Weeder 2.0 to Pscan/PscanChIP Matrix Converter
Weeder 2.0 outputs a file containing a list of matrices built using the occurrences of the motifs reported in the main output. The file is called inputfile.matrix.w2 where inputfile is the name of the input multifasta file. The format of this file has been designed to be "STAMP friendly" in order to allow a quick search of correspondences between the identified motifs and the ones in databases like Jaspar and Transfac using STAMP.
However, this format is slightly different and not compatible with the one used by our other tools Pscan and PscanChIP. The utility mat_converter makes possible converting Weeder 2.0 matrices file to the format adopted by Pscan and PscanChIP.
- Download this program (works under UNIX/LINUX/MacOSX), and save it anywhere you like.
- Compile the program: g++ mat_converter.cpp -o mat_converter -O3
- At this point you'll get an executable file called "mat_converter"
- To run it the syntax is:
./mat_converter inputfile.matrix.w2 >matrixfile.wil.
- The new file
matrixfile.wil now contains the motif matrices in a format compatible with Pscan and PscanChIP.