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.
SEE ALSO¶
afetch(1),
alistat(1),
compalign(1),
compstruct(1),
revcomp(1),
seqsplit(1),
seqstat(1),
sfetch(1),
shuffle(1),
sindex(1),
stranslate(1),
weight(1).
AUTHOR¶
Biosquid and its documentation are Copyright (C) 1992-2003 HHMI/Washington
University School of Medicine Freely distributed under the GNU General Public
License (GPL) See COPYING in the source code distribution for more details, or
contact me.
Sean Eddy
HHMI/Department of Genetics
Washington University School of Medicine
4444 Forest Park Blvd., Box 8510
St Louis, MO 63108 USA
Phone: 1-314-362-7666
FAX : 1-314-362-2157
Email: eddy@genetics.wustl.edu