closeProject

To close the current project without saving it.

(None available)

compactProject

Same as the Project > Update > Compact menu command.

We recommend using this command after using deleteContig or deleteSequence but before resaving the project using the saveProject command.

(None available)

exportConsensusEnds

To export the first 1000 bases and the last 1000 bases of contigs from a scaffold. The contigs are exported only in position order.

Any valid scaffold specifier

See Specifying Scaffolds.

file:"pathname\filename.ext"

Specifies the location and name for the output file. You must include the correct extension for the chosen file format k(as shown below). The pathname\filename must be enclosed in quotes.

To export Consensus Ends 1, 7 and 44 to an Extended FastA file named Consensi-1-7-44.fas:

exportConsensusEnds

          scaffolds:{1 7 44}

          file:"Consensi-1-7-44.fas"

          format:FAS

Specify the format for the output file by choosing of the following format parameters. If you do not use this parameter in your script, consensi will be exported into a single GenBank file (.gbk) by default.*

format:FAS

Extended FastA format (saves sequence info); use “.fas” as the filename extension in the file parameter.

format:Genbank

Genbank flatfile format; use “.gbk” as the filename extension in the file parameter.

exportContigInfo

To save information about a specific contig.

Any valid contig specifier

See Specifying Contigs.

openProject file: "Dual-End Sample.sqd"

exportContigInfo contigs: {all} file: "results/pairs0.txt" pairs:0

exportContigInfo contigs: {all} file: "results/pairs1.txt" pairs:1

exportContigInfo contigs: {all} file: "results/pairs2.txt" pairs:2

file:"pathname\filename.txt"

Specifies the location and name for the output file. The pathname\filename must be enclosed in quotes. Using this parameter is equivalent to using the File > Save Contig Info menu command with the file format as “tab-delimited.”

pairs

The values for this parameter are 0, 1, and 2.

0 = don't export pair info (default).

1 = export pair info for all sequences and include pair info where relevant.

2 = only export information for sequences with pair data.

When using pairs:1 and pairs:2, these columns are added to the report:

pairDist, pairColor, seqname, pairContID, pairID, pairScheme

exportContigs

To export the specified contigs into a single file (which can contain multiple sequences).

Any valid contig specifier

See Specifying Contigs.

Example 1: To export Contigs 1, 7 and 44 to a DNA Multi-Seq file named Consensi-1-7-44.mseq, and only include areas of the contigs with a depth of at least 3:

exportContigs

          contigs:{1 7 44}

          file:"Consensi-1-7-44.mseq"

          format:DNAMulti

coverage:3

Example 2: To save Contigs 1 and 9 as individual Lasergene DNA sequence files, you must use a separate exportContigs statement for each output file:

exportContigs

          contigs:{1}

          file:"C:\Data\contig1.seq"

          format:dna

exportContigs

          contigs:{9}

          file:"C:\Data\contig9.seq"

          format:dna

Example 3: To export only the segment of Contig 1 between 400-900 bp and to retain its consensus gaps:

exportContigs

          contigs:{1 (400>900)}

doGaps:true

doFeatures:true

file:"pathname\filename.ext"

Specifies the location and name for the output file. You must include the correct extension for the chosen file format. The pathname\filename must be enclosed in quotes.

Specify the format for the output file by choosing of the following format parameters. If you do not use this parameter in your script, consensi will be exported into a single multi-FastA file by default.*

format:DNA

Lasergene DNA sequence format; use “.seq” as the filename extension in the file parameter. This file type only supports one sequence per file. Attempting to use this format to export multiple contigs will result in exporting a DNA Multi Seq file (.mseq).

format:DNAMulti

DNA Multi-Seq format; use “.mseq” as the filename extension in the file parameter.

format:FASSimple

FastA format (saves sequence name only); use “.fas” as the filename extension in the file parameter.

format:FAS

Extended FastA format (saves sequence info); use “.fas” as the filename extension in the file parameter.

format:FasAndQual

Saves as two FastA files—one including the sequence(s) and one containing chromatogram information; use “.fas” as the filename extension in the file parameter.

format:Genbank

Genbank flatfile format; use “.gbk” as the filename extension in the file parameter.

format:GCG

GCG format; use “.gcg” as the filename extension in the file parameter. This file type only supports one sequence per file. Using this type to export multiple contigs will result in exporting only the first contig.

Additional optional parameters:

doGaps:true

Retains gaps in the consensus.

doGaps:false

Removes gaps in the consensus.

doFeature:true

Retains contig information and construction features so that you may view them in the comments pane of SeqBuilder Pro.

doFeature:false

Does not retain contig information or construction features.

coverage:3

The coverage required for an area of a contig to be exported. Portions of a contig not meeting this threshold will not be included in the exported data. Note that SeqMan will only export .seq (format:DNA) or .mseq (format:DNAMulti) files when the coverage parameter is used.

exportGenVision

To export a SeqMan project to GenVision.

file:"pathname\filename"

The pathname\filename where the GenVision project and associated .txt files will be saved must be enclosed in quotes. If the pathname\filename you enter already exists, it will be overwritten.

exportProjectInfo

To export the Project Statistics report to a specific file.

file:"pathname\filename.txt"

The pathname\filename where the report will be saved must be enclosed in quotes and terminate with a valid extension—usually “.txt” If the pathname\filename you enter already exists, it will be overwritten.

Additional optional parameters:

sortOrder:length

Sorts the Project Statistics report by contig length.

sortOrder:name

Sorts the Project Statistics report by contig name.

sortOrder:num

Sorts the Project Statistics report by the number of sequences in each contig.

sortOrder:position

Sorts the Project Statistics report by the contig position.

sortOrder:conflict

Sorts the Project Statistics report by the number of conflicts.

showSummary:true

Includes the summary for the Project Statistics report.

showSummary:false

Does not include the summary for the Project Statistics report.

showAmbig:true

Shows ambiguities for the Project Statistics report.

showAmbig:false

Does not show ambiguities for the Project Statistics report.

showContigInfo:true

Includes the individual contig info from the Project Statistics report.

showContigInfo:false

Excludes the individual contig info from the Project Statistics report.

seqnumthreshold:10

Excludes contigs from the Project Statistics reports that do not meet the threshold, in this example of having at least 10 sequences.

exportSequences

To export all of the sequences from one or more contigs.

Any valid contig specifier

See Specifying Contigs.

To export the sequences from all contigs into Extended FastA format while retaining consensus gaps:

exportSequences

contigs:all

          file:"C:\Datafolder\Mycontig.fas"

          format: FAS

          doGaps:true

file:"pathname\filename.ext"

Specifies the location and name for the output file. You must include the correct extension for the chosen file format. The pathname\filename must be enclosed in quotes.

exportQ_N:[true/false]

Specifies if Q Scores or Q/n Scores will be exported for trace data when format:FasAndQual is used. (See below.) When true, the Q/n scores are exported; when false, the Q Scores are exported.

Specify the format for the output file by choosing one of the following format parameters. If you do not use this parameter in your script, consensi will be exported into a single multi-FastA file by default.

format:DNAmulti

DNA Multi-Seq format; use “.mseq” as the filename extension in the file parameter.

format:FASSimple

FastA format (saves sequence name only); use “.fas” as the filename extension in the file parameter.

format:FAS

Extended FastA format (saves sequence info); use “.fas” as the filename extension in the file parameter.

format:FasAndQual

Saves as two FastA files—one including the sequence(s) and one containing chromatogram information; use “.fas” as the filename extension in the file parameter.

format:Genbank

Genbank flatfile format; use “.gbk” as the filename extension in the file parameter.

Additional optional parameters:

doGaps:true

Exports gaps in the consensus.

doGaps:false

Removes gaps in the consensus before exporting. This is the default value if neither parameter is chosen explicitly.

exportSNPInfo

To save variant information to a specific file.

file:"pathname\filename.txt"

The pathname\filename where the report will be saved must be enclosed in quotes and terminate with a valid extension—usually “.txt”

Any valid contig specifier

See Specifying Contigs. This parameter exports the variant information for only the contigs specified.

snpThresh: 50

This parameter applies the Heterozygous Peak Threshold to the exported variant information. Default 50.

Qscore: 5

This parameter applies the Q Score Threshold to the exported variant information. Default 5.

SNPscoreMin: 0

This parameter defines the minimum frequency a variant must occur at a position to be included in the exported variant information. Default 0.

SNPscoreMax: 100

This parameter defines the maximum frequency a variant can occur at a position to be included in the exported variant information. Default 100.

quit

To quit the SeqMan application without saving the current project.

(None available)

saveFOF

To save a file of filenames for unassembled sequences in the current project, without saving the project itself.

file:"pathname\filename.fof"

The pathname\filename you wish to save to must be enclosed in quotes and terminate with a valid extension—usually “.fof”. If the pathname\filename you enter already exists, it will be overwritten.

A file of filenames is saved in text format unless the sequences have been added using the assemble command with optimizeOrder set to true and DoAssemble set to false. If these last two conditions are true, the sequence order will be optimized and the output file of filenames will contain optimized order in binary format, which cannot be read by text editors.

Note: When using an .fof file, SeqMan assumes that the vector trim has already been completed.

saveProject

Same as the File > Save menu command. Saves the current project.

file:"pathname\filename.sqd"

The pathname\filename you wish to save to must be enclosed in quotes and terminate with the extension “.sqd”. If the pathname\filename you enter already exists, it will be overwritten.

saveReport

To save the specified report as a text file, without saving the project.

file:"pathname\filename.txt"

The pathname\filename where the report will be saved must be enclosed in quotes and terminate with a valid extension—usually “.txt”. If the pathname\filename you enter already exists, it will be overwritten.

Use one of the following parameters to specify which report you wish to save.

which:status

Saves the Project Report.

which:trim

Saves the Trim Report.

which:ABI_Info

Saves the data acquisition information for any ABI files in the Unassembled Sequences window in spreadsheet format. Note that you cannot retrieve this ABI_Info if you assemble the data, as the sequences will no longer be listed in the Unassembled Sequences window.