Class Importer_Sequences_FASTA

importer for fasta files. created predicted peptides.

cli_import\AbstractImporter implements CLI_Command, cli_import\Importer

Extended by

cli_import\Importer_Sequences_FASTA

Namespace: cli_import
Located at src/cli/import/commands/Importer_Sequences_FASTA.php

Methods summary
`public static list($description,$sequence)`	# `read_fasta( resource $fasta_handle )` reads the next fasta sequence from file handle $fasta_handle and returns a list of description and sequence (without whitespace and newlines) reads the next fasta sequence from file handle $fasta_handle and returns a list of description and sequence (without whitespace and newlines) Parameters `$fasta_handle` `resource` $fasta_handle Returns `list($description,$sequence)` $description,$sequence) Throws `ErrorException` with ErrorMsg ERRCODE_ILLEGAL_FILE_FORMAT: next non-empty line has to start with '>'
`public static string`	# `prepare_predpep_name( string $isoform_name, integer $left, integer $right, char $direction )` Converts values to String that would be stored as Name (Suffix of UniqueName) in DB Converts values to String that would be stored as Name (Suffix of UniqueName) in DB Parameters `$isoform_name` `string` $isoform_name `$left` `integer` $left `$right` `integer` $right `$direction` `char` $direction [+-] Returns `string`
`public static Array`	# `import( Array $options )` Parameters `$options` `Array` $options user-provided command-line options Returns `Array` results Throws `Exception` on error `ErrorException` on error InheritDoc
`public static`	# `CLI_commandDescription( )` InheritDoc
`public static`	# `CLI_commandName( )` InheritDoc
`public static`	# `CLI_longHelp( )` InheritDoc

Methods inherited from cli_import\AbstractImporter
`CLI_checkRequiredOpts(), CLI_execute(), CLI_getCommand(), dieOnMissingArg(), preCommitMsg(), setLineCount(), updateProgress()`

Properties inherited from cli_import\AbstractImporter
`$log`