Closed hepcat72 closed 6 years ago
weblogo --help
lists the supported formats. Neither of these formats is currently supported, although WebLogo will read transfac position weight matrix files.
OK. I'm still missing something though. I saw the list of formats for --datatype: clustal, fasta, msf, genbank, nbrf, nexus, phylip, stockholm, intelligenetics, table, array, transfac
. Where can I find the format description so that I can transform my data into one of those formats? E.g. What does table
format look like? Is it tab delimited? What are the rows? What are the columns? Does it take counts or percentages? Where is this information? Are there examples of the formats somewhere that I overlooked?
Descriptions of the different formats can be found in the parsing code.
https://github.com/WebLogo/weblogo/tree/master/corebio/seq_io
I have base position frequency files that look like this:
from which I generated meme motif files (to run ceqlogo) that look like this (different data):
But I cannot find a description of any of the formats listed in the usage for --datatype. Are either of these formats one of the formats accepted by --datatype?