sreformat(1)							  Biosquid Manual						      sreformat(1)

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  informa-
       tion).

       The  available aligned output file format codes include stockholm (PFAM/Stockholm format); msf (GCG MSF format); a2m (an aligned FASTA for-
       mat); 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 ambi-
	      guity  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  charac-
	      ters  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  nota-
	      tion,  <>. 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

Biosquid 1.9g							   January 2003 						      sreformat(1)