diff --git a/R/getAssemblyStats.R b/R/getAssemblyStats.R index a58ae26..5761ea0 100644 --- a/R/getAssemblyStats.R +++ b/R/getAssemblyStats.R @@ -139,14 +139,14 @@ getAssemblyStats <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | stringr::str_detect(assembly_accession, organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -323,7 +323,7 @@ getAssemblyStats <- ) - readr::write_tsv(doc, path = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) message( paste0( diff --git a/R/getCDS.R b/R/getCDS.R index 81da8df..63c833a 100644 --- a/R/getCDS.R +++ b/R/getCDS.R @@ -119,14 +119,14 @@ getCDS <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | stringr::str_detect(assembly_accession, organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -322,7 +322,7 @@ getCDS <- ) - readr::write_tsv(doc, path = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) message( paste0( @@ -504,7 +504,7 @@ getCDS <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) @@ -672,7 +672,7 @@ getCDS <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) diff --git a/R/getGFF.R b/R/getGFF.R index ef45447..947e358 100644 --- a/R/getGFF.R +++ b/R/getGFF.R @@ -134,14 +134,14 @@ getGFF <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | stringr::str_detect(assembly_accession, organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -322,7 +322,7 @@ getGFF <- ) - readr::write_tsv(doc, path = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) if (gunzip) { message( @@ -488,7 +488,7 @@ getGFF <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) @@ -659,7 +659,7 @@ getGFF <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) diff --git a/R/getGenome.R b/R/getGenome.R index 82c1aff..e0d53e5 100644 --- a/R/getGenome.R +++ b/R/getGenome.R @@ -161,14 +161,14 @@ getGenome <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | assembly_accession == organism, - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -339,12 +339,12 @@ getGenome <- ) - readr::write_tsv(doc, path = file.path(path, paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path, paste0("doc_",local.org,"_db_",db,".tsv"))) genome_summary_stats <- summary_genome(file = file.path(path, paste0(local.org, "_genomic_", db, ".fna.gz")), organism = organism) - readr::write_tsv(genome_summary_stats, path = file.path(path, paste0("doc_",local.org,"_db_",db,"_summary_statistics.tsv"))) + readr::write_tsv(genome_summary_stats, file = file.path(path, paste0("doc_",local.org,"_db_",db,"_summary_statistics.tsv"))) if (!gunzip) { message( @@ -529,7 +529,7 @@ getGenome <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) @@ -696,7 +696,7 @@ getGenome <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) diff --git a/R/getProteome.R b/R/getProteome.R index dbadc1c..5be44e9 100644 --- a/R/getProteome.R +++ b/R/getProteome.R @@ -141,14 +141,14 @@ getProteome <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | stringr::str_detect(assembly_accession, organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -325,7 +325,7 @@ getProteome <- ) - readr::write_tsv(doc, path = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) if (!gunzip) { message( @@ -506,7 +506,7 @@ getProteome <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) @@ -673,7 +673,7 @@ getProteome <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) diff --git a/R/getRNA.R b/R/getRNA.R index b2d97a0..794a266 100644 --- a/R/getRNA.R +++ b/R/getRNA.R @@ -115,14 +115,14 @@ getRNA <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | stringr::str_detect(assembly_accession, organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -319,7 +319,7 @@ getRNA <- ) - readr::write_tsv(doc, path = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) message( paste0( @@ -483,7 +483,7 @@ getRNA <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) @@ -628,7 +628,7 @@ getRNA <- ) - readr::write_tsv(doc, file.path( + readr::write_tsv(doc, file = file.path( path, paste0("doc_", new.organism, "_db_", db, ".tsv")) ) diff --git a/R/getRepeatMasker.R b/R/getRepeatMasker.R index 09b7267..c383360 100644 --- a/R/getRepeatMasker.R +++ b/R/getRepeatMasker.R @@ -123,14 +123,14 @@ getRepeatMasker <- AssemblyFilesAllKingdoms, stringr::str_detect(organism_name, organism) | stringr::str_detect(assembly_accession, organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } else { FoundOrganism <- dplyr::filter( AssemblyFilesAllKingdoms, taxid == as.integer(organism), - (version_status == "latest") + (version_status == "latest"), !is.na(ftp_path) ) } } @@ -308,7 +308,7 @@ getRepeatMasker <- ) - readr::write_tsv(doc, path = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) + readr::write_tsv(doc, file = file.path(path,paste0("doc_",local.org,"_db_",db,".tsv"))) message( paste0(