jnarayan81 / SyntenyParser

Parse the syntney

SyntenyParser

Report bug to Jitendra Narayan ( [e-mail] )

SyntenyParser script usage

  print "Usage: $0 --qfile --flip 1 \n\n";
  print	"Options:\n";
  print "	--qfile|-q	query Synteny blocks_coords file\n";
  print "	--flip|-f	flip the coordiantes if negative oriented | 1 for yes or 0 for no \n";
  print "	--core|-c	Number of core/core to use \n";
  print "	--ofile|-o	oufile/results file\n";
  print "	--ref|-r	reference name \n";
  print "	--tar|-t	target name\n";
  print "	--plot|-p	name of scaff to plot\n";
  print "	--block|-b	report block format : for default see below\n";
  print "     	--help|-h	brief help message\n";
  print "	--lfile|-l	provide chr length file\n";
  print "	--mode|-m	provide alingnment mode\n";
  print "     	--help|-h	brief help message\n";

print "For LastZ general-: perl SyntenyParser.pl -a seeALN_scaffold_15.lz -f 1 -c 1 -o see2 -r ref -t tar -p scaffold_15 -m lastz -l scaff15.fa.fai
";
print "For Sibelia: perl SyntenyParser.pl -a blocks_coords.txt -f 1 -c 1 -o see2 -r ref -t tar -p scaffold_1 -m sibelia";

Outfile format (default)

  +Col1		Name of the reference
  +Col2		Name of the reference chromosome/contig/sequence
  +Col3		Strand
  +Col4		Start coordinates
  +Col5		End coordinates
  +Col6		Length of alignments
  +Col7		Name of the target
  +Col8		Name of the target chromosome/contig/sequence
  +Col9		Strand
  +Col10	Start coordinates
  +Col11	End coordinates
  +Col12	Length of alignments
  +Col13	Others