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seqtools
Sequence operation utilities
Sequence search tools and sequence operation tools Sequence search tools and sequence operation tools Copyright © xie.guigang@gcmodeller.org 2014
Module AssemblyName: file:///D:/GCModeller/GCModeller/bin/seqtools.exe
Root namespace: seqtools.Utilities
If you are having trouble debugging this Error, first read the best practices tutorial for helpful tips that address many common problems:
The debugging facility Is helpful To figure out what's happening under the hood:
If you're still stumped, you can try get help from author directly from E-mail:
All of the command that available in this program has been list below:
| Function API | Info |
|---|---|
| /align | |
| /check.attrs | |
| /Clustal.Cut | |
| /gwANI | |
| /Loci.describ | Testing |
| /logo | * Drawing the sequence logo from the clustal alignment result. |
| /Mirrors.Context | This function will convert the mirror data to the simple segment object data |
| /Mirrors.Context.Batch | This function will convert the mirror data to the simple segment object data |
| /Mirrors.Group | |
| /Mirrors.Group.Batch | |
| /nw | RunNeedlemanWunsch |
| /Palindrome.BatchTask | |
| /Palindrome.Workflow | |
| /Sigma | |
| /SimpleSegment.AutoBuild | |
| /SimpleSegment.Mirrors | |
| /SimpleSegment.Mirrors.Batch | |
| /SNP | |
| /Time.Diffs | |
| /Write.Seeds | |
| -321 | Polypeptide sequence 3 letters to 1 lettes sequence. |
| --align | |
| --align.Self | |
| -complement | |
| --Drawing.ClustalW | |
| -pattern_search | Parsing the sequence segment from the sequence source using regular expression. |
| Repeats.Density | |
| -reverse | |
| rev-Repeats.Density | |
| Search.Batch | Batch search for repeats. |
| --translates | Translates the ORF gene as protein sequence. If any error was output from the console, please using > operator dump the output to a log file for the analysis. |
Tools command that works around the fasta format data.
| Function API | Info |
|---|---|
| /Compare.By.Locis | |
| /Distinct | Distinct fasta sequence by sequence content. |
| /Get.Locis | |
| /Gff.Sites | |
| /Merge | Only search for 1 level folder, dit not search receve. |
| /Merge.Simple | This tools just merge the fasta sequence into one larger file. |
| /Select.By_Locus | |
| /Split | |
| /subset | |
| /To_Fasta | Convert the sequence data in a excel annotation file into a fasta sequence file. |
| -segment | |
| --segments | |
| --Trim |
Tools command that using for finding Palindrome sites.
| Function API | Info |
|---|---|
| /Mirror.Batch | |
| /Mirror.Fuzzy | |
| /Mirror.Fuzzy.Batch | |
| /Mirror.Vector | |
| /Mirrors.Nt.Trim | |
| /Palindrome.Screen.MaxMatches | |
| /Palindrome.Screen.MaxMatches.Batch | |
| --Hairpinks | |
| --Hairpinks.batch.task | |
| --ImperfectsPalindrome.batch.Task | |
| --Mirror.From.Fasta | Mirror Palindrome, search from a fasta file. |
| --Mirror.From.NT | Mirror Palindrome, and this function is for the debugging test |
| --Palindrome.batch.Task | |
| --Palindrome.From.FASTA | |
| --Palindrome.From.NT | This function is just for debugger test, /nt parameter is the nucleotide sequence data as ATGCCCC |
| --Palindrome.Imperfects | |
| --PerfectPalindrome.Filtering | |
| --ToVector |
Prototype: seqtools.Utilities::Int32 Align2(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /align /query <query.fasta> /subject <subject.fasta> [/blosum <matrix.txt> /out <out.xml>]seqtoolsPrototype: seqtools.Utilities::Int32 CheckHeaders(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /check.attrs /in <in.fasta> /n <attrs.count> [/all]seqtoolsPrototype: seqtools.Utilities::Int32 CutMlAlignment(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Clustal.Cut /in <in.fasta> [/left 0.1 /right 0.1 /out <out.fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 CompareFile(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Compare.By.Locis /file1 <file1.fasta> /file2 </file2.fasta>seqtoolsDistinct fasta sequence by sequence content.
Prototype: seqtools.Utilities::Int32 Distinct(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Distinct /in <in.fasta> [/out <out.fasta> /by_Uid <uid_regexp>]seqtoolsPrototype: seqtools.Utilities::Int32 GetSimpleSegments(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Get.Locis /in <locis.csv> /nt <genome.nt.fasta> [/out <outDIR>]seqtoolsPrototype: seqtools.Utilities::Int32 GffSites(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Gff.Sites /fna <genomic.fna> /gff <genome.gff> [/out <out.fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 gwANI(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /gwANI /in <in.fasta> [/fast /out <out.Csv>]seqtoolsTesting
Prototype: seqtools.Utilities::Int32 LociDescript(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Loci.describ /ptt <genome-context.ptt> [/test <loci:randomize> /complement /unstrand]seqtools- Drawing the sequence logo from the clustal alignment result.
Prototype:
seqtools.Utilities::Int32 SequenceLogo(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /logo /in <clustal.fasta> [/out <out.png> /title ""]seqtoolsThe file path of the clustal output fasta file.
The output sequence logo image file path. default is the same name as the input fasta sequence file.
The display title on the sequence logo, default is using the fasta file name.
Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile Example:
[
]Only search for 1 level folder, dit not search receve.
Prototype: seqtools.Utilities::Int32 Merge(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Merge /in <fasta.DIR> [/out <out.fasta> /trim /unique /ext <*.fasta> /brief]seqtoolsThis tools just merge the fasta sequence into one larger file.
Prototype: seqtools.Utilities::Int32 SimpleMerge(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Merge.Simple /in <DIR> [/exts <default:*.fasta,*.fa> /line.break 120 /out <out.fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 MirrorBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirror.Batch /nt <nt.fasta> [/out <out.csv> /mp /min <3> /max <20> /num_threads <-1>]seqtoolsCalculation in the multiple process mode?
Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile Example:
[
]Decalre: System.Boolean Example:
trueDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}Prototype: seqtools.Utilities::Int32 FuzzyMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirror.Fuzzy /in <in.fasta> [/out <out.csv> /cut 0.6 /max-dist 6 /min 3 /max 20]seqtoolsDecalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:
{
"Extension": {
"DynamicHash": {
"Properties": {
},
"source": [
]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}Prototype: seqtools.Utilities::Int32 FuzzyMirrorsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirror.Fuzzy.Batch /in <in.fasta/DIR> [/out <out.DIR> /cut 0.6 /max-dist 6 /min 3 /max 20 /num_threads <-1>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}Prototype: seqtools.Utilities::Int32 MirrorsVector(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirror.Vector /in <inDIR> /size <genome.size> [/out out.txt]seqtoolsThis function will convert the mirror data to the simple segment object data
Prototype: seqtools.Utilities::Int32 MirrorContext(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirrors.Context /in <mirrors.csv> /PTT <genome.ptt> [/trans /strand <+/-> /out <out.csv> /stranded /dist <500bp>]seqtoolsEnable this option will using genome_size minus loci location for the location correction, only works in reversed strand.
This function will convert the mirror data to the simple segment object data
Prototype: seqtools.Utilities::Int32 MirrorContextBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirrors.Context.Batch /in <mirrors.csv.DIR> /PTT <genome.ptt.DIR> [/trans /strand <+/-> /out <out.csv> /stranded /dist <500bp> /num_threads -1]seqtoolsEnable this option will using genome_size minus loci location for the location correction, only works in reversed strand.
Prototype: seqtools.Utilities::Int32 MirrorGroups(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirrors.Group /in <mirrors.Csv> [/batch /fuzzy <-1> /out <out.DIR>]seqtools-1 means group sequence by string equals compared, and value of 0-1 means using string fuzzy compare.
Prototype: seqtools.Utilities::Int32 MirrorGroupsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirrors.Group.Batch /in <mirrors.DIR> [/fuzzy <-1> /out <out.DIR> /num_threads <-1>]seqtoolsPrototype: seqtools.Utilities::Int32 TrimNtMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Mirrors.Nt.Trim /in <mirrors.Csv> [/out <out.Csv>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}RunNeedlemanWunsch
Prototype: seqtools.Utilities::Int32 NW(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /nw /query <query.fasta> /subject <subject.fasta> [/out <out.txt>]seqtoolsDecalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:
{
"Extension": {
"DynamicHash": {
"Properties": {
},
"source": [
]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:
{
"Extension": {
"DynamicHash": {
"Properties": {
},
"source": [
]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}Decalre: System.String Example:
"System.String"Prototype: seqtools.Utilities::Int32 PalindromeBatchTask(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Palindrome.BatchTask /in <in.DIR> [/num_threads 4 /min 3 /max 20 /min-appears 2 /cutoff <0.6> /Palindrome /max-dist <1000 (bp)> /partitions <-1> /out <out.DIR>]seqtoolsOnly search for Palindrome, not includes the repeats data.
Prototype: seqtools.Utilities::Int32 FilteringMatches(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Palindrome.Screen.MaxMatches /in <in.csv> /min <min.max-matches> [/out <out.csv>]seqtoolsPrototype: seqtools.Utilities::Int32 FilteringMatchesBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Palindrome.Screen.MaxMatches.Batch /in <inDIR> /min <min.max-matches> [/out <out.DIR> /num_threads <-1>]seqtoolsPrototype: seqtools.Utilities::Int32 PalindromeWorkflow(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Palindrome.Workflow /in <in.fasta> [/batch /min-appears 2 /min 3 /max 20 /cutoff <0.6> /max-dist <1000 (bp)> /Palindrome /partitions <-1> /out <out.DIR>]seqtoolsThis is a single sequence fasta file.
Only search for Palindrome, not includes the repeats data.
Prototype: seqtools.Utilities::Int32 SelectByLocus(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Select.By_Locus /in <locus.txt> /fa <fasta/.inDIR> [/out <out.fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 Sigma(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Sigma /in <in.fasta> [/out <out.Csv> /simple /round <-1>]seqtoolsPrototype: seqtools.Utilities::Int32 ConvertsAuto(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /SimpleSegment.AutoBuild /in <locis.csv> [/out <out.csv>]seqtoolsDecalre: Microsoft.VisualBasic.Data.csv.DocumentStream.File Example:
[
]Decalre: SMRUCC.genomics.SequenceModel.NucleotideModels.SimpleSegment Example:
{
"Complement": "System.String",
"Ends": 0,
"ID": "System.String",
"SequenceData": "System.String",
"Start": 0,
"Strand": "System.String"
}Prototype: seqtools.Utilities::Int32 ConvertMirrors(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /SimpleSegment.Mirrors /in <in.csv> [/out <out.csv>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}Decalre: SMRUCC.genomics.SequenceModel.NucleotideModels.SimpleSegment Example:
{
"Complement": "System.String",
"Ends": 0,
"ID": "System.String",
"SequenceData": "System.String",
"Start": 0,
"Strand": "System.String"
}Prototype: seqtools.Utilities::Int32 ConvertMirrorsBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /SimpleSegment.Mirrors.Batch /in <in.DIR> [/out <out.DIR>]seqtoolsPrototype: seqtools.Utilities::Int32 SNP(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /SNP /in <nt.fasta> [/ref 0 /pure /monomorphic]seqtoolsDecalre: SMRUCC.genomics.SequenceModel.FASTA.FastaFile Example:
[
]Decalre: System.Int32 Example:
0Decalre: System.Boolean Example:
truePrototype: seqtools.Utilities::Int32 Split(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Split /in <in.fasta> [/n <4096> /out <outDIR>]seqtoolsPrototype: seqtools.Utilities::Int32 SubSet(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /subset /lstID <lstID.txt> /fa <source.fasta>seqtoolsPrototype: seqtools.Utilities::Int32 TimeDiffs(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Time.Diffs /in <aln.fasta> [/out <out.csv>]seqtoolsConvert the sequence data in a excel annotation file into a fasta sequence file.
Prototype: seqtools.Utilities::Int32 ToFasta(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /To_Fasta /in <anno.csv> [/out <out.fasta> /attrs <gene;locus_tag;gi;location,...> /seq <Sequence>]seqtoolsPrototype: seqtools.Utilities::Int32 WriteSeeds(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools /Write.Seeds /out <out.dat> [/prot /max <20>]seqtoolsPolypeptide sequence 3 letters to 1 lettes sequence.
Prototype: seqtools.Utilities::Int32 PolypeptideBriefs(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools -321 /in <sequence.txt> [/out <out.fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 Align(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --align /query <query.fasta> /subject <subject.fasta> [/out <out.DIR> /cost <0.7>]seqtoolsPrototype: seqtools.Utilities::Int32 AlignSelf(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --align.Self /query <query.fasta> /out <out.DIR> [/cost 0.75]seqtoolsPrototype: seqtools.Utilities::Int32 Complement(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools -complement -i <input_fasta> [-o <output_fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 DrawClustalW(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Drawing.ClustalW /in <align.fasta> [/out <out.png> /dot.Size 10]seqtoolsPrototype: seqtools.Utilities::Int32 Hairpinks(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Hairpinks /in <in.fasta> [/out <out.csv> /min <6> /max <7> /cutoff 3 /max-dist <35 (bp)>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.ImperfectPalindrome Example:
{
"Distance": 0,
"Evolr": "System.String",
"Left": 0,
"Matches": "System.String",
"MaxMatch": 0,
"Palindrome": "System.String",
"Paloci": 0,
"Score": 0,
"Site": "System.String"
}Prototype: seqtools.Utilities::Int32 HairpinksBatch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Hairpinks.batch.task /in <in.fasta> [/out <outDIR> /min <6> /max <7> /cutoff <0.6> /max-dist <35 (bp)> /num_threads <-1>]seqtoolsPrototype: seqtools.Utilities::Int32 BatchSearchImperfectsPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --ImperfectsPalindrome.batch.Task /in <in.fasta> /out <outDir> [/min <3> /max <20> /cutoff <0.6> /max-dist <1000 (bp)> /num_threads <-1>]seqtoolsMirror Palindrome, search from a fasta file.
Prototype: seqtools.Utilities::Int32 SearchMirrotFasta(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Mirror.From.Fasta /nt <nt-sequence.fasta> [/out <out.csv> /min <3> /max <20>]seqtoolsThis fasta file should contains only just one sequence.
Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:
{
"Extension": {
"DynamicHash": {
"Properties": {
},
"source": [
]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}Mirror Palindrome, and this function is for the debugging test
Prototype: seqtools.Utilities::Int32 SearchMirrotNT(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Mirror.From.NT /nt <nt-sequence> /out <out.csv> [/min <3> /max <20>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}Prototype: seqtools.Utilities::Int32 BatchSearchPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Palindrome.batch.Task /in <in.fasta> /out <outDir> [/min <3> /max <20> /num_threads <-1>]seqtoolsPrototype: seqtools.Utilities::Int32 SearchPalindromeFasta(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Palindrome.From.Fasta /nt <nt-sequence.fasta> [/out <out.csv> /min <3> /max <20>]seqtoolsFasta sequence file, and this file should just contains only one sequence.
Decalre: SMRUCC.genomics.SequenceModel.FASTA.FastaToken Example:
{
"Extension": {
"DynamicHash": {
"Properties": {
},
"source": [
]
}
},
"SequenceData": "System.String",
"Attributes": [
"System.String"
]
}Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}This function is just for debugger test, /nt parameter is the nucleotide sequence data as ATGCCCC
Prototype: seqtools.Utilities::Int32 SearchPalindromeNT(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Palindrome.From.NT /nt <nt-sequence> /out <out.csv> [/min <3> /max <20>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.PalindromeLoci Example:
{
"Loci": "System.String",
"MirrorSite": "System.String",
"PalEnd": 0,
"Palindrome": "System.String",
"Start": 0
}Prototype: seqtools.Utilities::Int32 ImperfectPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Palindrome.Imperfects /in <in.fasta> [/out <out.csv> /min <3> /max <20> /cutoff <0.6> /max-dist <1000 (bp)> /partitions <-1>]seqtoolsParsing the sequence segment from the sequence source using regular expression.
Prototype: seqtools.Utilities::Int32 PatternSearchA(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools -pattern_search -i <file_name> -p <regex_pattern>[ -o <output_directory> -f <format:fsa/gbk>]seqtools -pattern_search -i ~/xcc8004.txt -p TTA{3}N{1,2} -f fsaThe sequence input data source file, it can be a fasta or genbank file.
~/Desktop/xcc8004.txtThis switch specific the regular expression pattern for search the sequence segment, for more detail information about the regular expression please read the user manual.
N{1,5}TAOptional, this switch value specific the output directory for the result data, default is user Desktop folder.
~/Documents/Optional, specific the input file format for the sequence reader, default value is FASTA sequence file. fsa - The input sequence data file is a FASTA format file; gbk - The input sequence data file is a NCBI genbank flat file.
fsaPrototype: seqtools.Utilities::Int32 FilterPerfectPalindrome(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --PerfectPalindrome.Filtering /in <inDIR> [/min <8> /out <outDIR>]seqtoolsDecalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.ImperfectPalindrome Example:
{
"Distance": 0,
"Evolr": "System.String",
"Left": 0,
"Matches": "System.String",
"MaxMatch": 0,
"Palindrome": "System.String",
"Paloci": 0,
"Score": 0,
"Site": "System.String"
}Prototype: seqtools.Utilities::Int32 RepeatsDensity(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools Repeats.Density /dir <dir> /size <size> /ref <refName> [/out <out.csv> /cutoff <default:=0>]seqtoolsPrototype: seqtools.Utilities::Int32 Reverse(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools -reverse -i <input_fasta> [-o <output_fasta>]seqtoolsPrototype: seqtools.Utilities::Int32 revRepeatsDensity(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools rev-Repeats.Density /dir <dir> /size <size> /ref <refName> [/out <out.csv> /cutoff <default:=0>]seqtoolsBatch search for repeats.
Prototype: seqtools.Utilities::Int32 BatchSearch(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools Search.Batch /aln <alignment.fasta> [/min 3 /max 20 /min-rep 2 /out <./>]seqtoolsThe input fasta file should be the output of the clustal multiple alignment fasta output.
Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.RepeatsView Example:
{
"Left": 0,
"Locis": [
0
],
"SequenceData": "System.String"
}Decalre: SMRUCC.genomics.Analysis.SequenceTools.SequencePatterns.Topologically.RevRepeatsView Example:
{
"Left": 0,
"Locis": [
0
],
"SequenceData": "System.String",
"RevLocis": [
0
],
"RevSegment": "System.String"
}Prototype: seqtools.Utilities::Int32 GetSegment(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools -segment /fasta <Fasta_Token> [-loci <loci>] [/left <left> /length <length> /right <right> [/reverse]] [/ptt <ptt> /geneID <gene_id> /dist <distance> /downstream] -o <saved> [-line.break 100]seqtoolsPrototype: seqtools.Utilities::Int32 GetSegments(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --segments /regions <regions.csv> /fasta <nt.fasta> [/complement /reversed /brief-dump]seqtoolsIf the sequence is on the complement strand, reversed it after complement operation?
If this Boolean switch is set on, then all of the reversed strand segment will be complemenet and reversed.
If this parameter is set up true, then only the locus_tag of the ORF gene will be dump to the fasta sequence.
Prototype: seqtools.Utilities::Int32 ToVector(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --ToVector /in <in.DIR> /min <4> /max <8> /out <out.txt> /size <genome.size>seqtoolsTranslates the ORF gene as protein sequence. If any error was output from the console, please using > operator dump the output to a log file for the analysis.
Prototype: seqtools.Utilities::Int32 Translates(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --translates /orf <orf.fasta> [/transl_table 1 /force]seqtoolsORF gene nt sequence should be completely complement and reversed as forwards strand if it is complement strand.
This force parameter will force the translation program ignore of the stop code and continute sequence translation.
Available index value was described at http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=tgencodes#SG25
Prototype: seqtools.Utilities::Int32 Trim(Microsoft.VisualBasic.CommandLine.CommandLine)
seqtools --Trim /in <in.fasta> [/case <u/l> /break <-1/int> /out <out.fasta> /brief]seqtoolsAdjust the letter case of your sequence, l for lower case and u for upper case. Default value is upper case.
Adjust the sequence break when this program write the fasta sequence, default is -1 which means no break, write all sequence in one line.
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