---------
MAD1L1-201, MAD1L1-203
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(734:2695|393:2354), M(554:734|74:254), and perhaps more.
---------
---------
PMS2-201, PMS2-268
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(815, 815) and range(268, 268)
---------
---------
PHF14-215, PHF14-216
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
TMEM106B-201, TMEM106B-216
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(229, 229) and range(211, 211)
---------
---------
AEBP1-201, AEBP1-206
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(1727:1806|0:79), M(1806:1951|182:327), and perhaps more.
---------
---------
POLD2-202, POLD2-207
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 295, in from_transcripts
    assert anchor.length - position['anchor'] == other.length - position['other'], f'{position=}, {anchor.length=}, {other.length=}, {anchor=}'
AssertionError: position={'anchor': 2158, 'other': 1660}, anchor.length=2158, other.length=1659, anchor=POLD2-202
---------
---------
POLD2-202, POLD2-235
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 104, in process_gene
    tx_aln = TranscriptAlignment.from_transcripts(anchor, alternative)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 295, in from_transcripts
    assert anchor.length - position['anchor'] == other.length - position['other'], f'{position=}, {anchor.length=}, {other.length=}, {anchor=}'
AssertionError: position={'anchor': 2158, 'other': 1740}, anchor.length=2158, other.length=1739, anchor=POLD2-202
---------
---------
VOPP1-201, VOPP1-212
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(37, 37) and range(0, 0)
---------
---------
ZNF713-202, ZNF713-206
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
KCTD7-202, KCTD7-206
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(289, 289) and range(290, 290)
---------
---------
KCTD7-202, KCTD7-209
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(289, 289) and range(305, 305)
---------
---------
KCTD7-202, KCTD7-211
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(289, 289) and range(239, 239)
---------
---------
GALNT17-201, GALNT17-205
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(79, 79) and range(0, 0)
---------
---------
BCL7B-201, BCL7B-206
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 569, in from_proteins
    match_tblock = one(interval.data for interval in intervals if interval.data.category is SeqAlignCat.MATCH)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/more_itertools/more.py", line 555, in one
    raise too_long or ValueError(msg)
ValueError: Expected exactly one item in iterable, but got M(14:204|0:190), M(204:877|312:985), and perhaps more.
---------
---------
EFCAB10-205, EFCAB10-203
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(132, 132) and range(128, 128)
---------
---------
ST7-208, ST7-203
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(50, 50) and range(0, 0)
---------
---------
NDUFA5-201, NDUFA5-215
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(22, 22) and range(0, 0)
---------
---------
MKRN1-201, MKRN1-211
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(328, 328) and range(112, 112)
---------
---------
KRBA1-207, KRBA1-201
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(0, 0) and range(0, 0)
---------
---------
PAXIP1-201, PAXIP1-202
Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 216, in get_cblocks
    dfs[chr] = pd.read_csv(df_file, sep='\t')
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
    return _read(filepath_or_buffer, kwds)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 577, in _read
    parser = TextFileReader(filepath_or_buffer, **kwds)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1407, in __init__
    self._engine = self._make_engine(f, self.engine)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
    self.handles = get_handle(
                   ^^^^^^^^^^^
  File "/Users/mayankmurali/miniconda3/envs/biosurfer-install/lib/python3.11/site-packages/pandas/io/common.py", line 859, in get_handle
    handle = open(
             ^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'B_hybrid_aln_gencode_v42/cblock-tables/cblocks-chr7.tsv'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/analysis/genome_wide_alignment_analysis.py", line 105, in process_gene
    cd_aln = CodonAlignment.from_proteins(anchor.protein, alternative.protein)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 523, in from_proteins
    cblock = CodonAlignmentBlock(range(anchor_start, anchor_stop), range(other_start, other_stop), category=category)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<attrs generated init biosurfer.core.alignments.CodonAlignmentBlock>", line 12, in __init__
    self.__attrs_post_init__()
  File "/Users/mayankmurali/Desktop/Desktop - Mayank’s MacBook Pro/biosurfer_analysis_test_2/biosurfer/biosurfer/core/alignments.py", line 46, in __attrs_post_init__
    raise ValueError(f'Invalid ranges {self.anchor_range} and {self.other_range}')
ValueError: Invalid ranges range(1065, 1065) and range(1065, 1065)
---------
