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Mean score value by ID over a defined genomic region

 
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# 1  
Old 09-14-2015
Mean score value by ID over a defined genomic region
Hi,

I would like to know how can I get a mean score value by ID over a defined genomic region. Here it is an example:

file1
Code:
12 100 103 id1
12 110 112 id1
12 200 203 id2

file2
Code:
12 100 101 1
12 101 102 0.8
12 102 103 0.7
12 110 111 2.5
12 111 112 2.8
12 200 201 10.1
12 201 202 12.0
12 202 203 11.7

Desired output file
Code:
id1 1.56
id2 11.3


Thanks in advance
Moderator's Comments:
Mod Comment Please use CODE tags (not ICODE tags) for multiline displays.
Last edited by Don Cragun; 09-14-2015 at 10:13 PM.. Reason: Fix CODE tags.
# 2  
Old 09-14-2015
Please explain how file1 and ile2 are connected. Could there be lines in file2 that must not be counted?
How many decimal places do you need in the output?
Last edited by RudiC; 09-14-2015 at 06:23 AM..
# 3  
Old 09-14-2015
If the genomic regions in file 2 overlap any of the genomic regions of file 1, average the scores by ID

file1 fields explanation:
chromosome startPosition endPosition ID

file2 fields explanation:
chromosome startPosition endPosition score


One decimal place is enough. Thank you.
# 4  
Old 09-14-2015
Try
Code:
awk '
NR==FNR         {P1[NR]=$2
                 P2[NR]=$3
                 ID[NR]=$4
                 next
                }
                {for (i in ID)  {if ($2 >= P1[i] &&
                                     $3 <= P2[i])       {SUM[ID[i]]+=$4
                                                         CNT[ID[i]]++
                                                         break
                                                        }
                                }
                }

END             {for (s in SUM) printf "%s %.1f\n", s, SUM[s]/CNT[s]}
' file1 file2
id1 1.6
id2 11.3

# 5  
Old 09-14-2015
Thank you, but I only get the mean scores in the output, not the IDs.
# 6  
Old 09-14-2015
What if working on the sample files in post#1?
# 7  
Old 09-15-2015
Then the output is:

1.6
id2 11.3
 
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