#402 Utilitiy for multiple format sequence/feature outputs
From mailing list :
>>> (3) It would be great if fuzzpro can output multiple result files. This
>>> will benefit the down stream work a lot. For example, user like to have
>>> flat file and XML output at the same time. Would you consider this
>>> suggestion?
>>
>> Ummmm ... you mean "could we have a uitility that reads one report
>> format and writes another?" For example saving in a feature format and
>> rewriting. I'll have a look at the best options.
>
> The current default output format is "seqtable". My suggestion is to get
> fuzzpro produce default format ("seqtable") file, and at the same time,
> providing user options to generate an additional output file in
> different formats. Something like:
> fuzzpro [.....] -outfile outfile1 -rformat dbmotif -extraout outfile2
> For this, outfile1 is in "seqtable" format and outfile2 in "dbmotif".
We cannot allow an undefined number of output files. It breaks
pipelines, web interfaces, soap interfaces, etc. One output, one output
file. -ossingle (multiple sequences to individual files) was an anomaly
to cope with the transition for GCG users and is best turned off in
ointerfaces.
But we will add a utility to read a feature format or a sequence and
feature format and write a report so you can rewrite with another format.
We already have something similar with alignments, but could do better
with preserving other information for use in sequence sets.
