Fasta Utility¶ ↑
This is a pretty simple Thor application for performing a number of common tasks on fasta files.
So far, supported actions are:
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fasta_util lengths
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Calculates basic statistics on the lengths of the entries in the file.
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fasta_util filter
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Applies a variety of filter types to the entries in a fasta file.
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fasta_util clean
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Reformats each entry, wrapping long lines
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fasta_util sort
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Sorts the entries in a fasta file according to length.
Detailed help on each of the options can be accessed with
fasta_util help COMMAND
eg:
$ fasta_util help filter Usage: fasta_util filter FILENAME [options] Options: -l, [--length-cutoff=N] # Only entries with length >= cutoff will be returned. # Default: 0 -v, [--inverse-match] # Return the inverse of the match after all the other filters have been applied. -d, [--defline-grep=DEFLINE_GREP] # A regular expression, used to search the entry's definition line. Description: Impose a filter or set of filters on entries in a fasta file where each sequence in the file has to pass all of the filters to be printed.
Copyright¶ ↑
Copyright © 2011 Robert Syme. MIT Licence. See LICENSE.txt for further details.