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