Chapter 6. The EMBOSS Command Line
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Chapter 6. The EMBOSS Command Line

Table of Contents

6.1. Introduction to the EMBOSS Command Line
6.1.1. Finding and Running EMBOSS Applications
6.1.2. Application Options
6.1.3. Parameters and Qualifiers
6.1.4. Datatype-specific Qualifiers
6.1.4.1. Multiple Qualifiers
6.1.4.2. Numbering Qualifiers
6.1.5. Global Qualifiers
6.1.6. Command line Styles
6.1.7. Environment Variables
6.2. Specifying Values for Application Options
6.2.1. General Rules
6.2.2. Simple ACD Datatypes
6.2.2.1. Primitive Datatypes
6.2.2.2. Other Simple Datatypes
6.2.3. Input ACD Datatypes
6.2.3.1. Sequence Input
6.2.3.2. Feature Input
6.2.3.3. Files and Directories
6.2.3.4. Data Files
6.2.3.5. Datatypes for phylipnew EMBASSY Package
6.2.3.6. Other Biological Inputs
6.2.4. Output ACD Datatypes
6.2.4.1. Sequence Output
6.2.4.2. Features
6.2.4.3. Alignments
6.2.4.4. Output Files and Directories
6.2.4.5. Output Data Files
6.2.4.6. Datatypes for phylipnew EMBASSY Package
6.2.4.7. Other Biological Outputs
6.2.4.8. Report Output
6.2.5. Selection ACD Datatypes
6.2.5.1. list
6.2.5.2. selection
6.2.6. Graphics ACD Datatypes
6.2.6.1. graph
6.2.6.2. xygraph
6.3. Global Command Line Qualifiers
6.3.1. Introduction
6.3.2. Description of Global Qualifiers
6.3.2.1. -auto
6.3.2.2. -debug
6.3.2.3. -filter
6.3.2.4. -help
6.3.2.5. -options
6.3.2.6. -stdout
6.3.2.7. -warning, -error, -fatal
6.3.3. Global Qualifiers and Environment Variables
6.3.3.1. Negation
6.4. Datatype-specific Command Line Qualifiers
6.4.1. Introduction
6.4.2. Sequences
6.4.2.1. Sequence Input
6.4.2.2. Sequence Output
6.4.3. Sequence Features
6.4.3.1. Feature Input
6.4.3.2. Feature Output
6.4.4. Sequence Alignments
6.4.4.1. Specifying the Alignment File Format and Name
6.4.5. General Input
6.4.6. Patterns
6.4.6.1. Regular Expressions
6.4.6.2. Sequence Patterns
6.4.7. General Output
6.4.7.1. General Output
6.4.7.2. Output Files
6.4.8. Application Report Output
6.4.8.1. Usage Examples
6.5. Graphical Output
6.5.1. Description of Qualifiers
6.5.1.1. Usage Examples
6.6. The Uniform Sequence Address (USA)
6.6.1. Introduction
6.6.2. USA Syntax
6.6.2.1. Sequence
6.6.2.2. Format
6.6.2.3. ListFileName
6.6.2.4. DatabaseName
6.6.2.5. FileName
6.6.2.6. Entry
6.6.2.7. SearchField
6.6.2.8. Word
6.6.2.9. Program and ProgramParameters
6.6.2.10. [start : end : reverse]
6.6.3. Specifying the Format
6.6.4. Specifying a Database
6.6.4.1. Database Name
6.6.4.2. Database Entry
6.6.4.3. Set of Database Entries
6.6.4.4. Restrictions on Accessing Databases
6.6.5. Specifying a Sequence File
6.6.5.1. Multiple Sequence Files
6.6.5.2. Specifying One or More File Entries
6.6.5.3. Specifying a Set of Files
6.6.6. Specifying a Listfile
6.6.7. Specifying a Sequence "As Is"
6.6.8. Applications
6.6.9. Specifying Search Fields
6.6.9.1. ACC and ID
6.6.9.2. ORG, KEY and DES
6.6.9.3. SV
6.6.9.4. GI Number
6.6.9.5. Start, End, Reverse
6.6.10. USA Summary
6.6.10.1. USA Examples
6.7. The Uniform Feature Object (UFO)
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5.5. Introduction to Report Formats Home 6.1. Introduction to the EMBOSS Command Line