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Match column contents of one file and pasted whole line if match found

Hi,

I have two files.

bigfile1.txt

pos100  5   149275986   149275987   sample1
                                           1   NN
                                           15  NN
                                           18  NN
pos10   1   12907457    12907458    sample2
                                           1   NN
                                           2   NN
                                           3   NN
                                           18  NN
                                           191 NN
pos100  5   149275986   149275987   sample3
                                           17  NN
                                           15  NN
                                           18  NN

lookupfile2.txt

1269554 CA
1372268 AT
1849529 GC
149275986   TT
11854085    AG
11854476    GT
12837371    AA
12907457    TC
12907379    CA
12907457    GA

I want if first content of column 3 (149275986) of bigfile1.txt matches within the lookupfile2.txt, than the whole line is pasted in bigfile1.txt . Like:

pos100  5   149275986   149275987   sample1        149275986    TT
                                           1   NN
                                           15  NN
                                           18  NN
pos10   1   12907457    12907458    sample2        12907457     TC
                                           1   NN
                                           2   NN
                                           3   NN
                                           18  NN
                                           191 NN
pos100  5   149275986   149275987   sample3        149275986    TT
                                           17  NN
                                           15  NN
                                           18  NN

Due to the format I have for bigfile1.txt (it couldn't be sorted), I am getting difficulty in joining the things. I tired: https://stackoverflow.com/questions/18592736/awk-compare-columns-from-two-files-impute-values-of-another-column

and several other but no luck.

Thanks,

Waqas.

snp genome next-gen sequence
• 1,838 views • link
updated by cpad0112 cpad0112 • written by waqasnayab waqasnayab

2 answers

You can try this - see below. Note that you have a duplicate variant position (12907457). I decided to merge these together first, as you can see.

awk 'BEGIN{FS=" "}; {a[$1]=a[$1]==""? $2 : a[$1] "," $2 } END {for (i in a) print i, a[i]}' lookupfile2.txt > lookupfile2.VarsMerged.txt
cat lookupfile2.VarsMerged.txt
12907379 CA
12907457 TC,GA
12837371 AA
11854476 GT
149275986 TT
1269554 CA
1372268 AT
1849529 GC
11854085 AG

awk 'BEGIN {FS=" "} FNR==NR {values[NR]=$0; next} header=0; /^pos/{start=$3; end=$4; header=1} {for (i in values) {split(values[i],a," "); if (header==1 && start<=a[1] && end>=a[1]) {print $0"\t"values[i]}; if (header==0 && start<=a[1] && end>=a[1]) {print $0}}}' lookupfile2.VarsMerged.txt bigfile1.txt
pos100  5   149275986   149275987   sample1 149275986 TT
                                           1   NN
                                           15  NN
                                           18  NN
pos10   1   12907457    12907458    sample2 12907457 TC,GA
                                           1   NN
                                           2   NN
                                           3   NN
                                           18  NN
                                           191 NN
pos100  5   149275986   149275987   sample3 149275986 TT
                                           17  NN
                                           15  NN
                                           18  NN
• 0 views • link
written by Kevin Blighe Kevin Blighe

Hi Kevin,

Yeah, nice observation, I found four others positions within my lookup file that are repeated two times:

  2 23103039
  2 23103355
  2 38092026
  2 73717720

Further, I cross-checked with your first command, all fine, and than I run the last command. Seems to me it worked..,,,!!!! Thanks Kevin, once again...,,,!!!!!

• 0 views • link
written by waqasnayab waqasnayab

Hi Waqas, absolutely no problem.

• 0 views • link
written by Kevin Blighe Kevin Blighe

If you are okay with coordinates not being present twice:

$ sed '/pos/ s/\s\+/\t/g' file.txt | csvjoin -t  -c "3,1" --left - ids.txt | sed 's/,/\t/g' | datamash  -g 1 unique 2,3,4,5,6
pos100  5   149275986   149275987   sample1 CA
                                           1   NN                   
                                           15  NN                   
                                           18  NN                   
pos10   1   12907457    12907458    sample2 GA,TC
                                           1   NN                   
                                           2   NN                   
                                           3   NN                   
                                           18  NN                   
                                           191 NN                   
pos100  5   149275986   149275987   sample3 TT
                                           17  NN                   
                                           15  NN                   
                                           18  NN   

$ cat ids.txt 
1269554 CA
1372268 AT
1849529 GC
149275986   TT
11854085    AG
11854476    GT
12837371    AA
12907457    TC
12907379    CA
12907457    GA

$ cat file.txt 
pos100  5   149275986   149275987   sample1
                                           1   NN
                                           15  NN
                                           18  NN
pos10   1   12907457    12907458    sample2
                                           1   NN
                                           2   NN
                                           3   NN
                                           18  NN
                                           191 NN
pos100  5   149275986   149275987   sample3
                                           17  NN
                                           15  NN
                                           18  NN
• 0 views • link
written by cpad0112 cpad0112

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