Comparing Blast M8 Outputs

Question

[oussumenten]

Hi,

I want to compare BLAST outputs in m8 format to find out if any queries in the separate output files have the same subject hits to NCBI nr database.

For example, for the 2 BLAST outputs in m8 format below, displaying only the query and subject columns, I want to find PFD1 and GHT3 have the same hit (Hsp90):

BLAST Output 1:

PFD1 Hsp90

PFD2 Gan80

PFD5 Kan38

BLAST Output 2:

GHT1 Lsg70

GHT2 Jkl78

GHT3 Hsp90

GHT6 Odf45

Any help, suggestions or recommendations will be greatly appreciated. Also let me know if you have any questions.

[Pierre Lindenbaum]

cross posted on SE: http://seqanswers.com/forums/showthread.php?t=39775

Answer 1

[Pierre Lindenbaum]

sort both files on the 2nd column and join on the 2nd column (replace '\t' with a tab )..

join -t '\t' -1 2 -2 2 <(sort -t '\t' -k2,2 output1.tsv) <(sort -t '\t' -k2,2 output2.tsv)

[oussumenten]

Thanks. This will provide me with starting point

Answer 2

[Pavel Senin]

Let's do this in R:

table1 = data.frame(read.table("~/tmp/test1.out", header=F))
table2 = data.frame(read.table("~/tmp/test2.out", header=F))
names(table1) = c("gene","hit")
names(table2) = names(table1)
merge(table1, table2, by="hit")

output:

> merge(table1, table2, by="hit")
    hit gene.x gene.y
1 Hsp90   PFD1   GHT3

[oussumenten]

Thanks. This will provide me with a starting point.

Answer 3

[Prakki Rama]

Did this using Perl.

cat o1.txt o2.txt >o3.txt  ## combined both outputs

SCRIPT

open FH,"o3.txt";
%HoA=();
print "_______INPUT_DATA_________\n";
while(<FH>)
{
print "$_";
    @array=split;
    for($i=1;$i<=$#array;$i++)
    {
    push @{ $HoA{$array[$i]} }, "$array[0]";
    }
}
print "___________RESULT_________\n";
foreach $k (sort keys %HoA)
{
    print "$k\t@{$HoA{$k}}\n";
}

OUTPUT:

________INPUT_DATA_________
PFD1 Hsp90
PFD2 Gan80
PFD5 Kan38
GHT1 Lsg70
GHT2 Jkl78
GHT3 Hsp90
GHT6 Odf45
___________RESULT_________
Gan80    PFD2
Hsp90    PFD1 GHT3
Jkl78    GHT2
Kan38    PFD5
Lsg70    GHT1
Odf45    GHT6