I am wondering whether I can use the fisher test in pairwise module about my species(Arabidopsis thaliana)

[shangguandong1996]

Hi, Dr Khan I am wondering whether I can use the fisher test in pairwise module about my species(Arabidopsis thaliana). I have made it when I use the bedtools

$ bedtools fisher -a test.narrowPeak -b merge_peak.bed -g Athaliana.genome 
# Number of query intervals: 15732
# Number of db intervals: 25530
# Number of overlaps: 13743
# Number of possible intervals (estimated): 78334
# phyper(13743 - 1, 15732, 78334 - 15732, 25530, lower.tail=F)
# Contingency Table Of Counts
#_________________________________________
#           |  in -b       | not in -b    |
#     in -a | 13743        | 1989         |
# not in -a | 11787        | 50815        |
#_________________________________________
# p-values for fisher's exact test
left    right   two-tail    ratio
1   0   0   29.788

-----------------------------------------------------------
Athaliana.genome 

Chr1    30427671
Chr2    19698289
Chr3    23459830
Chr4    18585056
Chr5    26975502
ChrM    366924
ChrC    154478

--------------------------------------------------

But when I use the Athaliana.genome in intervene pairwise.It all failed (My intervene is installed by pip. The version is 0.6.4)

$ intervene pairwise -i * --compute=fisher --genome Athaliana.genome
ERROR 1064 (42000) at line 1: You have an error in your SQL syntax; check the manual that corresponds to your MariaDB server version for the right syntax to use near '.chromInfo' at line 1

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$ intervene pairwise -i * --compute=fisher --bedtools-option -g Athaliana.genome
usage: intervene pairwise [options]
intervene <subcommand> [options] pairwise: error: argument --bedtools-options: expected one argument
(intervene_module)

--------------------------------------------------------------------------------------------------------
$ intervene pairwise -i * --compute=fisher --bedtools-option g=Athaliana.genome
Fisher test requires genome name. Please set the --genome argument.
Type --help or read documentation for more details - http://intervene.readthedocs.io
(intervene_module)

It seems the intervene pairwise will get the genome info from uscs sql. But My species is not in USCS(it is a plant :D). So I am wondering if there is anotehr solution.

Guandong Shang