Error when using a custom data set

[PeiwenJi]

Hello! I'm trying to run samap with my own dataset, but something is wrong. My maps are exported directly from Ensembl and have been renamed as samap‘s blast, but when run

sm = SAMAP( filenames, f_maps = 'mydata/maps/' save_processed=True )

as described in Loading in raw data I get the following error. I don't know what to do.

---

IndexError Traceback (most recent call last) /tmp/ipykernel_3478998/777754579.py in 1 sm = SAMAP( 2 filenames, ----> 3 f_maps = 'mydata/maps/' 4 #save_processed=True #if False, do not save the processed results to *_pr.h5ad 5 )

/samap_directory/samap/mapping.py in init(self, sams, f_maps, names, keys, resolutions, gnnm, save_processed) 161 if gnnm is None: 162 gnnm, gns, gns_dict = _calculate_blast_graph( --> 163 ids, f_maps=f_maps, reciprocate=True 164 )
165 if names is not None:

/samap_directory/samap/mapping.py in _calculate_blast_graph(ids, f_maps, eval_thr, reciprocate) 1118 1119 A = A[A.index.astype("str") != "nan"] -> 1120 A = A[A.iloc[:, 0].astype("str") != "nan"] 1121 B = B[B.index.astype("str") != "nan"] 1122 B = B[B.iloc[:, 0].astype("str") != "nan"]

~/miniconda3/envs/SAMap/lib/python3.7/site-packages/pandas/core/indexing.py in getitem(self, key) 923 with suppress(KeyError, IndexError): 924 return self.obj._get_value(*key, takeable=self._takeable) --> 925 return self._getitem_tuple(key) 926 else: 927 # we by definition only have the 0th axis

~/miniconda3/envs/SAMap/lib/python3.7/site-packages/pandas/core/indexing.py in _getitem_tuple(self, tup) 1504 def _getitem_tuple(self, tup: tuple): 1505 -> 1506 self._has_valid_tuple(tup) 1507 with suppress(IndexingError): 1508 return self._getitem_lowerdim(tup)

~/miniconda3/envs/SAMap/lib/python3.7/site-packages/pandas/core/indexing.py in _has_valid_tuple(self, key) 752 for i, k in enumerate(key): 753 try: --> 754 self._validate_key(k, i) 755 except ValueError as err: 756 raise ValueError(

~/miniconda3/envs/SAMap/lib/python3.7/site-packages/pandas/core/indexing.py in _validate_key(self, key, axis) 1407 return 1408 elif is_integer(key): -> 1409 self._validate_integer(key, axis) 1410 elif isinstance(key, tuple): 1411 # a tuple should already have been caught by this point

~/miniconda3/envs/SAMap/lib/python3.7/site-packages/pandas/core/indexing.py in _validate_integer(self, key, axis) 1498 len_axis = len(self.obj._get_axis(axis)) 1499 if key >= len_axis or key < -len_axis: -> 1500 raise IndexError("single positional indexer is out-of-bounds") 1501 1502 # -------------------------------------------------------------------

IndexError: single positional indexer is out-of-bounds

[atarashansky]

Your tables are likely improperly formatted. Can you upload them so I can take a look?

[PeiwenJi]

Thank you very much for your prompt reply.

I thought it might be, too. This is my table.

---

,source,target,info,weight 4,MT-ND1,mt-Nd1,ortholog_one2one,1.0 8,MT-ND2,mt-Nd2,ortholog_one2one,1.0 14,MT-CO1,mt-Co1,ortholog_one2one,1.0 17,MT-CO2,mt-Co2,ortholog_one2one,1.0

How should I change it?

[atarashansky]

Yes, your formatting is not correct. Please inspect the mapping tables in the example data folder on the github and try to create something similar - same number of columns, same column IDs, etc. For columns that you don't have information for, just fill it with a dummy value.

[PeiwenJi]

Thank you very much for your help, I'm now able to run it properly.

I set all the dummy values to 0, (except for the last column which is the weight),

but I don't know which columns are used in the samap running and what effect it will have on the model results if I set them this way.

I would be very grateful for your answers.