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!

[brentp]

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!