mask didn't work in the call2plink workflow

[Zhenghongc]

I tried to use a mask file to exclude some individuals in the call2plink workflow. But the removal seemed not work and there were several other issues when using a mask file.

1. I gave a one-column mask file as follows to exclude these individuals. mask_type=sample-label.
   G4968
   G4969
   G4970
   G4971
   G4972
   sheet2fam.py reported an error at line 130. because the mask file doesn't have a second column.
   indivs[(data[0],data[1])]=data[-1]
   so modify the code to:
   indivs[(data[0],data[0])]=data[-1]

2. the plink log file shows that a --remove command was added to the process, but no individuals were removed. no idea about this bug.
   PLINK v1.90b7 64-bit (16 Jan 2023)
   Options in effect:
   --a2-allele emptyZ0ref.txt
   --bed raw.bed
   --bim raw.bim
   --fam raw.fam
   --flip flips.lst
   --make-bed
   --out plink_out
   --remove mask.inds
   4819 people (0 males, 0 females, 4819 ambiguous) loaded from .fam.
   --remove: 4819 people remaining.

3. the fixfam process marked mask individuals with 'MSK', but why they are not removed?
   G4969_MSK__ G4969 0 0 1 0
   G4970_MSK__ G4970 0 0 1 0
   G4971_MSK__ G4971 0 0 2 0
   G4972_MSK__ G4972 0 0 2 0

[Zhenghongc]

I checked the scripts in call2plin/bin and have solved the issues.

1. indivs[(data[0],data[0])]=data[-1]will not report error.
2. list_error_inds.py line 28 should be return (data,data)to correctly extract sample id if your mask file only has one column.
3. sheet2fam.py line 214 if (ofid,oiid) != (fid,real_id): , (ofid,oiid,fid,real_id) write to wrn. I added continue to skip the write. this may affect the result if paramater.replicate is set.
4. an additional finding. mask file in CSV format will cause an error in reading first line. no idea about this.

hope this will help others who want to use call2plink workflow. thanks for the great work of h3abionet