matteops/easyprimer

Identify the best regions to design primers in your alignment

easyprimer's Issues

'U' mode is deprecated

Hi there,
I got the following issue when running EasyPrimer on Linux:

/opt/Programs/EasyPrimer/EasyPrimer.py:97: DeprecationWarning: 'U' mode is deprecated
with open(inputpath + genename_ext, "rU") as handle:

Is that concerning?

Error for complete genomes.

Dear team EasyPrimer

I tried to use the program with my data dengue genomes completed.

But I have a error

administrador@dengue02:~/programas/EasyPrimer$ python3 EasyPrimer.py -out denv3 -in DENV3_final.fas
Traceback (most recent call last):
File "EasyPrimer.py", line 449, in
main()
File "EasyPrimer.py", line 445, in main
args.func(args)
File "EasyPrimer.py", line 407, in run
primerHRM(out_folder, tmp_folder, inputfile, conslimit, prilen, amplen, prim_thr, amp_thr, n_adj, w_adj, alg, jobname, snp, minpri, maxpri, minamp, maxamp)
File "EasyPrimer.py", line 150, in primerHRM
snptab[k][5] = float(snptab[k][0]) / totalleles # freqA
ZeroDivisionError: float division by zero

Please help !!