stat.mageck breaks when combined data is not in csv format

[dchiu911]

After MAGeCK version 0.5.4, changes where made to mageckCount.py and caused an error here when trying to run caRpools::stat.mageck().

The error traceback:

INFO  @ Tue, 27 Feb 2018 13:30:49: Processing 1 lines.. 
WARNING @ Tue, 27 Feb 2018 13:30:49: Line 1 of the read count table has fewer than 3 columns. Skip this line ... 
Traceback (most recent call last):
  File "/home/dchiu/bin/mageck", line 66, in <module>
    main();
  File "/home/dchiu/bin/mageck", line 51, in main
    magecktest_main(args);
  File "/home/dchiu/lib/python2.7/site-packages/mageck/crisprFunction.py", line 562, in magecktest_main
    mapres=getcounttablefromfile(args.count_table)
  File "/home/dchiu/lib/python2.7/site-packages/mageck/mageckCount.py", line 372, in getcounttablefromfile
    geneid=field[1]

Forcing the output to be in CSV format seems to fix the issue:

# In stat.mageck, change these lines
dataset.combined.file = paste(dirstore, "/", filename, "_MAGeCK_sgRNA.tab", 
                              sep = "")
write.table(dataset.combined, file = dataset.combined.file, 
            row.names = FALSE, quote = FALSE)

# to these lines
dataset.combined.file = paste(dirstore, "/", filename, "_MAGeCK_sgRNA.csv", 
                              sep = "")
write.table(dataset.combined, file = dataset.combined.file, 
            row.names = FALSE, quote = FALSE, sep = ",")