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 Multiple Qualifiers 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 Primitive Datatypes Other Simple Datatypes
6.2.3. Input ACD Datatypes Sequence Input Feature Input Files and Directories Data Files Datatypes for phylipnew EMBASSY Package Other Biological Inputs
6.2.4. Output ACD Datatypes Sequence Output Features Alignments Output Files and Directories Output Data Files Datatypes for phylipnew EMBASSY Package Other Biological Outputs Report Output
6.2.5. Selection ACD Datatypes list selection
6.2.6. Graphics ACD Datatypes graph xygraph
6.3. Global Command Line Qualifiers
6.3.1. Introduction
6.3.2. Description of Global Qualifiers -auto -debug -filter -help -options -stdout -warning, -error, -fatal
6.3.3. Global Qualifiers and Environment Variables Negation
6.4. Datatype-specific Command Line Qualifiers
6.4.1. Introduction
6.4.2. Sequences Sequence Input Sequence Output
6.4.3. Sequence Features Feature Input Feature Output
6.4.4. Sequence Alignments Specifying the Alignment File Format and Name
6.4.5. General Input
6.4.6. Patterns Regular Expressions Sequence Patterns
6.4.7. General Output General Output Output Files
6.4.8. Application Report Output Usage Examples
6.5. Graphical Output
6.5.1. Description of Qualifiers Usage Examples
6.6. The Uniform Sequence Address (USA)
6.6.1. Introduction
6.6.2. USA Syntax Sequence Format ListFileName DatabaseName FileName Entry SearchField Word Program and ProgramParameters [start : end : reverse]
6.6.3. Specifying the Format
6.6.4. Specifying a Database Database Name Database Entry Set of Database Entries Restrictions on Accessing Databases
6.6.5. Specifying a Sequence File Multiple Sequence Files Specifying One or More File Entries 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 ACC and ID ORG, KEY and DES SV GI Number Start, End, Reverse
6.6.10. USA Summary USA Examples
6.7. The Uniform Feature Object (UFO)