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
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.
|-f||file||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.|
|-s||suffix||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.|
|-off||position||Print sequences starting at position.||The sequences are printed from their start which is equivalent to giving -off a value of 1.|
|-len||length||Print up to length characters of the sequence.||The entire sequence is printed.|