional) should domain titles be included in the results? (Set
to FALSE by default.)
maxhit
(integer, optional) maximum number of results per query that should be retrieved.
Only matters if smode is set to "live".
nseqs
(integer, mandatory) number of sequences being submitted to the CD-SEARCH
server. This value should be automatically calculated and passed on from cdsearchr.
(Set to NULL by default.)
Value
A httr response object containing (among other things, but most importantly) the
unique cdsid referring to the submitted queries and search request which can subsequently
be used to query the server.
vragh/seqvisr documentation built on April 20, 2024, 10:06 a.m.
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| cdssubmit | R Documentation |
Submit a set of queries to NCBI's CD-SEARCH via R.
Description
Core internal cdsearchr function that prepares and submit queries to the
CD-SEARCH webserver located at a specified URL. Uses httr for POST\'ing to
the server.
Usage
cdssubmit(queries = NA, cdsurl = NULL,
db = c("cdd", "pfam", "smart", "tigrfam", "cog", "kog"),
smode = c("auto", "prec", "live"), evalue = 0.01, useid1 = TRUE, compbasedadj = 1,
biascompfilter = TRUE, tdata = c("hits", "aligns", "feats"), alnfmt = NA,
dmode = c("rep", "std", "full"), qdefl = TRUE, cddefl = TRUE, maxhit = 500,
nseqs = NULL)
Arguments
queries |
(character string, mandatory) path to a FASTA file containing the query protein sequences. |
cdsurl |
(character string, mandatory) the URL at which the remote CD-SEARCH
server is accessible. Should be inherited from |
db |
(character string, optional) controls which databases CD-SEARCH should
search the queries against. Please refer to "database selection" under the URL
https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd_help.shtml#BatchRPSBSearchMode
for particulars on the databases. This parameter only has an effect if |
smode |
(character string, optional) controls which search mode CD-SEARCH should use. "auto" will check the queries first against a set of precalculated results (by checking query identifiers; really only works if these are sequences in NCBI already), and if that fails, it performs a "live" search against the CD-SEARCH database. "prec" would return results only for queries that have a result in the precalculated database. "live" will search every query anew against its databases even if precalculated results exist for that query. (Set to "auto" by default.) |
evalue |
(numeric, optional) expect value (statistical significance threshold) used for filtering and reporting annotation matches. (Set to 0.01 by default.) |
useid1 |
(binary, optional) controls whether queries should also be searched against archived sequence identifiers if the query's identifier (if it happens to be an NCBI identifier) does not match anything in the current Entrez Protein database records. (Set to TRUE by default.) |
compbasedadj |
(integer, optional) should CD-SEARCH use compositionally- corrected scoring? (0 - correction turned off; 1 - correction turned on.) (Set to 1 by default.) |
biascompfilter |
(binary, optional) should compositionally biased regions of the queries be filtered out? (Set to TRUE by default.) |
tdata |
(character string, optional) what type of target data should be
returned: "hits" (domain hits), "aligns" (domain alignments), or "feats" (domain
features). Changing from the default might break functionality as of the current
version of |
alnfmt |
(character string, optional) data format to be used for downloading
alignment data in the event |
dmode |
(character string, optional) which data mode must be used for the results. This dictates what set of domains are returned: the highest scoring hit for each region of the sequence ("rep"), the best hits from each database available in CD-SEARCH (so multiple hits per query region are possible; "std"), or all hits ("full"). (Set to "rep" by default.) |
qdefl |
(binary, optional) should query titles be included in the results? (Set to TRUE by default.) |
cddefl |
(binary, optional) should domain titles be included in the results? (Set to FALSE by default.) |
maxhit |
(integer, optional) maximum number of results per query that should be retrieved.
Only matters if |
nseqs |
(integer, mandatory) number of sequences being submitted to the CD-SEARCH
server. This value should be automatically calculated and passed on from |
Value
A httr response object containing (among other things, but most importantly) the
unique cdsid referring to the submitted queries and search request which can subsequently
be used to query the server.
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