Can this software create an abundance table?

[slvrshot]

Hi Brian I have used your software for many years but was wondering if it had this capability.

I have a directory of files (48 files, 4 groups each containing 12 samples) containing the output from diamond. I used diamond to perform a blastx search of reads against a protein database. All I want to be able to do is generate counts for each occurrence of each gene identified per sample and create an abundance table containing these counts for all samples.

3TFCDRXX:2:1101:19180:1172	BAC0211|mdtB/yegN|sp|P76398|MDTB_ECOLI	52.0	50	24	0	1	150	741	790	1.2e-08	50.1
A00484:57:H3TFCDRXX:2:1101:9598:1204	BAC0316|pstB|sp|P0AAH0|PSTB_ECOLI	72.9	48	13	0	150	7	155	202	9.2e-17	77.0
A00484:57:H3TFCDRXX:2:1101:29939:1611	BAC0619|copA|tr|Q7WYH1|Q7WYH1_PSEPU	65.2	46	16	0	6	143	132	177	3.3e-16	75.1
A00484:57:H3TFCDRXX:2:1101:29595:1642	BAC0211|mdtB/yegN|sp|P76398|MDTB_ECOLI	85.2	27	4	0	3	83	889	915	4.5e-08	48.1
A00484:57:H3TFCDRXX:2:1101:16242:1689	BAC0467|zraR/hydH|sp|P14375|ZRAR_ECOLI	58.3	48	20	0	146	3	284	331	1.7e-10	56.2
A00484:57:H3TFCDRXX:2:1101:9516:1752	BAC0646|mdtB|tr|D0ZND9|D0ZND9_SALT1	64.5	31	11	0	58	150	42	72	5.1e-07	44.7
The 

Above is what the file looks...It basically has the sequence id extracted from a .fasta file and its corresponding blastx hit.

A buddy created a simple script to do this:

cut –f 2 diamond_output.tab > diamond_output_ids
Then:
sort diamond_output_ids | uniq –c | sort –n > ids_counts

The output of ids_counts looks like this (the numbers represent the number of times the gene was observed):

86 BAC0269|nia|tr|Q92Z60|Q92Z60_RHIME
  87 BAC0504|farB|tr|Q9RQ29|Q9RQ29_NEIGO
  88 BAC0078|copA|sp|O32220|COPA_BACSU
  89 BAC0487|pmrA|sp|Q70FH0|PMRA_PECSS

But I feel like BBMap could do this far more efficiently than doing each sample serially. Can BBMap help me?