I am trying to use the script MuMRescueLite.py from http://genome.gsc.riken.jp/osc/english/dataresource/. That's the link for the software: http://genome.gsc.riken.jp/osc/english/software/src/MuMRescueLite_090522.tar.gz What it does more or less: After mapping, it examines the mapping locations of all reads (single and multi mapping reads) and using the information from single mapping reads, it probabilistically assigns where a multi mapping read maps The script needs a specific input of the format:

#ID locations   chromosome  strand  start   end count
read_x  1   chr1    +   100 126 100
read_y  2   chr1    +   102 128 100
read_y  2   chrX    +   102 128 100

While the .bed format output of an aligner (such as bowtie,bwa) looks like:

 chr6   135135525   135135550   HWI-ST897:159:C1ACKACXX:1:1101:1127:2068    255 +
chr5    140027416   140027441   HWI-ST897:159:C1ACKACXX:1:1101:1280:2087    255 +
chr16   57219907    57219932    HWI-ST897:159:C1ACKACXX:1:1101:1414:2089    255 -

I am using awk to turn the second(.bed format) in to the first format, as: awk '/./ {print $1"\t"$7 + 1"\t"$3"\t"$2"\t"$4"\t"$4 + length($5)"\t1"}3333' < <mapping output> > <MuM Input>

or awk '{$7=$7+1;end=$4+length($5);}{OFS="\t";print$1,$7,$3,$2,$4,end,"1"}'

Nevertheless MuMrescueLite.py keeps failing with the following message:

Traceback (most recent call last):
  File "../../tools/MuMRescueLite_090522/MuMRescueLite.py", line 194, in <module>
    remainSingleMapper(inFile, singleMappers, inputHeaderFlag)
  File "../../tools/MuMRescueLite_090522/MuMRescueLite.py", line 55, in remainSingleMapper
    chromosome, strand, position = retPosition(columns)
  File "../../tools/MuMRescueLite_090522/MuMRescueLite.py", line 39, in retPosition
    raise Exception 
Exception

I guess my issue is at the awk command as i am pretty new in using awk for file manipulations! Anyone that has previously used MumRescueLite or any awk expert that could help me out???

Thanks in advance