bede / kindel Goto Github PK

Hi,
For very bad alignments with a lot of gaps, is it possible to fill them using the reference instead N's?
Thanks!

Depend on aligner? Segemehl, BBMap? Graphmap?

Accept reference as an optional argument and use to calculate length in absense of LN field

Throw exception with missing LN field and no reference

Function should return instance of Consensus object etc.

When I run Kindel using --realign on the test data. I get the following error. Has something not installed correctly?

kindel consensus --realign -t 6.1.sub_test.bam
loading sequences: 16457it [00:01, 14571.11it/s]
Traceback (most recent call last):
File "/usr/local/bin/kindel", line 11, in
sys.exit(main())
File "/home/.local/lib/python3.6/site-packages/kindel/cli.py", line 79, in main
parser.dispatch()
File "/home/.local/lib/python3.6/site-packages/argh/helpers.py", line 55, in dispatch
return dispatch(self, *args, **kwargs)
File "/home/.local/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
for line in lines:
File "/home/.local/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
for line in result:
File "/home/.local/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
result = function(*positional, **keywords)
File "/home/.local/lib/python3.6/site-packages/kindel/cli.py", line 24, in consensus
uppercase)
File "/home/.local/lib/python3.6/site-packages/kindel/kindel.py", line 377, in bam_to_consensus
clip_decay_threshold, mask_ends)
NameError: name 'mask_ends' is not defined

Hi, thanks for making this software available!

I am running into an error with kindel consensus:

kindel consensus align.sam > test.fasta
...
building consensus: 100%|████████████████████████████████████████████████████████████| 90/90 [00:00<00:00, 140853.49it/s]
Traceback (most recent call last):
  File "/env/kindel/bin/kindel", line 8, in <module>
    sys.exit(main())
  File "/env/kindel/lib/python3.6/site-packages/kindel/cli.py", line 83, in main
    parser.dispatch()
  File "/env/kindel/lib/python3.6/site-packages/argh/helpers.py", line 55, in dispatch
    return dispatch(self, *args, **kwargs)
  File "/env/kindel/lib/python3.6/site-packages/argh/dispatching.py", line 174, in dispatch
    for line in lines:
  File "/env/kindel/lib/python3.6/site-packages/argh/dispatching.py", line 277, in _execute_command
    for line in result:
  File "/env/kindel/lib/python3.6/site-packages/argh/dispatching.py", line 260, in _call
    result = function(*positional, **keywords)
  File "/env/kindel/lib/python3.6/site-packages/kindel/cli.py", line 28, in consensus
    uppercase)
  File "/env/kindel/lib/python3.6/site-packages/kindel/kindel.py", line 417, in bam_to_consensus
    uppercase)
  File "/env/kindel/lib/python3.6/site-packages/kindel/kindel.py", line 385, in build_report
    report += '- min, max observed depth[50:-50]: {}, {}\n'.format(min(aligned_depth[50:-50]),
ValueError: min() arg is an empty sequence

I suspect the problem must be in the data somewhere because I am running kindel consensus over a list of files, and it only errors out on some of them. If it would help with troubleshooting I can send the sam file.

name: kindel
channels:
  - bioconda
  - defaults
dependencies:
  - _libgcc_mutex=0.1=main
  - ca-certificates=2020.10.14=0
  - certifi=2020.6.20=py36_0
  - ld_impl_linux-64=2.33.1=h53a641e_7
  - libedit=3.1.20191231=h14c3975_1
  - libffi=3.3=he6710b0_2
  - libgcc-ng=9.1.0=hdf63c60_0
  - libstdcxx-ng=9.1.0=hdf63c60_0
  - ncurses=6.2=he6710b0_1
  - openssl=1.1.1h=h7b6447c_0
  - pip=20.2.3=py36_0
  - python=3.6.12=hcff3b4d_2
  - readline=8.0=h7b6447c_0
  - setuptools=50.3.0=py36hb0f4dca_1
  - sqlite=3.33.0=h62c20be_0
  - tk=8.6.10=hbc83047_0
  - wheel=0.35.1=py_0
  - xz=5.2.5=h7b6447c_0
  - zlib=1.2.11=h7b6447c_3
  - pip:
    - argh==0.26.2
    - biopython==1.78
    - kindel==0.4.2
    - numpy==1.19.2
    - ordereddict==1.1
    - pandas==1.1.3
    - python-dateutil==2.8.1
    - pytz==2020.1
    - scipy==1.5.2
    - simplesam==0.1.3.1
    - six==1.15.0
    - tqdm==4.50.2

14.1

Reproducer

from kindel import kindel
r = kindel.bam_to_consensus(f'{r_root}/kindel/bam/14.1.100k.bam')
str(r[0][0].seq)

Review handling of N, H, P, X and = ops. X and = were introduced in 1.4 and remove the need to concurrently examine the MD tag
https://samtools.github.io/hts-specs/SAMv1.pdf

Fix regression in v0.2.0+ reported by @tomas-fer via email

Temporary solution: $ pip3 install -Iv kindel==0.1.4

Maybe just replace with bokeh?

Thank you for providing this useful tool to the community. I was wondering if base quality is considered when determining min-depth for the consensus call such as iVar (https://andersen-lab.github.io/ivar/html/manualpage.html#autotoc_md19)?

Add before next release

   classifiers=[
        "Programming Language :: Python :: 3.5",
        "Programming Language :: Python :: 3.6"]