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Munge tables of data

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To explain regref I will walk through the following example:

./ test-data/ '${2}' '${3}' < test-data/z.fna

z.fna is a FASTA file with mangled headers where all non-letter or number characters have been replaced with underscores. is a table that contains the mangled names (in column 2) and the original names (in column 3).

The regref command reads the FASTA file from standard input and then replaces every occurance of the mangled string with the original string.

The arguments '${2}' and '${3}' refer to columns in by column number.

regref will replace every occurance of each pattern. The example below replaces the mangled string in a tree with a single-quoted orginal string.

./ test-data/ '${2}' "'\${3}'" < test-data/z.tre

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