Peddy run error: AttributeError: 'DataFrame' object has no attribute 'ix'

[yusmile0618]

Hi , everyone, I install peddy through conda [ conda install -y peddy ]

1. $ python -m peddy --plot -p 4 --prefix merge4fam merge4fam.vcf.gz merge4fam.ped
   VCF header:
   #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A24173 A24173F A24173M C5140 C5140F C5140M P8491 P8491F P8491M P8505 P8505F P8505M
   ped file:
   A24173fam A24173 A24173F A24173M 2 1
   A24173fam A24173F 0 0 1 0
   A24173fam A24173M 0 0 2 0
   C5140fam C5140 C5140F C5140M 2 1
   C5140fam C5140F 0 0 1 0
   C5140fam C5140M 0 0 2 0
   P8491fam P8491 P8491F P8491M 2 1
   P8491fam P8491F 0 0 1 0
   P8491fam P8491M 0 0 2 0
   P8505fam P8505 P8505F P8505M 1 1
   P8505fam P8505F 0 0 1 0
   P8505fam P8505M 0 0 2 0

Then I got the following error:

2020-03-20 10:40:48 dell-PowerEdge-R930 peddy.cli[31318] INFO Running Peddy version 0.4.3
Traceback (most recent call last):
File "/home/yu/anaconda3/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/home/yu/anaconda3/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/yu/anaconda3/lib/python3.7/site-packages/peddy/main.py", line 14, in
sys.exit(cli())
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/yu/anaconda3/lib/python3.7/site-packages/peddy/cli.py", line 198, in peddy
ped_df = ped_df.ix[samples, :]
File "/home/yu/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

Is there anything wrong with my vcf or ped file?

2. $ python -m peddy --plot -p 4 --prefix merge4fam merge4fam.vcf.gz merge.plink.fam
   with same vcf
   fam file:
   A24173fam A24173 A24173F A24173M 2 1
   A24173fam A24173F 0 0 1 0
   A24173fam A24173M 0 0 2 0
   C5140fam C5140 C5140F C5140M 2 1
   C5140fam C5140F 0 0 1 0
   C5140fam C5140M 0 0 2 0
   P8491fam P8491 P8491F P8491M 2 1
   P8491fam P8491F 0 0 1 0
   P8491fam P8491M 0 0 2 0
   P8505fam P8505 P8505F P8505M 1 1
   P8505fam P8505F 0 0 1 0
   P8505fam P8505M 0 0 2 0

Then I got the following same? error:

2020-03-20 10:56:48 dell-PowerEdge-R930 peddy.cli[31423] INFO Running Peddy version 0.4.3
2020-03-20 10:56:48 dell-PowerEdge-R930 peddy.cli[31423] WARNING 12 samples in vcf not in ped:
A24173,C5140,P8491,A24173F,P8491M,P8505,P8505M,P8505F,C5140F,C5140M,P8491F,A24173M

2020-03-20 10:56:48 dell-PowerEdge-R930 peddy.cli[31423] WARNING 1 samples in ped not in vcf:
nan

Traceback (most recent call last):
File "/home/yu/anaconda3/lib/python3.7/runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "/home/yu/anaconda3/lib/python3.7/runpy.py", line 85, in _run_code
exec(code, run_globals)
File "/home/yu/anaconda3/lib/python3.7/site-packages/peddy/main.py", line 14, in
sys.exit(cli())
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 764, in call
return self.main(*args, **kwargs)
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 717, in main
rv = self.invoke(ctx)
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 956, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/yu/anaconda3/lib/python3.7/site-packages/click/core.py", line 555, in invoke
return callback(*args, **kwargs)
File "/home/yu/anaconda3/lib/python3.7/site-packages/peddy/cli.py", line 198, in peddy
ped_df = ped_df.ix[samples, :]
File "/home/yu/anaconda3/lib/python3.7/site-packages/pandas/core/generic.py", line 5274, in getattr
return object.getattribute(self, name)
AttributeError: 'DataFrame' object has no attribute 'ix'

Actually the ped and fam files are same content, and I use same vcf files, but why the error info showed 2 more line than the first command?
please help me figure out the error reason, thanks!

[Brent Pedersen]

hi, this is fixed in master, it happens due to deprecated use of ix. But master has conflicts in conda which I don't know how to fix. You can clone the repo and run python setup.py install

[yusmile0618]

@brentp Thanks a lot. I download and reinstall peddy (v0.4.5), this bug was fixed!