fasta-center

Usage:

fasta-center [options]

Description

Reads sequences in FASTA format. For each sequence, it outputs the central portion of the sequence. The flanking regions can also be output to a separate file. When the alphabet is specified and the central portion of a sequence consists of nothing but the wildcard it is not output.

Input

Sequences in FASTA format from standard input.

Output

Writes a FASTA format file to standard output.

Options

Option Parameter Description Default Behavior
Alphabet Options
General Options
-lenlen Length of central region to output. If this is larger than the length of a sequence, the entire sequence is output. 100
-flankfilename Output the regions flanking the central regions to a file named filename. The FASTA IDs of the flanking regions on the left (right) are the original FASTA ID with '-L' ('-R') appended. Flanking regions are not output.
-rejectfilename Output any rejected central regions to a file named filename. Rejected central regions are not output.
-no-pgc Suppress parsing of genomic coordinates in FASTA header lines and output sequences with their FASTA headers unmodified. Output centered (and flanking) sequences with FASTA headers containing their correct genomic coordinates.