p3-get-feature-regions

Display DNA Regions for Features

p3-get-feature-regions.pl [options]

This script takes as input a list of feature IDs and displays the DNA region surrounding each feature. The portion of each region occupied by the feature itself and the feature’s neighbors will be shown in upper case, the rest in lower case. The output will be in FASTA format.

Parameters

There are no positional parameters

The standard input can be overridden using the options in Input Options.

The input column can be specified using Column Options. Additional command-line options are as follows.

• distance

The distance in base pairs to show around the specified feature. The default is 100.

• comment

If specified, a field to put in the FASTA comments. If multiple fields are desired, the option should be specified multiple times.

• consolidated

If a requested feature’s region includes another requested feature, the region will be expanded to include it. If this is done, a description of the features in each sequence and their locations will be appended to the comment field. Note that there will still be one output sequence per incoming feature; however, some may be duplicated.