cannot access local variable 'leftcheck' where it is not associated with a value

[xiekunwhy]

Describe the bug
v0.0.5 error

/public2/home/sl_qybio/sl_qybio/miniforge3/envs/samtools/bin/samtools view -@ 10 -h -F 0x100 /public2/home/sl_qybio/sl_qybio/project/2024/QY240622GA064_GangLiu_T2T/QY240622GA064_std_2_assemble/t2t/03.telomere/hifisplit/Chr01.sortn.bam|/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/bin/teloclip --motifs CCCTAAA --refIdx /public2/home/sl_qybio/sl_qybio/project/2024/QY240622GA064_GangLiu_T2T/QY240622GA064_std_2_assemble/t2t/03.telomere/pse.gapfill.fa.fai|/public2/home/sl_qybio/sl_qybio/miniforge3/envs/samtools/bin/samtools sort > /public2/home/sl_qybio/sl_qybio/project/2024/QY240622GA064_GangLiu_T2T/QY240622GA064_std_2_assemble/t2t/03.telomere/hifisoftclip/Chr01.overhangs.bam
Traceback (most recent call last):
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/bin/teloclip", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/lib/python3.12/site-packages/teloclip/app.py", line 138, in main
    processSamlines(
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/lib/python3.12/site-packages/teloclip/samops.py", line 105, in processSamlines
    if isMotifInClip(
       ^^^^^^^^^^^^^^
  File "/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/lib/python3.12/site-packages/teloclip/seqops.py", line 152, in isMotifInClip
    return any(leftcheck, rightcheck)
               ^^^^^^^^^
UnboundLocalError: cannot access local variable 'leftcheck' where it is not associated with a value

but v0.0.4 run successfully.

/public2/home/sl_qybio/sl_qybio/miniforge3/envs/samtools/bin/samtools view -@ 10 -h -F 0x100 /public2/home/sl_qybio/sl_qybio/project/2024/QY240622GA064_GangLiu_T2T/QY240622GA064_std_2_assemble/t2t/03.telomere/hifisplit/Chr01.sortn.bam|/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/bin/teloclip --motifs CCCTAAA --refIdx /public2/home/sl_qybio/sl_qybio/project/2024/QY240622GA064_GangLiu_T2T/QY240622GA064_std_2_assemble/t2t/03.telomere/pse.gapfill.fa.fai|/public2/home/sl_qybio/sl_qybio/miniforge3/envs/samtools/bin/samtools sort > /public2/home/sl_qybio/sl_qybio/project/2024/QY240622GA064_GangLiu_T2T/QY240622GA064_std_2_assemble/t2t/03.telomere/hifisoftclip/Chr01.overhangs.bam
Processed 243435 SAM records.
Found 1 alignments soft-clipped at contig ends.
Output 1 alignments containing motif matches.
Discarded 170105 terminal alignments after filtering.

Best,
Kun

[Adamtaranto]

Hi Kun,

Thanks for reporting this. I'll look into it!

If you could provide a single contig with associated reads in sam/bam format that reproduces this error that would be useful for debugging.

[Adamtaranto]

@xiekunwhy, can you please re-install teloclip from the patch branch and let me know if it runs AND if it gives you the same output as for v0.0.4 ?

# Uninstall current version
pip uninstall teloclip

# Install from patch branch
pip install git+https://github.com/adamtaranto/teloclip.git@patch_missing_overhangs

[xiekunwhy]

Yes, it works.

/public2/home/sl_qybio/sl_qybio/miniforge3/envs/samtools/bin/samtools view -@ 10 -h -F 0x100 hifisplit/Chr01.sortn.bam |/public2/home/sl_qybio/sl_qybio/miniforge3/envs/teloclip/bin/teloclip --motifs CCCTAAA --refIdx ../pse.gapfill.fa.fai |/public2/home/sl_qybio/sl_qybio/miniforge3/envs/samtools/bin/samtools sort > hifisoftclip/Chr01.overhangs.bam
2024-11-13 09:33:11,112 | INFO | samops:122:processSamlines() | Processed 243435 SAM records.
Found 1 alignments soft-clipped at contig ends.
Output 1 alignments containing motif matches.
Discarded 170105 terminal alignments after filtering.