- sreformat - convert sequence file to different format
-
sreformat [options] format seqfile
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.
- -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.
-
--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.
afetch(1),
alistat(1),
compalign(1),
compstruct(1),
revcomp(1),
seqsplit(1),
seqstat(1),
sfetch(1),
shuffle(1),
sindex(1),
stranslate(1),
weight(1).
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: [email protected]