Failure to parse (compressed) Bed file in computeMatrix

[IanSudbery]

I recieve the following error message when using computeMatrix preference-point with a bed file:

Traceback (most recent call last): 
   File "<redacted>/mamba/PAS_metagene/bin/computeMatrix", line 10, in <module> 
      sys.exit(main()) 
              ^^^^^^ 
   File "/<redacted>/mamba/PAS_metagene/lib/python3.12/site-packages/deeptools/computeMatrix.py", line 413, in main 
      cmo.sortMatrix(hm, args.regionsFileName, args.transcriptID, args.transcript_id_designator, verbose=not args.quiet) 
   File "<redacted>/mamba/PAS_metagene/lib/python3.12/site-packages/deeptools/computeMatrixOperations.py", line 722, in sortMatrix 
      loadBED(line, fp, fname, labelColumn, labels, regions, defaultGroup) 
   File "<redacted>/mamba/PAS_metagene/lib/python3.12/site-packages/deeptools/computeMatrixOperations.py", line 598, in loadBED 
       if line.startswith("#") and labelColumn is None: 
         ^^^^^^^^^^^^^^^^^^^^ 
TypeError: startswith first arg must be bytes or a tuple of bytes, not str 

Deeptools is run with the following command:

$ computeMatrix reference-point
                   --referencePoint center
                   -R peaks.intronic.bed.gz
                   -S Rp12.rev.cov.bw
                   --outFileNameMatrix Rp12.rev.cov.matrix.tsv
                   --outFileName Rp12.rev.cov.matrix.tsv.computematrix.tsv 
                  -p 4                   
> Rp12.rev.cov.matrix.tsv.log 

using deeptools v3.5.5 on SUSE 7.9, python 3.12.3, installation via conda.

My guess is that which ever library is doing your depcompression, its passing bytes back, while the standard uncompressed bed parsing returns str?

[IanSudbery]

My hypothesis is supported by the fact that it works fine with an uncompressed bed file.

[dpryan79]

Indeed, it's returning things earlier on correctly but not decoding later on. @WardDeb You want something like https://github.com/deeptools/deeptools_intervals/blob/master/deeptoolsintervals/parse.py#L15