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I have this script 

annotatepeaks.pl file mm9 -annStats filename > output

I use this script to run one job: 

annotatepeaks.pl file.xls mm9 -annStats file_stat.xls > file_ann.xls

Since I have multiple files and want to run in batch (add Batchparallel.pl)

Batchparallel.pl annotatepeaks.pl ann.xls mm9 -annStats filename -f *.xls

that basically runs parallel command for the one job. The problem is -annStats only give me one output file. How to specify the file name so that it takes the input name and use it for output for that specific flag (-annStats).

I am very new to this so hopefully my question makes sense for everyone.

Thanks for your help!

Hcorg
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Duy Pham
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  • I can't give very specific help without seeing your code, but if you modify annotatepeaks.pl to write to a file instead of printing to STDOUT, you can use something like "my $outfile = $infile . '_out.xls'" to use base the output name on the input name. – heathobrien Jul 20 '15 at 11:56
  • Thanks! The script is quite long so I don't know how to to attach the perl file here otherwise I can copy and paste. – Duy Pham Jul 20 '15 at 22:10

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