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sheynkman-lab / biosurfer

"Surf" the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.
MIT License
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EXITC detection raises error when aligning some transcripts #78

Closed jsaquing closed 3 years ago

jsaquing commented 3 years ago

example: ETFA|PB.13537.14 and ETFA|PB.13537.12 (bone.sqlite3)

from biosurfer.core.models import Transcript
from biosurfer.core.alignments import TranscriptBasedAlignment as Alignment
tx1 = Transcript.from_name('ETFA|PB.13537.12')
tx2 = Transcript.from_name('ETFA|PB.13537.14')
>>> Alignment(tx1.protein, tx2.protein)
ETFA|PB.13537.12:protein|ETFA|PB.13537.14:protein
>>> Alignment(tx2.protein, tx1.protein)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "biosurfer/core/alignments.py", line 210, in __init__
    self._annotate()
  File "biosurfer/core/alignments.py", line 458, in _annotate
    exon_extension_introduces_stop = upstream_cterm_tblock._prev_match_or_frame_tblock[-1].other.codon[0].exon is upstream_cterm_res_aln.other.codon[2].exon
TypeError: 'NoneType' object is not subscriptable