Traceback (most recent call last):
File "/Users/bgold/HemTools/bin/bed2vcf.py", line 137, in <module>
main()
File "/Users/bgold/HemTools/bin/bed2vcf.py", line 101, in main
out = df[[chr,pos,ID,ref,alt]]
File "/Users/bgold/opt/anaconda3/lib/python3.8/site-packages/pandas/core/frame.py", line 3030, in __getitem__
indexer = self.loc._get_listlike_indexer(key, axis=1, raise_missing=True)[1]
File "/Users/bgold/opt/anaconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1266, in _get_listlike_indexer
self._validate_read_indexer(keyarr, indexer, axis, raise_missing=raise_missing)
File "/Users/bgold/opt/anaconda3/lib/python3.8/site-packages/pandas/core/indexing.py", line 1308, in _validate_read_indexer
raise KeyError(f"None of [{key}] are in the [{axis_name}]")
KeyError: "None of [Index(['chr', 'pos', 'ID', 'ref', 'alt'], dtype='object')] are in the [columns]"
Here are the first ~30 lines of my input, space-delimited, no headers input file:
Hello,
Here is my command:
python /Users/bgold/HemTools/bin/bed2vcf.py -f PanelBmosaik.bed --required_cols chr,pos,ID,ref,alt --info_col QUAL,DP,VD,AD,AF,RD,ALD,Func.refGene,REFGENE,GeneDetail.refGene,ExonicFunc.refGene,AAChange.refGene,Func.ensGene,Gene.ensGene,GeneDetail.ensGene,ExonicFunc.ensGene,AAChange.ensGene,Func.knownGene,Gene.knownGene,GeneDetail.knownGene,ExonicFunc.knownGene,AAChange.knownGene --info_types STRING,INTEGER,INTEGER,STRING,FLOAT,INTEGER,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING,STRING -o PanelBmosaik.vcf
Here is the reply:
Here are the first ~30 lines of my input, space-delimited, no headers input file:
OK, so where am I messing up?
Suggestions welcomed.