fasta-fetch <FASTA file> [-f <file> | <id>+] [options]


Fetch sequences from a FASTA sequence file. Requires an index file made by fasta-make-index.

Reads sequence identifiers from the command line, from a file and from standard input, in that order.


Sequences in FASTA format from the <FASTA file>.

An index generated from the sequences with fasta-make-index which is named the same as the FASTA file but with ".index" appended.

Sequence identifiers, either listed on the command line, from a file specified with -f option or provided on standard input.


Writes a FASTA format file to standard output.


Option Parameter Description Default Behavior
General Options
-ffile Specifiy a file containing a list of sequence identifiers. The sequence identifiers must be specified on the command line or on standard input.
-c Check that the index actually references the expected sequence. This is intended to help catch cases when the sequence file has changed but the index has not been updated. The index file is assumed to be correct for the sequence file.
-ssuffix Put each sequence in its own file named with the sequence identifier with ".suffix" appended. Any pipe characters in the identifier will be substituted with underscores. The sequences are written to standard output.
-offposition Print sequences starting at position. The sequences are printed from their start which is equivalent to giving -off a value of 1.
-lenlength Print up to length characters of the sequence. The entire sequence is printed.