fasta-center [options]
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.
Sequences in FASTA format from standard input.
Writes a FASTA format file to standard output.
| Option | Parameter | Description | Default Behavior |
|---|---|---|---|
| Alphabet Options | |||
| -alph | alphabet file | The alphabet file contains the alphabet definition of a (possibly non-standard) alphabet. The sequences are verified using the alphabet definition, and sequences consisting of nothing but ambiguous symbols are rejected and optionally written to the reject file. Incompatible with options -dna, -rna and -protein. | When no alphabet is specified, the sequence content is ignored. |
| -dna | Same as specifying the -alph option with the standard DNA alphabet definition file. Incompatible with options -alph, -rna, and -protein. | When no alphabet is specified, the sequence content is ignored. | |
| -rna | Same as specifying the -alph option with the standard RNA alphabet definition file. Incompatible with options -alph, -dna, and -protein. | When no alphabet is specified, the sequence content is ignored. | |
| -protein | Same as specifying the -alph option with the standard protein alphabet definition file. Incompatible with options -alph, -dna, and -rna. | When no alphabet is specified, the sequence content is ignored. | |
| General Options | |||
| -len | len | Length of central region to output. If this is larger than the length of a sequence, the entire sequence is output. | 100 |
| -flank | filename | 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. |
| -reject | filename | 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. | |
| -h | Display the usage message and exit. | Run as normal. | |