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FAST-1.06
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/ fastr

NAME

fastr - character-based transformations on sequence records

SYNOPSIS

fastr [OPTION]... [SEARCHLIST] [REPLACELIST] [MULTIFASTA-FILE...]

fastr -n [OPTION]... [SEARCHLIST] [MULTIFASTA-FILE...]

fastr --strict [--ambig=<char>] [MULTIFASTA-FILE...]

fastr --iupac [--ambig=<char>] [MULTIFASTA-FILE...]

fastr --degap [MULTIFASTA-FILE...]

DESCRIPTION

fastr takes multifasta format sequence or alignment data as input, and faciliates character transliterations on identifiers (by default), sequences or descriptions using the Perl tr/// character transliteration operator. This faciliates character remapping, case changes, character deletions, degapping, squashing of repeated characters, and more. Special modes --strict, --iupac, and --degap automatically direct transliterations on facilitate enforcement of sequence alphabets, and remapping illegal characters to 'N' or 'X' or a user-defined character.

Options specific to fastr: -s, --sequence transliterate sequences -d, --description transliterate descriptions -D, --delete delete found characters not replaced -S, --squash squash duplicate replaced characters -n, --no-replace squash/delete characters in searchlist -c, --complement complement searchlist as a character set --strict map ambiguous/invalid nongap chars in sequences --iupac map invalid nongap chars (to N/X by default) -N, -X, --ambig=<char> map ambig/invalid chars to <char> --degap delete gap characters '-' -j, --join=<string> use <string> to join data annotation

Options general to FAST: -h, --help print a brief help message --man print full documentation --version print version -l, --log create/append to logfile -L, --logname=<string> use logfile name <string> -C, --comment=<string> save comment <string> to log --format=<format> use alternative format for input --moltype=<[dna|rna|protein]> specify input sequence type -q, --fastq fastq format for input and output

SEARCHLIST AND REPLACELIST

These arguments are strings of characters, or character ranges with hyphens (like "A-Z" "0-9"), separated by the empty string. Characters are remapped in corresponding order. If SEARCHLIST is longer than REPLACELIST, the last character of REPLACELIST is repeated unless in "delete-mode," in which case unmatched characters are deleted. In "squash-mode" transliteration happens before squashing. With the "no-replace" option, only SEARCHLIST is provided, no transliteration occurs, and SEARCHLIST characters are directly squashed and deleted. For more information see documentation for tr/// in the perlop manpage.

INPUT AND OUTPUT

fastr is part of FAST, the FAST Analysis of Sequences Toolbox, based on Bioperl. Most core FAST utilities expect input and return output in multifasta format. Input can occur in one or more files or on STDIN. Output occurs to STDOUT. The FAST utility fasconvert can reformat other formats to and from multifasta.

OPTIONS

-s --sequence

Transliterate sequences (identifiers by default).

-d --description

Transliterate descriptions.

-D --delete

Delete found but unreplaced characters.

-S --squash

Squash duplicate replaced characters.

-c --complement

Character complement SEARCHLIST. The last character of REPLACELIST replaces all characters not in SEARCHLIST.

-n --no-replace

Delete or squash characters in SEARCHLIST.

--strict

Transliterate illegal sequence characters to "N" (DNA or RNA) or "X" (protein). Takes precedence over --iupac. Other options disallowed in combination except --ambig and --fastq. For DNA, equivalent to: fastr -sc ACTGactg\- N

--iupac

Transliterate illegal sequence characters (including IUPAC ambiguities) to "N" (DNA or RNA) or "X" (protein). Other options disallowed in combination except --ambig and --fastq. For DNA, equivalent to:

fastr -sc ACTGactgMRWSYKVHDBXNmrwsykvhdbxn\- N

--degap

Delete gap characters "-" from each sequence. May only be combined with no other option except the --fastq option. Equivalent to:

fastr -snD -- -

-N <char>, -X <char>, --ambig=<char>

Use <char> to replace illegal characters instead of "N" or "X" with --strict or --iupac

-h, --help

Print a brief help message and exit.

--man

Print the manual page and exit.

--version

Print version information and exit.

-l, --log

Creates, or appends to, a generic FAST logfile in the current working directory. The logfile records date/time of execution, full command with options and arguments, and an optional comment.

-L [string], --logname=[string]

Use [string] as the name of the logfile. Default is "FAST.log.txt".

-C [string], --comment=[string]

Include comment [string] in logfile. No comment is saved by default.

--format=[format]

Use alternative format for input. See man page for "fasconvert" for allowed formats. This is for convenience; the FAST tools are designed to exchange data in Fasta format, and "fasta" is the default format for this tool.

-m [dna|rna|protein], --moltype=[dna|rna|protein]

Specify the type of sequence on input (should not be needed in most cases, but sometimes Bioperl cannot guess and complains when processing data).

-q --fastq

Use fastq format as input and output.

EXAMPLES

Change all bars "|" to hashes ("#") in IDs:

    fastr '|' '#' t/data/P450.fas

Change all square brackets to parens in description:

    fastr -d '[]' '()' t/data/P450.fas

Lower-case all sequence data:

    fastr -s 'A-Z' 'a-z' t/data/P450.fas

Delete all bars "|" in GenBank IDs:

    fastr -D '|' '' t/data/P450.fas

    fastr -nD '|' t/data/P450.fas

Delete all non-strict characters from a DNA sequence:

    fastr -nscD 'ACGT' t/data/P450.fas

Control and check the function of --strict:

    fastr --strict t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fascomp -t cat t/data/ArdellEtAl03_ncbi_popset_32329588.fas | fascomp -t

SEE ALSO

man perlre
perldoc perlre

Documentation on perl regular expressions.

man FAST
perldoc FAST

Introduction and cookbook for FAST

The FAST Home Page"

CITING

If you use FAST, please cite Lawrence et al. (2015). FAST: FAST Analysis of Sequences Toolbox. and Bioperl Stajich et al..