Cruzdb in Python3

Question

[whyaberrate]

Hello everyone, I'm trying to convert a bed file into a list of Gene IDs. I'm using the cruzdb module, to convert coordinates into the gene name, but I keep encountering issues. Here is a snippet of the bed file:

chr3    180984538   180984632   CPEB4_K562_IDR  1000    -   4.97411347309479    6.05868285076205    -1  -1
chr1    203853992   203854048   CPEB4_K562_IDR  1000    +   5.76313501648548    7.95820203088544    -1  -1
chr7    119716099   119716134   CPEB4_K562_IDR  1000    -   5.28139795449803    4.78621165693166    -1  -1

and here's the python script I'm using:

from cruzdb import Genome
genomedatabase = Genome(db='hg19')
cpeb4_peaks = open("/Users/ya8eb/Documents/Research/cpeb4/rna_binding_protein_data/cpeb4_clipseq_peaks.txt")
for i, line in enumerate(cpeb4_peaks):
    toks = line.split()
    if i == 0:
        print("\t".join(['gene'] + toks))
    else:
        chrom, posns = toks[0].split(":")
        start, end = map(int, posns.rstrip("|").split("-"))
        genes = genomedatabase.bin_query('refGene', chrom, start, end)
        print("\t".join(["|".join(set(g.name2 for g in genes))] + toks))

the error I'm getting is:

Traceback (most recent call last):
  File "/Users/ya8eb/Documents/Research/cpeb4/rna_binding_protein_data/convert_bed_to_genes.py", line 1, in <module>
    from cruzdb import Genome
  File "/Users/ya8eb/opt/anaconda3/lib/python3.7/site-packages/cruzdb/__init__.py", line 5, in <module>
    from . import soup
  File "/Users/ya8eb/opt/anaconda3/lib/python3.7/site-packages/cruzdb/soup.py", line 1, in <module>
    from . import sqlsoup
  File "/Users/ya8eb/opt/anaconda3/lib/python3.7/site-packages/cruzdb/sqlsoup.py", line 458
    except KeyError, ke:
                   ^
SyntaxError: invalid syntax

I'm guessing this has something to do with cruzdb compatibility for Python 2 vs Python 3, but I'm not sure. Does anyone have a work around for this, or suggestion for a different way to convert bed files into a gene list? I'm open to using something else, I just thought this would be the most convenient. Thanks so much for the help!