Improve IMGT numbering

[benjiemc]

I have modified the annotations to improve the IMGT numbering for molecules. Previously, MHC class I were only being half numbered because anarci would find the first hit, and then that would be passed back and used as annotations. Now, anarci keeps going until no more annotations can be found for a sequence, and these are used to number the whole molecule. These changes also update how scTCRs are identified.

These changes also rely on a fix that is staged as a PR in anarci (https://github.com/npqst/anarci-mhc/pull/5). There is an issue with how CD1 molecules are currently identified by anarci.

I also added a fix for interaction profiling that addresses #75, because the updated numbering uncovered some potential issues with how the conversion between PLIP and PDB numbering was working.

[benjiemc]

Ran into an issue that needs to be resolved caused by this change before the PR is ready to be merged.

File "/Users/bmcmaster/code/STCRpy/stcrpy/tcr_processing/TCRParser.py", line 288, in get_tcr_structure
    numbering, chain_type, germline_info, scTCR = annotate(chain)
                                                  ^^^^^^^^^^^^^^^
  File "/Users/bmcmaster/code/STCRpy/stcrpy/tcr_processing/annotate.py", line 108, in annotate
    aligned_numbering = align_numbering(numbering, sequence_list)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/bmcmaster/code/STCRpy/stcrpy/tcr_processing/annotate.py", line 297, in align_numbering
    raise AlignmentError(numbered_sequence_ali, input_sequence_ali)
stcrpy.tcr_processing.annotate.AlignmentError: Could not align sequences: -----------------------------DSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVERDKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLTGDYAEQFFGPGTRLTVL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- and MSNTVLADSAWGITLLSWVTVFLLGTSSADSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVERDKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLTGDYAEQFFGPGTRLTVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADCGITSASYHQGVLSATILYEILLGKATLYAVLVSGLVLMAMVKKKNS

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[benjiemc]

Ran into an issue that needs to be resolved caused by this change before the PR is ready to be merged.

File "/Users/bmcmaster/code/STCRpy/stcrpy/tcr_processing/TCRParser.py", line 288, in get_tcr_structure
    numbering, chain_type, germline_info, scTCR = annotate(chain)
                                                  ^^^^^^^^^^^^^^^
  File "/Users/bmcmaster/code/STCRpy/stcrpy/tcr_processing/annotate.py", line 108, in annotate
    aligned_numbering = align_numbering(numbering, sequence_list)
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/bmcmaster/code/STCRpy/stcrpy/tcr_processing/annotate.py", line 297, in align_numbering
    raise AlignmentError(numbered_sequence_ali, input_sequence_ali)
stcrpy.tcr_processing.annotate.AlignmentError: Could not align sequences: -----------------------------DSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVERDKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLTGDYAEQFFGPGTRLTVL----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- and MSNTVLADSAWGITLLSWVTVFLLGTSSADSGVVQSPRHIIKEKGGRSVLTCIPISGHSNVVWYQQTLGKELKFLIQHYEKVERDKGFLPSRFSVQQFDDYHSEMNMSALELEDSAMYFCASSLTGDYAEQFFGPGTRLTVLEDLRNVTPPKVSLFEPSKAEIANKQKATLVCLARGFFPDHVELSWWVNGKEVHSGVSTDPQAYKESNYSYCLSSRLRVSATFWHNPRNHFRCQVQFHGLSEEDKWPEGSPKPVTQNISAEAWGRADCGITSASYHQGVLSATILYEILLGKATLYAVLVSGLVLMAMVKKKNS

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This issue is fine because it happened from expected behaviour. The error message has now been improved to include more details.