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compare and merge two txt files.

Hi, I have two SNP files. I want to compare and merge them.

File1

chrA01  2024    G       A       10      11
chrA01  2026    T       A       10      11
chrA01  2289    A       T       3       3
chrA01  2314    C       T       3       3
chrA01  2323    T       C       3       3
chrA01  26034   A       G       4       5

file2

chrA01  2024    G       A       10      12
chrA01  2026    T       A       10      12
chrA01  2300    A       G       3       3
chrA01  26034   A       G       5       6

I want to get the results:

chrA01  2024    G       A       10      11     10      12
chrA01  2026    T       A       10      11     10      12
chrA01  26034   A       G       4       5      5       6

I have tried command as like:

comm -12 <( sort BR.txt ) <( sort BS.txt )
awk -F'|' 'NR==FNR{c[$1$2$3$4]++;next};c[$1$2$3$4] > 0' BR.txt  BS.txt

kdiff3 BR.txt  BS.txt -m
kdiff3 BR.txt  BS.txt -o SNP.txt
awk 'NR==FNR{tgts[$1$2$3$4]; next} $1$2$3$4 in tgts' BR.txt  BS.txt > BRS.txt

join -1 1 -2 1 -3 1 -4 1 BR.txt  BS.txt | awk '{print $1}' > BRS.txt.

But it does not work well. Could you help modified my commands?

Thanks, Fuyou

snp
• 2,811 views • link
updated by bioguy24 bioguy24 • written by fufuyou fufuyou

3 answers

Just one command with csvtk, another cross-platform, efficient, practical and pretty CSV/TSV toolkit in Golang.

Suppose that the file 1 and file 2 are tab-delimited/tabular files, use this

csvtk -H -t join -f 1,2,3,4 file1 file2

Let me explain the command:

-H           global option, means no header line
-t           global option, means input files are tab-delimited/tabular
join         subcommand
-f 1,2,3,4   the keys columns
file1 file2  input files, support more!

The results are exactly what you want:

chrA01  2024    G       A       10      11      10      12
chrA01  2026    T       A       10      11      10      12
chrA01  26034   A       G       4       5       5       6

If the input files are space delimited, use csvtk space2tab for pre-processing.

• 1 views • link
written by shenwei356 shenwei356

Thanks. It works well. Fuyou

• 1 views • link
written by fufuyou fufuyou

Maybe this awk:

awk 'NR==FNR{A[$2];next}$2 in A' file1 file2
chrA01  2024    G       A       10      12
chrA01  2026    T       A       10      12
chrA01  26034   A       G       5       6
• 1 views • link
written by bioguy24 bioguy24

I have tried this. It does not work well.

• 1 views • link
written by fufuyou fufuyou

no tested:

join -t '\t' -1 1 -2 1 \
                  <(awk '{printf("%s_%s_%s_%s\t%s\n",$1,$2,$3,$4,$0);}' BR.txt | sort -t '\t' -k1,1 ) \
                  <(awk '{printf("%s_%s_%s_%s\t%s\n",$1,$2,$3,$4,$0);}' BS.txt | sort -t '\t' -k1,1 ) \
| cut -f 2-
• 1 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, It does not work. sort: multi-character tab \\t' sort: multi-character tab\t' Fuyou

• 1 views • link
written by fufuyou fufuyou

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