Find flanking positions Post: 302969434

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Top Forums Shell Programming and Scripting Find flanking positions Post 302969434 by RudiC on Tuesday 22nd of March 2016 04:30:33 PM

03-22-2016

Registered User

How come your ch1 400 line is "flanked" by the ch2 567 line? If the chromosome doesn't need to match, why then wouldn't ch3 456 flank the 400 line?

---------- Post updated at 21:30 ---------- Previous update was at 21:26 ----------

SHOULD the chromosome matter, this might work:

Code:

awk '
BEGIN           {print "QueryMarker     Chromosome      Position        Left    pos     Right   Pos"}
NR == FNR       {T1[NR] = $1
                 T2[NR] = $2
                 T3[NR] = $3
                 MX     = NR
                 next
                }

                {for (m=1; m<=MX; m++)  {if (T2[m] != $2) continue
                                         if (T3[m] <= $3) continue 
                                         print $0, T1[m-1], T3[m-1], T1[m], T3[m]
                                        }
                }
' file1 OFS="\t" file2
QueryMarker     Chromosome      Position        Left    pos     Right   Pos
Q1      ch1     43      m2      5       m3      50
Q3      ch3     2000    m9      456     m10     2315

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CURL_MULTI_STRERROR(3)							 1						    CURL_MULTI_STRERROR(3)

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