Hi. No, never automatically. And its gone be taken out of usage soon as we move towards bcbio-nextgen.


On Nov 27, 2013, at 1:10 PM, Johannes Alneberg wrote:

> In scripts/RNA_analysis/make_tophat_sbatch.py:
> 
> > +                        file_info[lane_run] = {}
> > +                    if not file_info[lane_run].has_key(tag):
> > +                        file_info[lane_run][tag] = {}
> > +                if (fname.split('.fastq')[0][-1] == "1"):
> > +                    file_info[lane_run][tag]['R1'] = fname
> > +                else:
> > +                    file_info[lane_run][tag]['R2'] = fname
> > +            except:
> > +                sys.exit('files missing? '+fname)
> > +        print file_info.keys()
> > +
> > +        print "Best guess for sample names: "
> > +        for lane in file_info:
> > +            print lane
> > +            print sorted(file_info[lane].keys())
> > +        try_names = raw_input("Press y if the sample names are wrong.")
> Is this robust? Will this script ever be ran automatically?
> 
> —
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