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Use aligntools #1068

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merged 3 commits into from
Mar 19, 2024
Merged

Use aligntools #1068

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1727e95
Add aligntools to the list of dependencies
Donaim Mar 19, 2024
ba01749
Switch to using aligntools instead of utils.cigar_tools
Donaim Mar 19, 2024
2c799fd
Remove cigar_tools.py
Donaim Mar 19, 2024
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3 changes: 3 additions & 0 deletions .mypy.ini
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Expand Up @@ -9,6 +9,9 @@ check_untyped_defs = True
[mypy-micall.core.plot_contigs]
check_untyped_defs = False

[mypy-aligntools]
ignore_missing_imports = true

[mypy-mappy]
ignore_missing_imports = true

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2 changes: 1 addition & 1 deletion micall/core/aln2counts.py
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Expand Up @@ -29,7 +29,7 @@
from micall.data.landmark_reader import LandmarkReader
from micall.utils.big_counter import BigCounter
from micall.utils.consensus_aligner import ConsensusAligner
from micall.utils.cigar_tools import CigarActions
from aligntools import CigarActions
from micall.utils.report_amino import ReportAmino, MAX_CUTOFF, SeedAmino, AMINO_ALPHABET, ReportNucleotide, \
SeedNucleotide
from micall.utils.spring_beads import Wire, Bead
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2 changes: 1 addition & 1 deletion micall/core/contig_stitcher.py
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Expand Up @@ -11,8 +11,8 @@
import logging
from fractions import Fraction
from operator import itemgetter
from aligntools import Cigar, connect_cigar_hits, CigarHit

from micall.utils.cigar_tools import Cigar, connect_cigar_hits, CigarHit
from micall.utils.contig_stitcher_context import context, StitcherContext
from micall.utils.contig_stitcher_contigs import GenotypedContig, AlignedContig
import micall.utils.contig_stitcher_events as events
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2 changes: 1 addition & 1 deletion micall/core/plot_contigs.py
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Expand Up @@ -11,6 +11,7 @@
import logging

import yaml
from aligntools import CigarHit
from genetracks import Figure, Track, Multitrack, Coverage
# noinspection PyPep8Naming
import drawsvg as draw
Expand All @@ -21,7 +22,6 @@
from micall.core.project_config import ProjectConfig
from micall.utils.alignment_wrapper import align_nucs
from micall.utils.contig_stitcher_contigs import Contig, GenotypedContig, AlignedContig
from micall.utils.cigar_tools import CigarHit
import micall.utils.contig_stitcher_events as events
from micall.data.landmark_reader import LandmarkReader

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