Impl log collection opt#29
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… put PepSIRF's log files. Moved code to collect logs from diffEnrich.py to a new utilities file called "utils.py".
… make a call to collect_logs. Ran into exit status 64 when trying to call log collection funtion.
…ctory specified by the user. Default directory is "logs".
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Adds a new option to specify a directory into which autopepsirf will collect PepSIRF's log files. The default directory name is "logs". This should improve the user experience since *.log files will not be scattered after running autopepsirf.