Report bug to Jitendra Narayan ( jnarayan81@gmail.com )
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