R/Rvsearch.R
In lerch-a/Rvsearch: R vsearch Wrapper
Defines functions
.execute
.vsearchBin
vsearch_version
vsearch_usage
chimeraDetectionDenovo
Documented in
chimeraDetectionDenovo
vsearch_usage
vsearch_version
## Example
# "Usage: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rvsearch/vsearch [OPTIONS]"
# [6] "General options"
# [7] " --fasta_width INT width of FASTA seq lines, 0 for no wrap (80)"
# [9] " --log FILENAME write messages, timing and memory info to file"
# [10] " --maxseqlength INT maximum sequence length (50000)"
# [11] " --minseqlength INT min seq length (clust/derep/search: 32, other:1)"
# [12] " --notrunclabels do not truncate labels at first space"
# [13] " --quiet output just warnings and fatal errors to stderr"
# [14] " --threads INT number of threads to use, zero for all cores (0)"
## The main wrapper around vsearch
# Chimera detection using a reference database
# chimeraDetectionRef <- function()
# {
# # [19] " --uchime_ref FILENAME detect chimeras"
# # [25] " --db FILENAME reference database for --uchime_ref"
# # [36] " --self exclude identical labels for --uchime_ref"
# # [37] " --selfid exclude identical sequences for --uchime_ref"
# }
# Chimera detection de novo
chimeraDetectionDenovo <- function(filename, abskew=2.0, mindiffs=3L, mindiv=0.8, minh=0.28,
nonchimeras=sub(".fasta", "_nonchimera.fasta", filename),
chimeras=sub(".fasta", "_chimera.fasta", filename),
borderline=sub(".fasta", "_bordchimera.fasta", filename),
uchimeout=sub(".fasta", "_chimeraResults.txt", filename))
{
syscall <- paste("--uchime_denovo ", filename,
"--abskew", abskew,
"--mindiffs", mindiffs,
"--mindiv", mindiv,
"--minh", minh,
"--nonchimeras", nonchimerafile,
"--chimeras", chimerafile,
"--borderline", borderfile,
"--uchimeout", uchimeout, sep=" ")
# System call parameters
# [18] " --uchime_denovo FILENAME detect chimeras "
# [20] "Options"
# [21] " --abskew REAL min abundance ratio of parent vs chimera (2.0)"
# [28] " --mindiffs INT minimum number of differences in segment (3)"
# [29] " --mindiv REAL minimum divergence from closest parent (0.8)"
# [30] " --minh REAL minimum score (0.28)"
# [23] " --borderline FILENAME output borderline chimeric sequences to file"
# [24] " --chimeras FILENAME output chimeric sequences to file"
# [31] " --nonchimeras FILENAME output non-chimeric sequences to file"
# [40] " --uchimeout FILENAME output to chimera info to tab-separated file"
# Not supported in this function
# [26] " --dn REAL 'no' vote pseudo-count (1.4)"
# [27] " --fasta_score include chimera score in fasta output"
# [32] " --relabel STRING relabel nonchimeras with this prefix string"
# [33] " --relabel_keep keep the old label after the new when relabelling"
# [34] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [35] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [38] " --sizeout include abundance information when relabelling"
# [39] " --uchimealns FILENAME output chimera alignments to file"
# [22] " --alignwidth INT width of alignment in uchimealn output (80)"
# [41] " --uchimeout5 make output compatible with uchime version 5"
# [42] " --xn REAL 'no' vote weight (8.0)"
# [43] " --xsize strip abundance information in output"
return(invisible(.vsearchBin(args=syscall)))
}
## Helper function that return a description of the intended usage for vsearch
vsearch_usage <- function(){
print(.vsearchBin(args="--help"))
}
## Helper function that return the version of vsearch
vsearch_version <- function(){
print(.vsearchBin(args="--version"))
}
## A helper function to call the vsearch binaries with additional arguments.
.vsearchBin <- function(args="")
{
if(is.null(args) || args=="")
stop("The vsearch binaries need to be called with additional arguments")
args <- gsub("^ *| *$", "", args)
call <- paste(shQuote(file.path(system.file(package="Rvsearch"), "vsearch")), args)
return(system(call, intern=TRUE))
}
## The direct binary call function
.execute <- function(callstr, ...){
call <- file.path(shQuote(system.file(package="Rvsearch")), callstr)
return(system(call, ...))
}
# [45] "Clustering"
# [46] " --cluster_fast FILENAME cluster sequences after sorting by length"
# [47] " --cluster_size FILENAME cluster sequences after sorting by abundance"
# [48] " --cluster_smallmem FILENAME cluster already sorted sequences (see -usersort)"
# [49] "Options (most searching options also apply)"
# [50] " --centroids FILENAME output centroid sequences to FASTA file"
# [51] " --clusterout_id add cluster id info to consout and profile files"
# [52] " --clusterout_sort order msaout, consout, profile by decr abundance"
# [53] " --clusters STRING output each cluster to a separate FASTA file"
# [54] " --consout FILENAME output cluster consensus sequences to FASTA file"
# [55] " --cons_truncate do not ignore terminal gaps in MSA for consensus"
# [56] " --id REAL reject if identity lower"
# [57] " --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)"
# [58] " --msaout FILENAME output multiple seq. alignments to FASTA file"
# [59] " --profile FILENAME output sequence profile of each cluster to file"
# [60] " --qmask none|dust|soft mask seqs with dust, soft or no method (dust)"
# [61] " --relabel STRING relabel centroids with this prefix string"
# [62] " --relabel_keep keep the old label after the new when relabelling"
# [63] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [64] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [65] " --sizein propagate abundance annotation from input"
# [66] " --sizeorder sort accepted centroids by abundance (AGC)"
# [67] " --sizeout write cluster abundances to centroid file"
# [68] " --strand plus|both cluster using plus or both strands (plus)"
# [69] " --uc FILENAME specify filename for UCLUST-like output"
# [70] " --usersort indicate sequences not pre-sorted by length"
# [71] " --xsize strip abundance information in output"
# [73] "Dereplication and rereplication"
# [74] " --derep_fulllength FILENAME dereplicate sequences in the given FASTA file"
# [75] " --derep_prefix FILENAME dereplicate sequences in file based on prefixes"
# [76] " --rereplicate FILENAME rereplicate sequences in the given FASTA file"
# [77] "Options"
# [78] " --maxuniquesize INT maximum abundance for output from dereplication"
# [79] " --minuniquesize INT minimum abundance for output from dereplication"
# [80] " --output FILENAME output FASTA file"
# [81] " --relabel STRING relabel with this prefix string"
# [82] " --relabel_keep keep the old label after the new when relabelling"
# [83] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [84] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [85] " --sizein propagate abundance annotation from input"
# [86] " --sizeout write abundance annotation to output"
# [87] " --strand plus|both dereplicate plus or both strands (plus)"
# [88] " --topn INT output only n most abundant sequences after derep"
# [89] " --uc FILENAME filename for UCLUST-like dereplication output"
# [90] " --xsize strip abundance information in derep output"
# [92] "FASTQ filtering"
# [93] " --fastq_filter FILENAME filter FASTQ file, output to FASTQ or FASTA file"
# [94] "Options"
# [95] " --eeout include expected errors in FASTQ filter output"
# [96] " --fastaout FILENAME FASTA output filename for passed sequences"
# [97] " --fastaout_discarded FNAME FASTA filename for discarded sequences"
# [98] " --fastqout FILENAME FASTQ output filename for passed sequences"
# [99] " --fastqout_discarded FNAME FASTQ filename for discarded sequences"
# [100] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [101] " --fastq_maxee REAL maximum expected error value for FASTQ filter"
# [102] " --fastq_maxee_rate REAL maximum expected error rate for FASTQ filter"
# [103] " --fastq_maxns INT maximum number of N's for FASTQ filter"
# [104] " --fastq_minlen INT minimum length for FASTQ filter"
# [105] " --fastq_stripleft INT bases on the left to delete for FASTQ filter"
# [106] " --fastq_trunclen INT read length for FASTQ filter truncation"
# [107] " --fastq_truncqual INT base quality value for FASTQ filter truncation"
# [108] " --relabel STRING relabel filtered sequences with given prefix"
# [109] " --relabel_keep keep the old label after the new when relabelling"
# [110] " --relabel_md5 relabel filtered sequences with md5 digest"
# [111] " --relabel_sha1 relabel filtered sequences with sha1 digest"
# [112] " --sizeout include abundance information when relabelling"
# [113] " --xsize strip abundance information in output"
# [115] "FASTQ format conversion"
# [116] " --fastq_convert FILENAME convert between FASTQ file formats"
# [117] "Options"
# [118] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [119] " --fastq_asciiout INT FASTQ output quality score ASCII base char (33)"
# [120] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [121] " --fastq_qmaxout INT maximum base quality value for FASTQ output (41)"
# [122] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [123] " --fastq_qminout INT minimum base quality value for FASTQ output (0)"
# [124] ""
# [125] "FASTQ format detection and quality analysis"
# [126] " --fastq_chars FILENAME analyse FASTQ file for version and quality range"
# [127] "Options"
# [128] " --fastq_tail INT min length of tails to count for fastq_chars (4)"
# [130] "FASTQ paired-end reads merging"
# [131] " --fastq_mergepairs FILENAME merge paired-end reads into one sequence"
# [132] "Options:"
# [133] " --eetabbedout FILENAME output error statistics to specified file"
# [134] " --fastaout FILENAME FASTA output filename for merged sequences"
# [135] " --fastaout_notmerged_fwd FN FASTA filename for non-merged forward sequences"
# [136] " --fastaout_notmerged_rev FN FASTA filename for non-merged reverse sequences"
# [137] " --fastq_allowmergestagger Allow merging of staggered reads"
# [138] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [139] " --fastq_eeout include expected errors in FASTQ output"
# [140] " --fastq_maxdiffs maximum number of different bases in overlap (5)"
# [141] " --fastq_maxee REAL maximum expected error value for merged sequence"
# [142] " --fastq_maxmergelen maximum length of entire merged sequence"
# [143] " --fastq_maxns INT maximum number of N's"
# [144] " --fastq_minlen INT minimum input read length after truncation (1)"
# [145] " --fastq_minmergelen minimum length of entire merged sequence"
# [146] " --fastq_minovlen minimum length of overlap between reads (16)"
# [147] " --fastq_nostagger disallow merging of staggered reads (default)"
# [148] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [149] " --fastq_qmaxout INT maximum base quality value for FASTQ output (41)"
# [150] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [151] " --fastq_qminout INT minimum base quality value for FASTQ output (0)"
# [152] " --fastq_truncqual INT base quality value for truncation"
# [153] " --fastqout FILENAME FASTQ output filename for merged sequences"
# [154] " --fastqout_notmerged_fwd F FASTQ filename for non-merged forward sequences"
# [155] " --fastqout_notmerged_rev F FASTQ filename for non-merged reverse sequences"
# [156] " --label_suffix suffix to append to label of merged sequences"
# [157] " --reverse FILENAME specify FASTQ file with reverse reads"
# [159] "FASTQ quality statistics"
# [160] " --fastq_stats FILENAME report FASTQ file statistics"
# [161] " --fastq_eestats FILENAME quality score and expected error statistics"
# [162] "Options"
# [163] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [164] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [165] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [167] "Masking (new)"
# [168] " --fastx_mask FILENAME mask sequences in the given FASTA or FASTQ file"
# [169] "Options"
# [170] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [171] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [172] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [173] " --fastaout FILENAME output to specified FASTA file"
# [174] " --fastqout FILENAME output to specified FASTQ file"
# [175] " --hardmask mask by replacing with N instead of lower case"
# [176] " --max_unmasked_pct max unmasked % of sequences to keep (100.0)"
# [177] " --min_unmasked_pct min unmasked % of sequences to keep (0.0)"
# [178] " --qmask none|dust|soft mask seqs with dust, soft or no method (dust)"
# [180] "Masking (old)"
# [181] " --maskfasta FILENAME mask sequences in the given FASTA file"
# [182] "Options"
# [183] " --hardmask mask by replacing with N instead of lower case"
# [184] " --output FILENAME output to specified FASTA file"
# [185] " --qmask none|dust|soft mask seqs with dust, soft or no method (dust)"
# [186] ""
# [187] "Pairwise alignment"
# [188] " --allpairs_global FILENAME perform global alignment of all sequence pairs"
# [189] "Options (most searching options also apply)"
# [190] " --alnout FILENAME filename for human-readable alignment output"
# [191] " --acceptall output all pairwise alignments"
# [193] "Reverse complementation"
# [194] " --fastx_revcomp FILENAME Reverse-complement seqs in FASTA or FASTQ file"
# [195] "Options"
# [196] " --fastaout FILENAME FASTA output filename"
# [197] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [198] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [199] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [200] " --fastqout FILENAME FASTQ output filename"
# [201] " --label_suffix STRING Label to append to identifier in the output"
# [203] "Searching"
# [204] " --search_exact FILENAME filename of queries for exact match search"
# [205] " --usearch_global FILENAME filename of queries for global alignment search"
# [206] "Options"
# [207] " --alnout FILENAME filename for human-readable alignment output"
# [208] " --blast6out FILENAME filename for blast-like tab-separated output"
# [209] " --db FILENAME filename for FASTA formatted database for search"
# [210] " --dbmask none|dust|soft mask db with dust, soft or no method (dust)"
# [211] " --dbmatched FILENAME FASTA file for matching database sequences"
# [212] " --dbnotmatched FILENAME FASTA file for non-matching database sequences"
# [213] " --fastapairs FILENAME FASTA file with pairs of query and target"
# [214] " --fulldp full dynamic programming alignment (always on)"
# [215] " --gapext STRING penalties for gap extension (2I/1E)"
# [216] " --gapopen STRING penalties for gap opening (20I/2E)"
# [217] " --hardmask mask by replacing with N instead of lower case"
# [218] " --id REAL reject if identity lower"
# [219] " --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)"
# [220] " --idprefix INT reject if first n nucleotides do not match"
# [221] " --idsuffix INT reject if last n nucleotides do not match"
# [222] " --leftjust reject if terminal gaps at alignment left end"
# [223] " --match INT score for match (2)"
# [224] " --matched FILENAME FASTA file for matching query sequences"
# [225] " --maxaccepts INT number of hits to accept and show per strand (1)"
# [226] " --maxdiffs INT reject if more substitutions or indels"
# [227] " --maxgaps INT reject if more indels"
# [228] " --maxhits INT maximum number of hits to show (unlimited)"
# [229] " --maxid REAL reject if identity higher"
# [230] " --maxqsize INT reject if query abundance larger"
# [231] " --maxqt REAL reject if query/target length ratio higher"
# [232] " --maxrejects INT number of non-matching hits to consider (32)"
# [233] " --maxsizeratio REAL reject if query/target abundance ratio higher"
# [234] " --maxsl REAL reject if shorter/longer length ratio higher"
# [235] " --maxsubs INT reject if more substitutions"
# [236] " --mid REAL reject if percent identity lower, ignoring gaps"
# [237] " --mincols INT reject if alignment length shorter"
# [238] " --minqt REAL reject if query/target length ratio lower"
# [239] " --minsizeratio REAL reject if query/target abundance ratio lower"
# [240] " --minsl REAL reject if shorter/longer length ratio lower"
# [241] " --mintsize INT reject if target abundance lower"
# [242] " --minwordmatches INT minimum number of word matches required (10)"
# [243] " --mismatch INT score for mismatch (-4)"
# [244] " --notmatched FILENAME FASTA file for non-matching query sequences"
# [245] " --output_no_hits output non-matching queries to output files"
# [246] " --pattern STRING option is ignored"
# [247] " --qmask none|dust|soft mask query with dust, soft or no method (dust)"
# [248] " --query_cov REAL reject if fraction of query seq. aligned lower"
# [249] " --rightjust reject if terminal gaps at alignment right end"
# [250] " --rowlen INT width of alignment lines in alnout output (64)"
# [251] " --samheader include a header in the SAM output file"
# [252] " --samout FILENAME filename for SAM format output"
# [253] " --self reject if labels identical"
# [254] " --selfid reject if sequences identical"
# [255] " --sizeout write abundance annotation to dbmatched file"
# [256] " --slots INT option is ignored"
# [257] " --strand plus|both search plus or both strands (plus)"
# [258] " --target_cov REAL reject if fraction of target seq. aligned lower"
# [259] " --top_hits_only output only hits with identity equal to the best"
# [260] " --uc FILENAME filename for UCLUST-like output"
# [261] " --uc_allhits show all, not just top hit with uc output"
# [262] " --userfields STRING fields to output in userout file"
# [263] " --userout FILENAME filename for user-defined tab-separated output"
# [264] " --weak_id REAL include aligned hits with >= id; continue search"
# [265] " --wordlength INT length of words for database index 3-15 (8)"
# [267] "Shuffling and sorting"
# [268] " --shuffle FILENAME shuffle order of sequences in FASTA file randomly"
# [269] " --sortbylength FILENAME sort sequences by length in given FASTA file"
# [270] " --sortbysize FILENAME abundance sort sequences in given FASTA file"
# [271] "Options"
# [272] " --maxsize INT maximum abundance for sortbysize"
# [273] " --minsize INT minimum abundance for sortbysize"
# [274] " --output FILENAME output to specified FASTA file"
# [275] " --randseed INT seed for PRNG, zero to use random data source (0)"
# [276] " --relabel STRING relabel sequences with this prefix string"
# [277] " --relabel_keep keep the old label after the new when relabelling"
# [278] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [279] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [280] " --sizeout include abundance information when relabelling"
# [281] " --topn INT output just first n sequences"
# [282] " --xsize strip abundance information in output"
# [284] "Subsampling"
# [285] " --fastx_subsample FILENAME subsample sequences from given FASTA/FASTQ file"
# [286] "Options"
# [287] " --fastaout FILENAME output FASTA file for subsamples"
# [288] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [289] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [290] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [291] " --fastqout FILENAME output FASTQ file for subsamples"
# [292] " --randseed INT seed for PRNG, zero to use random data source (0)"
# [293] " --relabel STRING relabel sequences with this prefix string"
# [294] " --relabel_keep keep the old label after the new when relabelling"
# [295] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [296] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [297] " --sample_pct REAL sampling percentage between 0.0 and 100.0"
# [298] " --sample_size INT sampling size"
# [299] " --sizein consider abundance info from input, do not ignore"
# [300] " --sizeout update abundance information in output"
# [301] " --xsize strip abundance information in output"
lerch-a/Rvsearch documentation built on Aug. 3, 2020, 5:30 p.m.
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Defines functions .execute .vsearchBin vsearch_version vsearch_usage chimeraDetectionDenovo
Documented in chimeraDetectionDenovo vsearch_usage vsearch_version
## Example
# "Usage: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rvsearch/vsearch [OPTIONS]"
# [6] "General options"
# [7] " --fasta_width INT width of FASTA seq lines, 0 for no wrap (80)"
# [9] " --log FILENAME write messages, timing and memory info to file"
# [10] " --maxseqlength INT maximum sequence length (50000)"
# [11] " --minseqlength INT min seq length (clust/derep/search: 32, other:1)"
# [12] " --notrunclabels do not truncate labels at first space"
# [13] " --quiet output just warnings and fatal errors to stderr"
# [14] " --threads INT number of threads to use, zero for all cores (0)"
## The main wrapper around vsearch
# Chimera detection using a reference database
# chimeraDetectionRef <- function()
# {
# # [19] " --uchime_ref FILENAME detect chimeras"
# # [25] " --db FILENAME reference database for --uchime_ref"
# # [36] " --self exclude identical labels for --uchime_ref"
# # [37] " --selfid exclude identical sequences for --uchime_ref"
# }
# Chimera detection de novo
chimeraDetectionDenovo <- function(filename, abskew=2.0, mindiffs=3L, mindiv=0.8, minh=0.28,
nonchimeras=sub(".fasta", "_nonchimera.fasta", filename),
chimeras=sub(".fasta", "_chimera.fasta", filename),
borderline=sub(".fasta", "_bordchimera.fasta", filename),
uchimeout=sub(".fasta", "_chimeraResults.txt", filename))
{
syscall <- paste("--uchime_denovo ", filename,
"--abskew", abskew,
"--mindiffs", mindiffs,
"--mindiv", mindiv,
"--minh", minh,
"--nonchimeras", nonchimerafile,
"--chimeras", chimerafile,
"--borderline", borderfile,
"--uchimeout", uchimeout, sep=" ")
# System call parameters
# [18] " --uchime_denovo FILENAME detect chimeras "
# [20] "Options"
# [21] " --abskew REAL min abundance ratio of parent vs chimera (2.0)"
# [28] " --mindiffs INT minimum number of differences in segment (3)"
# [29] " --mindiv REAL minimum divergence from closest parent (0.8)"
# [30] " --minh REAL minimum score (0.28)"
# [23] " --borderline FILENAME output borderline chimeric sequences to file"
# [24] " --chimeras FILENAME output chimeric sequences to file"
# [31] " --nonchimeras FILENAME output non-chimeric sequences to file"
# [40] " --uchimeout FILENAME output to chimera info to tab-separated file"
# Not supported in this function
# [26] " --dn REAL 'no' vote pseudo-count (1.4)"
# [27] " --fasta_score include chimera score in fasta output"
# [32] " --relabel STRING relabel nonchimeras with this prefix string"
# [33] " --relabel_keep keep the old label after the new when relabelling"
# [34] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [35] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [38] " --sizeout include abundance information when relabelling"
# [39] " --uchimealns FILENAME output chimera alignments to file"
# [22] " --alignwidth INT width of alignment in uchimealn output (80)"
# [41] " --uchimeout5 make output compatible with uchime version 5"
# [42] " --xn REAL 'no' vote weight (8.0)"
# [43] " --xsize strip abundance information in output"
return(invisible(.vsearchBin(args=syscall)))
}
## Helper function that return a description of the intended usage for vsearch
vsearch_usage <- function(){
print(.vsearchBin(args="--help"))
}
## Helper function that return the version of vsearch
vsearch_version <- function(){
print(.vsearchBin(args="--version"))
}
## A helper function to call the vsearch binaries with additional arguments.
.vsearchBin <- function(args="")
{
if(is.null(args) || args=="")
stop("The vsearch binaries need to be called with additional arguments")
args <- gsub("^ *| *$", "", args)
call <- paste(shQuote(file.path(system.file(package="Rvsearch"), "vsearch")), args)
return(system(call, intern=TRUE))
}
## The direct binary call function
.execute <- function(callstr, ...){
call <- file.path(shQuote(system.file(package="Rvsearch")), callstr)
return(system(call, ...))
}
# [45] "Clustering"
# [46] " --cluster_fast FILENAME cluster sequences after sorting by length"
# [47] " --cluster_size FILENAME cluster sequences after sorting by abundance"
# [48] " --cluster_smallmem FILENAME cluster already sorted sequences (see -usersort)"
# [49] "Options (most searching options also apply)"
# [50] " --centroids FILENAME output centroid sequences to FASTA file"
# [51] " --clusterout_id add cluster id info to consout and profile files"
# [52] " --clusterout_sort order msaout, consout, profile by decr abundance"
# [53] " --clusters STRING output each cluster to a separate FASTA file"
# [54] " --consout FILENAME output cluster consensus sequences to FASTA file"
# [55] " --cons_truncate do not ignore terminal gaps in MSA for consensus"
# [56] " --id REAL reject if identity lower"
# [57] " --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)"
# [58] " --msaout FILENAME output multiple seq. alignments to FASTA file"
# [59] " --profile FILENAME output sequence profile of each cluster to file"
# [60] " --qmask none|dust|soft mask seqs with dust, soft or no method (dust)"
# [61] " --relabel STRING relabel centroids with this prefix string"
# [62] " --relabel_keep keep the old label after the new when relabelling"
# [63] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [64] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [65] " --sizein propagate abundance annotation from input"
# [66] " --sizeorder sort accepted centroids by abundance (AGC)"
# [67] " --sizeout write cluster abundances to centroid file"
# [68] " --strand plus|both cluster using plus or both strands (plus)"
# [69] " --uc FILENAME specify filename for UCLUST-like output"
# [70] " --usersort indicate sequences not pre-sorted by length"
# [71] " --xsize strip abundance information in output"
# [73] "Dereplication and rereplication"
# [74] " --derep_fulllength FILENAME dereplicate sequences in the given FASTA file"
# [75] " --derep_prefix FILENAME dereplicate sequences in file based on prefixes"
# [76] " --rereplicate FILENAME rereplicate sequences in the given FASTA file"
# [77] "Options"
# [78] " --maxuniquesize INT maximum abundance for output from dereplication"
# [79] " --minuniquesize INT minimum abundance for output from dereplication"
# [80] " --output FILENAME output FASTA file"
# [81] " --relabel STRING relabel with this prefix string"
# [82] " --relabel_keep keep the old label after the new when relabelling"
# [83] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [84] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [85] " --sizein propagate abundance annotation from input"
# [86] " --sizeout write abundance annotation to output"
# [87] " --strand plus|both dereplicate plus or both strands (plus)"
# [88] " --topn INT output only n most abundant sequences after derep"
# [89] " --uc FILENAME filename for UCLUST-like dereplication output"
# [90] " --xsize strip abundance information in derep output"
# [92] "FASTQ filtering"
# [93] " --fastq_filter FILENAME filter FASTQ file, output to FASTQ or FASTA file"
# [94] "Options"
# [95] " --eeout include expected errors in FASTQ filter output"
# [96] " --fastaout FILENAME FASTA output filename for passed sequences"
# [97] " --fastaout_discarded FNAME FASTA filename for discarded sequences"
# [98] " --fastqout FILENAME FASTQ output filename for passed sequences"
# [99] " --fastqout_discarded FNAME FASTQ filename for discarded sequences"
# [100] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [101] " --fastq_maxee REAL maximum expected error value for FASTQ filter"
# [102] " --fastq_maxee_rate REAL maximum expected error rate for FASTQ filter"
# [103] " --fastq_maxns INT maximum number of N's for FASTQ filter"
# [104] " --fastq_minlen INT minimum length for FASTQ filter"
# [105] " --fastq_stripleft INT bases on the left to delete for FASTQ filter"
# [106] " --fastq_trunclen INT read length for FASTQ filter truncation"
# [107] " --fastq_truncqual INT base quality value for FASTQ filter truncation"
# [108] " --relabel STRING relabel filtered sequences with given prefix"
# [109] " --relabel_keep keep the old label after the new when relabelling"
# [110] " --relabel_md5 relabel filtered sequences with md5 digest"
# [111] " --relabel_sha1 relabel filtered sequences with sha1 digest"
# [112] " --sizeout include abundance information when relabelling"
# [113] " --xsize strip abundance information in output"
# [115] "FASTQ format conversion"
# [116] " --fastq_convert FILENAME convert between FASTQ file formats"
# [117] "Options"
# [118] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [119] " --fastq_asciiout INT FASTQ output quality score ASCII base char (33)"
# [120] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [121] " --fastq_qmaxout INT maximum base quality value for FASTQ output (41)"
# [122] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [123] " --fastq_qminout INT minimum base quality value for FASTQ output (0)"
# [124] ""
# [125] "FASTQ format detection and quality analysis"
# [126] " --fastq_chars FILENAME analyse FASTQ file for version and quality range"
# [127] "Options"
# [128] " --fastq_tail INT min length of tails to count for fastq_chars (4)"
# [130] "FASTQ paired-end reads merging"
# [131] " --fastq_mergepairs FILENAME merge paired-end reads into one sequence"
# [132] "Options:"
# [133] " --eetabbedout FILENAME output error statistics to specified file"
# [134] " --fastaout FILENAME FASTA output filename for merged sequences"
# [135] " --fastaout_notmerged_fwd FN FASTA filename for non-merged forward sequences"
# [136] " --fastaout_notmerged_rev FN FASTA filename for non-merged reverse sequences"
# [137] " --fastq_allowmergestagger Allow merging of staggered reads"
# [138] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [139] " --fastq_eeout include expected errors in FASTQ output"
# [140] " --fastq_maxdiffs maximum number of different bases in overlap (5)"
# [141] " --fastq_maxee REAL maximum expected error value for merged sequence"
# [142] " --fastq_maxmergelen maximum length of entire merged sequence"
# [143] " --fastq_maxns INT maximum number of N's"
# [144] " --fastq_minlen INT minimum input read length after truncation (1)"
# [145] " --fastq_minmergelen minimum length of entire merged sequence"
# [146] " --fastq_minovlen minimum length of overlap between reads (16)"
# [147] " --fastq_nostagger disallow merging of staggered reads (default)"
# [148] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [149] " --fastq_qmaxout INT maximum base quality value for FASTQ output (41)"
# [150] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [151] " --fastq_qminout INT minimum base quality value for FASTQ output (0)"
# [152] " --fastq_truncqual INT base quality value for truncation"
# [153] " --fastqout FILENAME FASTQ output filename for merged sequences"
# [154] " --fastqout_notmerged_fwd F FASTQ filename for non-merged forward sequences"
# [155] " --fastqout_notmerged_rev F FASTQ filename for non-merged reverse sequences"
# [156] " --label_suffix suffix to append to label of merged sequences"
# [157] " --reverse FILENAME specify FASTQ file with reverse reads"
# [159] "FASTQ quality statistics"
# [160] " --fastq_stats FILENAME report FASTQ file statistics"
# [161] " --fastq_eestats FILENAME quality score and expected error statistics"
# [162] "Options"
# [163] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [164] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [165] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [167] "Masking (new)"
# [168] " --fastx_mask FILENAME mask sequences in the given FASTA or FASTQ file"
# [169] "Options"
# [170] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [171] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [172] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [173] " --fastaout FILENAME output to specified FASTA file"
# [174] " --fastqout FILENAME output to specified FASTQ file"
# [175] " --hardmask mask by replacing with N instead of lower case"
# [176] " --max_unmasked_pct max unmasked % of sequences to keep (100.0)"
# [177] " --min_unmasked_pct min unmasked % of sequences to keep (0.0)"
# [178] " --qmask none|dust|soft mask seqs with dust, soft or no method (dust)"
# [180] "Masking (old)"
# [181] " --maskfasta FILENAME mask sequences in the given FASTA file"
# [182] "Options"
# [183] " --hardmask mask by replacing with N instead of lower case"
# [184] " --output FILENAME output to specified FASTA file"
# [185] " --qmask none|dust|soft mask seqs with dust, soft or no method (dust)"
# [186] ""
# [187] "Pairwise alignment"
# [188] " --allpairs_global FILENAME perform global alignment of all sequence pairs"
# [189] "Options (most searching options also apply)"
# [190] " --alnout FILENAME filename for human-readable alignment output"
# [191] " --acceptall output all pairwise alignments"
# [193] "Reverse complementation"
# [194] " --fastx_revcomp FILENAME Reverse-complement seqs in FASTA or FASTQ file"
# [195] "Options"
# [196] " --fastaout FILENAME FASTA output filename"
# [197] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [198] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [199] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [200] " --fastqout FILENAME FASTQ output filename"
# [201] " --label_suffix STRING Label to append to identifier in the output"
# [203] "Searching"
# [204] " --search_exact FILENAME filename of queries for exact match search"
# [205] " --usearch_global FILENAME filename of queries for global alignment search"
# [206] "Options"
# [207] " --alnout FILENAME filename for human-readable alignment output"
# [208] " --blast6out FILENAME filename for blast-like tab-separated output"
# [209] " --db FILENAME filename for FASTA formatted database for search"
# [210] " --dbmask none|dust|soft mask db with dust, soft or no method (dust)"
# [211] " --dbmatched FILENAME FASTA file for matching database sequences"
# [212] " --dbnotmatched FILENAME FASTA file for non-matching database sequences"
# [213] " --fastapairs FILENAME FASTA file with pairs of query and target"
# [214] " --fulldp full dynamic programming alignment (always on)"
# [215] " --gapext STRING penalties for gap extension (2I/1E)"
# [216] " --gapopen STRING penalties for gap opening (20I/2E)"
# [217] " --hardmask mask by replacing with N instead of lower case"
# [218] " --id REAL reject if identity lower"
# [219] " --iddef INT id definition, 0-4=CD-HIT,all,int,MBL,BLAST (2)"
# [220] " --idprefix INT reject if first n nucleotides do not match"
# [221] " --idsuffix INT reject if last n nucleotides do not match"
# [222] " --leftjust reject if terminal gaps at alignment left end"
# [223] " --match INT score for match (2)"
# [224] " --matched FILENAME FASTA file for matching query sequences"
# [225] " --maxaccepts INT number of hits to accept and show per strand (1)"
# [226] " --maxdiffs INT reject if more substitutions or indels"
# [227] " --maxgaps INT reject if more indels"
# [228] " --maxhits INT maximum number of hits to show (unlimited)"
# [229] " --maxid REAL reject if identity higher"
# [230] " --maxqsize INT reject if query abundance larger"
# [231] " --maxqt REAL reject if query/target length ratio higher"
# [232] " --maxrejects INT number of non-matching hits to consider (32)"
# [233] " --maxsizeratio REAL reject if query/target abundance ratio higher"
# [234] " --maxsl REAL reject if shorter/longer length ratio higher"
# [235] " --maxsubs INT reject if more substitutions"
# [236] " --mid REAL reject if percent identity lower, ignoring gaps"
# [237] " --mincols INT reject if alignment length shorter"
# [238] " --minqt REAL reject if query/target length ratio lower"
# [239] " --minsizeratio REAL reject if query/target abundance ratio lower"
# [240] " --minsl REAL reject if shorter/longer length ratio lower"
# [241] " --mintsize INT reject if target abundance lower"
# [242] " --minwordmatches INT minimum number of word matches required (10)"
# [243] " --mismatch INT score for mismatch (-4)"
# [244] " --notmatched FILENAME FASTA file for non-matching query sequences"
# [245] " --output_no_hits output non-matching queries to output files"
# [246] " --pattern STRING option is ignored"
# [247] " --qmask none|dust|soft mask query with dust, soft or no method (dust)"
# [248] " --query_cov REAL reject if fraction of query seq. aligned lower"
# [249] " --rightjust reject if terminal gaps at alignment right end"
# [250] " --rowlen INT width of alignment lines in alnout output (64)"
# [251] " --samheader include a header in the SAM output file"
# [252] " --samout FILENAME filename for SAM format output"
# [253] " --self reject if labels identical"
# [254] " --selfid reject if sequences identical"
# [255] " --sizeout write abundance annotation to dbmatched file"
# [256] " --slots INT option is ignored"
# [257] " --strand plus|both search plus or both strands (plus)"
# [258] " --target_cov REAL reject if fraction of target seq. aligned lower"
# [259] " --top_hits_only output only hits with identity equal to the best"
# [260] " --uc FILENAME filename for UCLUST-like output"
# [261] " --uc_allhits show all, not just top hit with uc output"
# [262] " --userfields STRING fields to output in userout file"
# [263] " --userout FILENAME filename for user-defined tab-separated output"
# [264] " --weak_id REAL include aligned hits with >= id; continue search"
# [265] " --wordlength INT length of words for database index 3-15 (8)"
# [267] "Shuffling and sorting"
# [268] " --shuffle FILENAME shuffle order of sequences in FASTA file randomly"
# [269] " --sortbylength FILENAME sort sequences by length in given FASTA file"
# [270] " --sortbysize FILENAME abundance sort sequences in given FASTA file"
# [271] "Options"
# [272] " --maxsize INT maximum abundance for sortbysize"
# [273] " --minsize INT minimum abundance for sortbysize"
# [274] " --output FILENAME output to specified FASTA file"
# [275] " --randseed INT seed for PRNG, zero to use random data source (0)"
# [276] " --relabel STRING relabel sequences with this prefix string"
# [277] " --relabel_keep keep the old label after the new when relabelling"
# [278] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [279] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [280] " --sizeout include abundance information when relabelling"
# [281] " --topn INT output just first n sequences"
# [282] " --xsize strip abundance information in output"
# [284] "Subsampling"
# [285] " --fastx_subsample FILENAME subsample sequences from given FASTA/FASTQ file"
# [286] "Options"
# [287] " --fastaout FILENAME output FASTA file for subsamples"
# [288] " --fastq_ascii INT FASTQ input quality score ASCII base char (33)"
# [289] " --fastq_qmax INT maximum base quality value for FASTQ input (41)"
# [290] " --fastq_qmin INT minimum base quality value for FASTQ input (0)"
# [291] " --fastqout FILENAME output FASTQ file for subsamples"
# [292] " --randseed INT seed for PRNG, zero to use random data source (0)"
# [293] " --relabel STRING relabel sequences with this prefix string"
# [294] " --relabel_keep keep the old label after the new when relabelling"
# [295] " --relabel_md5 relabel with md5 digest of normalized sequence"
# [296] " --relabel_sha1 relabel with sha1 digest of normalized sequence"
# [297] " --sample_pct REAL sampling percentage between 0.0 and 100.0"
# [298] " --sample_size INT sampling size"
# [299] " --sizein consider abundance info from input, do not ignore"
# [300] " --sizeout update abundance information in output"
# [301] " --xsize strip abundance information in output"
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