searchProjectID: Search SRR project accession ID using query

In paodan/SRRDownloader: Download Raw Fastq Files from SRA Database.

Search SRR project accession ID using query

Description

Search SRR project accession ID using query

Usage

searchProjectID(
 
    query = "IFN-\u03b3 selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate macrophage activation",
  timeout = 60
)

Arguments

query	character, the title or keywords to search in BioProject database (https://www.ncbi.nlm.nih.gov/bioproject)
timeout	numeric, the number of seconds to wait before killing the searching process.

Details

Format Selection

-format Format of record or report
-mode text, xml, asn.1, json
-style withparts, conwithfeat

Direct Record Selection

-db Database name
-id Unique identifier or accession number

Sequence Range

-seq_start First sequence position to retrieve
-seq_stop Last sequence position to retrieve
-strand Strand of DNA to retrieve

Gene Range

-chr_start Sequence range from 0-based coordinates
-chr_stop in gene docsum GenomicInfoType object

Sequence Flags

-complexity 0 = default, 1 = bioseq, 3 = nuc-prot set
-extend Extend sequence retrieval in both directions
-extrafeat Bit flag specifying extra features

Miscellaneous

-raw Skip database-specific XML modifications
-json Convert adjusted XML output to JSON

Format Examples

-db -format -mode Report Type
___ _______ _____ ___________

(all)
docsum DocumentSummarySet XML
docsum json DocumentSummarySet JSON
full Same as native except for mesh
uid Unique Identifier List
url Entrez URL
xml Same as -format full -mode xml

bioproject
native BioProject Report
native xml RecordSet XML

biosample
native BioSample Report
native xml BioSampleSet XML

biosystems
native xml Sys-set XML

gds
native xml RecordSet XML
summary Summary

gene
full_report Detailed Report
gene_table Gene Table
native Gene Report
native asn.1 Entrezgene ASN.1
native xml Entrezgene-Set XML
tabular Tabular Report

homologene
alignmentscores Alignment Scores
fasta FASTA
homologene Homologene Report
native Homologene List
native asn.1 HG-Entry ASN.1
native xml Entrez-Homologene-Set XML

mesh
full Full Record
native MeSH Report
native xml RecordSet XML

nlmcatalog
native Full Record
native xml NLMCatalogRecordSet XML

pmc
medline MEDLINE
native xml pmc-articleset XML

pubmed
abstract Abstract
medline MEDLINE
native asn.1 Pubmed-entry ASN.1
native xml PubmedArticleSet XML

(sequences)
acc Accession Number
est EST Report
fasta FASTA
fasta xml TinySeq XML
fasta_cds_aa FASTA of CDS Products
fasta_cds_na FASTA of Coding Regions
ft Feature Table
gb GenBank Flatfile
gb xml GBSet XML
gbc xml INSDSet XML
gene_fasta FASTA of Gene
gp GenPept Flatfile
gp xml GBSet XML
gpc xml INSDSet XML
gss GSS Report
ipg Identical Protein Report
ipg xml IPGReportSet XML
native text Seq-entry ASN.1
native xml Bioseq-set XML
seqid Seq-id ASN.1

snp
chr Chromosome Report
docset Summary
fasta FASTA
flt Flat File
native asn.1 Rs ASN.1
native xml ExchangeSet XML
rsr RS Cluster Report
ssexemplar SS Exemplar List

sra
native xml EXPERIMENT_PACKAGE_SET XML
runinfo xml SraRunInfo XML

structure
mmdb Ncbi-mime-asn1 strucseq ASN.1
native MMDB Report
native xml RecordSet XML

taxonomy
native Taxonomy List
native xml TaxaSet XML

Examples

{
## Not run: 
searchProjectID()
searchProjectID("IFN-γ T cells")

## End(Not run)
}

paodan/SRRDownloader documentation built on Aug. 25, 2023, 3:23 a.m.