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Shell Programming and Scripting

Find flanking positions

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# 1  
Old 03-22-2016
Find flanking positions
I have a positions file with markers in col1 and position defined by chromosome and location in col2 and col3

Code:
m1	ch1	1
m2	ch1	5
m3	ch1	50
m4	ch2	567
m5	ch2	4567
m6	ch2	7766
m7	ch2	554433
m8	ch3	76
m9	ch3	456
m10	ch3	2315

Given a set of query marker, I would like to know what are the flanking markers (just before and just after).


If My query is

Code:
QueryMarker	Chromosome	Position
Q1	ch1	43
Q2	ch1	400
Q3	ch3	2000
Q4	ch3	5000

How can I return flanking markers from the previous file, when such information is available

Code:
QueryMarker	Chromosome	Position	Left	pos	Right	Pos
Q1	ch1	43	m2	5	m3	50
Q2	ch1	400	m3	50	m4	567
Q3	ch3	2000	m9	456	m10	2315
Q4	ch3	5000	m10	2315	NA	NA


Here is what I tried maybe a little lost in the syntax,

Code:
awk 'NR==FNR{m[$1]=$2 FS $3;next} { prev=$0; mark=0;} { for (ms in m) { if ($2 FS $3 < ms[$2 FS $3]) mark=1; nextl=ms[$1 FS $2]} ; if (mark==0); posl="NA"; print $0 , prev, posl, nextl, posl}' marker query

# 2  
Old 03-22-2016
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

This User Gave Thanks to RudiC For This Post:
jianp83
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