[gt-users] some questions

[Giorgio Gonnella]

Thank you for answering so quickly. So, now I am writing a tool that I named "gt simreads" to simulate a set of sequencing reads for a given sequence. Maybe a combination of tools (shredder, filter, mutate) could already almost do what I am going to do, but it is quite complicated, so I think this could be useful.

I thought to make the tool work as follow:
- input: a sequence
- output: newline separated list of fragments (the simulated reads)
- options: fragment lenght (-lenght) or lenght range (-minlenght/-maxlenght), number of fragments (-num)

And here are my questions, regarding conventions in gt:
- Are all tools that accept a sequence as input actually accepting multiple sequences? At the moment I used GtBioSeqIterator, but I don't really know what should be the expected behaviour for a genometools tool if the input is multiple (concatenate input sequences before starting? return "-num" sequences for each input sequence?). Or should I better accept only a single sequence as input?
- Is the output format as written up here acceptable for a genometools tool?
- I was thinking to implement an error rate option, is it ok (i.e. mutate sequences inside the tool) or is it better to chain the tool with "gt mutate"?

Giorgio