SEQIO -- A Package for Sequence File I/O
Table of Contents for the SEQIO Package Documentation
Contents of the User's Section
A Description of the SEQIO Package
fmtseq - A File Conversion Program
Differences from readseq
Interactive Mode
Program Options
Option Format and Use
Program Input and File Formats
Sequence Selection and Transformation
A "Big Alignment" Example
idxseq - A Database Indexing Program
Program Options
Program Operation
Index File Format
Example Programs
example1 - A simple keyword searching program
example2 - A sequence information display program
example3 - A feature extraction program
typeseq - A sequence output (`cat' or `fetch') program
wcseq - A sequence/entry counting program
grepseq - A fixed-width motif searching program
User's Guide to Programs Using the SEQIO Package
Specifying Files and Databases to a Program
The Supported File Formats
Database Identifiers and Identifier Prefixes
One-line Sequence Descriptions
The BIOSEQ Standard for Describing Databases
Simple BIOSEQ Files
The BIOSEQ Environment Variable
Extending the Simple Format
Alternate Database Names
A Root Directory for the Database Files
Adding Comments to the BIOSEQ File
Information Fields Giving Information about the Database
Virtual BIOSEQ Entries
A Shorthand for Listing a Sub-Directory's Files
Wildcards in the Filenames
Aliases
Database Search Specifiers
Search Specifier Format
Specifier-Filename Matching Process
A Complete BIOSEQ File Example
Contents of the Programmer's Section
The SEQIO Package Interface
Opening and Closing Files/Database-Searches
Reading Sequences/Entries
The SEQINFO Structure
SEQINFO Field Access Functions
Writing Sequences/Entries
BIOSEQ Database Functions
Miscellaneous Functions
Error Handling/Reporting
Quick Reference Guide to the SEQIO Interface
Functions, Structures, Variables and Constants Defined by the Package
Opening and Closing Files/Database-Searches
Reading Sequences/Entries
The SEQINFO Structure
Writing Sequences/Entries
BIOSEQ Database Functions
Miscellaneous Functions
Error Handling/Reporting
Programmer's Guide to Using the SEQIO Package
Reading Sequences and Performing Database Searches
Differences between SEQIO and stdio
Extracting Information from Entries
The Raw Sequence
The SEQINFO Structure
Seqfmainid, Seqfmainacc, Seqfoneline and Seqfallinfo
Extracting Other Information
Writing, Creating and Annotating Entries
Writing Entries
Creating New Entries
Annotating Existing Entries
BIOSEQ Stuff (Database Information Processing)
Error Handling
Porting the Package to Another Machine
The Supported File Formats (in detail)
File Format Types
Automatically Determining the Format Type
The SEQIO File Format Implementations
Raw Format
Plain Format
GenBank Flat-File Format
GBFAST variation of GenBank
PIR/CODATA Format
PIRFAST Variation of PIR
EMBL/Swiss-Prot File Formats
EMBLFAST/SPFAST Variation of EMBL/Swiss-Prot
FASTA/FASTA-old File Formats
NBRF/NBRF-old File Formats
IG/Stanford, IG-old/Stanford-old File Formats
ASN.1 Text File Format
GCG Format
GCG-* Formats
MSF Multiple Sequence Format
PHYLIP Interleaved and Sequential File Formats
Clustalw Format
FASTA-output Formats
BLAST-output Formats
Other Information
The Package README File
List of Files in the Release
Installation Notes
Using the SEQIO Package in a Program
Author and Acknowledgements
COPYRIGHT NOTICE
The Package CHANGES File
The Package TODO File
James R. Knight,
knight@cs.ucdavis.edu
June 29, 1996