SYNOPSIS

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.

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: [email protected]