sreformat - Online in the Cloud

PROGRAM:

NAME

sreformat - convert sequence file to different format

SYNOPSIS

sreformat [options] format seqfile

DESCRIPTION

sreformat reads the sequence file seqfile in any supported format, reformats it into a new
format specified by format, then prints the reformatted text.

Supported input formats include (but are not limited to) the unaligned formats FASTA,
Genbank, EMBL, SWISS-PROT, PIR, and GCG, and the aligned formats Stockholm, Clustal, GCG
MSF, and Phylip.

Available unaligned output file format codes include fasta (FASTA format); embl
(EMBL/SWISSPROT format); genbank (Genbank format); gcg (GCG single sequence format);
gcgdata (GCG flatfile database format); pir (PIR/CODATA flatfile format); raw (raw
sequence, no other information).

The available aligned output file format codes include stockholm (PFAM/Stockholm format);
msf (GCG MSF format); a2m (an aligned FASTA format); PHYLIP (Felsenstein's PHYLIP format);
and clustal (Clustal V/W/X format); and selex (the old SELEX/HMMER/Pfam annotated
alignment format);

All thee codes are interpreted case-insensitively (e.g. MSF, Msf, or msf all work).

Unaligned format files cannot be reformatted to aligned formats. However, aligned formats
can be reformatted to unaligned formats -- gap characters are simply stripped out.

This program was originally named reformat, but that name clashes with a GCG program of
the same name.

OPTIONS

-d DNA; convert U's to T's, to make sure a nucleic acid sequence is shown as DNA not
RNA. See -r.

-h Print brief help; includes version number and summary of all options, including
expert options.

-l Lowercase; convert all sequence residues to lower case. See -u.

-n For DNA/RNA sequences, converts any character that's not unambiguous RNA/DNA (e.g.
ACGTU/acgtu) to an N. Used to convert IUPAC ambiguity codes to N's, for software
that can't handle all IUPAC codes (some public RNA folding codes, for example). If
the file is an alignment, gap characters are also left unchanged. If sequences are
not nucleic acid sequences, this option will corrupt the data in a predictable
fashion.

-r RNA; convert T's to U's, to make sure a nucleic acid sequence is shown as RNA not
DNA. See -d.

-u Uppercase; convert all sequence residues to upper case. See -l.

-x For DNA sequences, convert non-IUPAC characters (such as X's) to N's. This is for
compatibility with benighted people who insist on using X instead of the IUPAC
ambiguity character N. (X is for ambiguity in an amino acid residue).

Warning: like the -n option, the code doesn't check that you are actually giving it
DNA. It simply literally just converts non-IUPAC DNA symbols to N. So if you
accidentally give it protein sequence, it will happily convert most every amino
acid residue to an N.

EXPERT OPTIONS

--gapsym <c>
Convert all gap characters to <c>. Used to prepare alignment files for programs
with strict requirements for gap symbols. Only makes sense if the input seqfile is
an alignment.

--informat <s>
Specify that the sequence file is in format <s>, rather than allowing the program
to autodetect the file format. Common examples include Genbank, EMBL, GCG, PIR,
Stockholm, Clustal, MSF, or PHYLIP; see the printed documentation for a complete
list of accepted format names.

--mingap
If seqfile is an alignment, remove any columns that contain 100% gap characters,
minimizing the overall length of the alignment. (Often useful if you've extracted
a subset of aligned sequences from a larger alignment.)

--nogap
Remove any aligned columns that contain any gap symbols at all. Useful as a prelude
to phylogenetic analyses, where you only want to analyze columns containing 100%
residues, so you want to strip out any columns with gaps in them. Only makes sense
if the file is an alignment file.

--pfam For SELEX alignment output format only, put the entire alignment in one block
(don't wrap into multiple blocks). This is close to the format used internally by
Pfam in Stockholm and Cambridge.

--sam Try to convert gap characters to UC Santa Cruz SAM style, where a . means a gap in
an insert column, and a - means a deletion in a consensus/match column. This only
works for converting aligned file formats, and only if the alignment already
adheres to the SAM convention of upper case for residues in consensus/match
columns, and lower case for residues in insert columns. This is true, for instance,
of all alignments produced by old versions of HMMER. (HMMER2 produces alignments
that adhere to SAM's conventions even in gap character choice.) This option was
added to allow Pfam alignments to be reformatted into something more suitable for
profile HMM construction using the UCSC SAM software.

--samfrac <x>
Try to convert the alignment gap characters and residue cases to UC Santa Cruz SAM
style, where a . means a gap in an insert column and a - means a deletion in a
consensus/match column, and upper case means match/consensus residues and lower
case means inserted resiudes. This will only work for converting aligned file
formats, but unlike the --sam option, it will work regardless of whether the file
adheres to the upper/lower case residue convention. Instead, any column containing
more than a fraction <x> of gap characters is interpreted as an insert column, and
all other columns are interpreted as match columns. This option was added to allow
Pfam alignments to be reformatted into something more suitable for profile HMM
construction using the UCSC SAM software.

--wussify
Convert RNA secondary structure annotation strings (both consensus and individual)
from old "KHS" format, ><, to the new WUSS notation, <>. If the notation is already
in WUSS format, this option will screw it up, without warning. Only SELEX and
Stockholm format files have secondary structure markup at present.

--dewuss
Convert RNA secondary structure annotation strings from the new WUSS notation, <>,
back to the old KHS format, ><. If the annotation is already in KHS, this option
will corrupt it, without warning. Only SELEX and Stockholm format files have
secondary structure markup.

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