Concatenation of int with str throws error for gene symbols and ids

[pcm32]

Apparently I have run into a case where a gene symbol or id is being intepreted as a numpy int, so I guess we need to be more defensive on that concatenation line:

INFO:root:Writing gene-by-gene, without using pandas
Traceback (most recent call last):
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.7.10/bin/cbImportScanpy", line 10, in <module>
    sys.exit(cbImportScanpyCli())
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.7.10/lib/python3.8/site-packages/cellbrowser/convert.py", line 565, in cbImportScanpyCli
    scanpyToCellbrowser(ad, outDir, datasetName, skipMatrix=options.skipMatrix, useRaw=(not options.useProc),
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.7.10/lib/python3.8/site-packages/cellbrowser/cellbrowser.py", line 3869, in scanpyToCellbrowser
    anndataMatrixToTsv(adata, matFname, useRaw=useRaw)
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.7.10/lib/python3.8/site-packages/cellbrowser/cellbrowser.py", line 3778, in anndataMatrixToTsv
    genes = [x+"|"+y for (x,y) in geneIdAndSyms]
  File "/Users/pmoreno/miniconda3/envs/__ucsc-cell-browser@0.7.10/lib/python3.8/site-packages/cellbrowser/cellbrowser.py", line 3778, in <listcomp>
    genes = [x+"|"+y for (x,y) in geneIdAndSyms]
TypeError: can only concatenate str (not "numpy.int16") to str

I have seen this in 0.7.9 as well.

Thanks!

[maximilianh]

Thanks! Fixed on the develop branch. I knew about this, but didn't apply it to the symbol case.

Note, this should not happen on real datasets. If you define genes to be symbols, they can not be numbers. If they are numbers, then they are entrez gene IDs. But I've changed it anyways, just to avoid the crash.