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BP_SREFORMAT(1)	      User Contributed Perl Documentation      BP_SREFORMAT(1)

       bpsreformat - convert sequence formats

       This script uses	the SeqIO system that allows conversion	of sequence
       formats either sequence data or multiple	sequence alignment data.  The
       name comes from the fact	that Sean Eddy's program sreformat (part of
       the HMMER pkg) already does this.  Sean's program tries to guess	the
       input formats while in our code we currently require your to specify
       what the	input and output formats are and if the	data is	from a
       multiple	sequence alignment or from straight sequence files.


       bpsreformat -if INFORMAT	-of OUTFORMAT -i FILENAME -o output.FORMAT

	 -h/--help	  Print	this help

	 -if/--informat	  Specify the input format

	 -of/--outformat  Specify the output format

	 -i/--input	  Specify the input file name
			  (to pass in data on STDIN use	minus sign as filename)
	 -o/--output	  Specify the output file name
			  (to pass data	out on STDOUT use minus	sign as	filename)

	 --msa		  Specify this is multiple sequence alignment data

	 --special	  Will pass on special parameters to the AlignIO/SeqIO
			  object -- most of these are for Bio::AlignIO objects
			  Comma	separated list of the following
			  nointerleaved	  -- for phylip,non-interleaved	format
			  idlinebreak	  -- for phylip, makes it molphy format
			  percentages	  -- for clustalw, show	% id per line

perl v5.32.1			  2019-12-07		       BP_SREFORMAT(1)


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