extracting blast hit whith the highest bit score
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4.0 years ago
Ric ▴ 360

Hi, I have the following blast out

tig00007144     chr03   97.352  7742    145     22      23113   30824   33203431        33211142        0.0     13106
tig00007144     chr03   96.995  5590    82      31      1       5564    33172892        33178421        0.0     9313
tig00007144     chr03   96.028  5488    101     38      30947   36357   33211132        33216579        0.0     8818
tig00007144     chr03   98.062  4541    43      19      36363   40867   33216622        33221153        0.0     7856
tig00026480     chr03   99.707  48449   70      54      1       48387   35010628        34962190        0.0     88616
tig00026480     chr03   98.286  5951    92      8       56515   62455   34956358        34950408        0.0     10416
tig00026480     chr03   94.484  5040    255     22      90660   95689   15384926        15389952        0.0     7745
tig00026480     chr03   94.483  5039    256     21      90661   95689   18433238        18428212        0.0     7745

Is there a quick way to extract each queary line with the highest bit score in order to get

tig00007144     chr03   97.352  7742    145     22      23113   30824   33203431        33211142        0.0     13106
tig00026480     chr03   99.707  48449   70      54      1       48387   35010628        34962190        0.0     88616

?

Thank you in advance

blast • 553 views
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Entering edit mode
4.0 years ago
5heikki 10.0k
export LANG=C; sort -t $'\t' -k1,1 -k12,12gr tabularBlastOutput | sort -t $'\t' -uk1,1
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4.0 years ago
Bioaln ▴ 350

Maybe something in the lines of: sort --key 2 --numeric-sort results.txt | head -n 5 # this gets top 5 results. I didn't really test it tho.

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