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License: GNU General Public License v3.0

Python 9.78% Jupyter Notebook 88.08% R 2.14%

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ibseq ditag yemilawal glaand aukehaver ztsin

cojac's Issues

configurable mutation list

provide a YAML file for each variant of concern featuring the mutation list we want to watch for

bioconda package

we need to make a bioconda package

our smallegenomeutility package is a good example.

Paired end 150?

Hi,

I just read your paper introducing this tool- very well done!

I'm getting set up to run COJAC myself on our own data. The amplicon was generated with the ARTIC 3 method, so we should be set on that front. However, sequencing was paired end 150, rather than 250. I know that this will create some gaps within reads, but am still curious to see how this algorithm performs. Are there any settings I will need to adjust to make COJAC run on our data?

Thanks

issue with overlapping amplicons

I run cojac on wastewater samples which are sequenced using NimagenV3 primer amplicons. It worked well for most variant profile however I encountered this error while using a profile which has co-occurrence in amplicon 120:
File "/usr/local/bin/cooc-mutbamscan2", line 245, in
table[sample]=scanbam(alnfname, amplicons)
File "/usr/local/bin/cooc-mutbamscan2", line 155, in scanbam
amplicon_iter = alnfile.fetch(rq_chr, rq_b, rq_e)
File "pysam/libcalignmentfile.pyx", line 1091, in pysam.libcalignmentfile.AlignmentFile.fetch
File "pysam/libchtslib.pyx", line 688, in pysam.libchtslib.HTSFile.parse_region
ValueError: invalid coordinates: start (22867) > stop (22846)

and here are the corresponding NimagenV3 insert coordinates:
amplicon_119 [22595-22837]
amplicon_120 [22804-22976]
amplicon_121 [22876-23119]
amplicon_122 [23072-23288]
According to the cooc-mutbamscan script, the boundaries are defined by +30 from previous amplicon end (22867) and -30 from next amplicon start (22846) which lead to this error.
Could you implement a fix for it?
Irene Bassano with you had contact with about cojac used to work with me. Thanks Hubert

add the notebooks

we need to create a folder notebooks/ and upload there the jupyter / rstudio notebooks that were used in the publication.

and add documentation describing them.

it's less urgent, but it's a nice to have.

yaml module not found

Hello,
I installed cojac using conda within a virtual environment (mac monterey)
conda create -n cojac
conda activate cojac
conda install cojac
but am now encountering the following error when testing:
cooc-mutbamscan --help
Traceback (most recent call last):
File "/Users/susanne/opt/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 10, in
import yaml
ModuleNotFoundError: No module named 'yaml'
I tried to install yaml via conda and pip, as well as homebrew. When I just use python within the cojac environment I can import the module, but I can't appear to solve the error.
Thank you and any help is appreciated,
Susanne

blank cooc.test.json file

Hi,
I was trying to use cojac for analysing SARS-CoV-2 sequenced wastewater samples.
When I was checking for co-occurrance using a standalone file,
(cojac) opentrons-b10@AirdiOptronsB10 cojac % cooc-mutbamscan -b QIAseqDIRECTSARSCoV2ampliconsfinal.bed -m voc/ -a read_mapping_21BL54986-TO_S3_L001.bam -j cooc-test.json

This message appears:

insertions not supported (yet): +ACT : ACT
insertions not supported (yet): +GAGCCAGAA : GAGCCAGAA
insertions not supported (yet): +AACA : AACA
autodecting reference as MN908947.3

and the cooc-test.json is empty:

What do you reckon is the problem here?
Many thanks for the help and for this amazing pipeline!!

cooc-curate TypeError: 'NoneType' object is not iterable

Hello,
I am trying to use cojac for my research and encountering the issue.
When I run in command line
cooc-curate voc/omicron_ba2_mutations.yaml (this command is also mentioned as an example in https://github.com/cbg-ethz/cojac#input-data-requirements)
or
cooc-curate voc/omicron_ba2_mutations.yaml voc/omicron_ba1_mutations.yaml voc/delta_mutations.yaml -a amplicons.yaml -m
(where amplicons.yaml is produced by cooc-nutbamscan)

In both cases I get the error

File ".../bin/cooc-curate", line 140, in listalllineages
    return {s['pangoLineage']:s['count'] for s in aggregated(fields='pangoLineage')}
TypeError: 'NoneType' object is not iterable

Can you please help me?
Thanks in advance.

Best wishes,
Polina

number of bam files for comparison

Hi all,
is the comparison done only two bam files at the time? can we add a longer list?

thanks
ibseq

updated yamls files

Hi, I am new to Cojac, it's a great tool, thanks!!

I was wondering where I can find an updated yamsl file with the list of all the variant? For this comand
-m DIR, --vocdir DIR directory containing the yamls defining the variant of concerns
usually what's a good number to chose for -# COOC, --cooc COOC minimum number of cooccurences to search for?

Thanks a lot!!
Carlotta

TypeError: unsupported operand type(s) for -: 'NoneType' and 'int'

Hello,

I am attempting to use cojac for a research project and have created a conda environment (conda version 4.13.0) for this, but when supplying *.bam files to test the package I have encountered an error.

First I will list my conda environment for your reference in case you notice important versioning differences (cojac and pysam in bold ):

packages in environment at /home/evan/anaconda3/envs/cojac:

So firstly, the command I used was:

cooc-mutbamscan -b ../SARS-CoV-2.insert.V4.txt -m ../voc/ -a NIRE-002f80_S267.sorted.bam NIRE-002f81_S268.sorted.bam -j ../out/cooc-test.json

The bams and bam indices are attached as .txt files for your testing.

NIRE-002f81_S268.sorted.bam.bai.txt
NIRE-002f81_S268.sorted.bam.txt
NIRE-002f80_S267.sorted.bam.bai.txt
NIRE-002f80_S267.sorted.bam.txt

I used the SARS-CoV-2.insert.V4.txt as from GitHub (and also tested V3 in case I was wrong about the primer version used).
The voc/ folder is mirrored from GitHub.

The output was:
insertions not supported (yet): +AACA : AACA
insertions not supported (yet): +ACT : ACT
insertions not supported (yet): +GAGCCAGAA : GAGCCAGAA
76_B16173 is identical to 76_ka
77_ga is identical to 77_be
76_de is identical to 76_AY42
92_de is identical to 92_AY42
78_BA1 is identical to 78_BA2
79_BA1 is identical to 79_BA2
82_BA1 is identical to 82_om1
88_BA1 is identical to 88_om1
94_BA1 is identical to 94_BA2
95_BA1 is identical to 95_BA2
autodecting reference as MN908947.3
amplicon_31_om2 9336 9467 {9424: 'G', 9534: 'T'} amplion: 410
Traceback (most recent call last):
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 479, in
main()
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 451, in main
table[sample]=scanbam(alnfname, amplicons,rq_chr)
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 184, in scanbam
amp_results[amp_name] = scanamplicon(amplicon_iter, mut_dict)
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 134, in scanamplicon
(t_pos, t_read) = test_read(R, mut_dict)
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 82, in test_read
found_site = [p for p,m in mut_dict.items() if read.reference_start <= (p-1) <= (read.reference_end-len(m))]
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 82, in
found_site = [p for p,m in mut_dict.items() if read.reference_start <= (p-1) <= (read.reference_end-len(m))]
TypeError: unsupported operand type(s) for -: 'NoneType' and 'int'

The program execution issue may be resolved by rolling back some to previous versions of some packages/using an earlier version of python, so if you could please advise me as to this, I would appreciate it. Alternatively if you can discern something about my input files that makes cojac unsuitable to analyse them, this would also be useful information.

I also get a similar output when running the V3 primer:
cooc-mutbamscan -b ../nCoV-2019.insert.V3.bed -m ../voc/ -a NIRE-002f80_S267.sorted.bam NIRE-002f81_S268.sorted.bam -j ../out/cooc-test.json
insertions not supported (yet): +AACA : AACA
insertions not supported (yet): +ACT : ACT
insertions not supported (yet): +GAGCCAGAA : GAGCCAGAA
76_B16173 is identical to 76_ka
76_ga is identical to 76_be
76_de is identical to 76_AY42
91_de is identical to 91_AY42
78_BA1 is identical to 78_BA2
93_BA1 is identical to 93_BA2
autodecting reference as MN908947.3
amplicon_31_om2 9275 9472 {9424: 'G', 9534: 'T'} amplion: 460
Traceback (most recent call last):
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 479, in
main()
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 451, in main
table[sample]=scanbam(alnfname, amplicons,rq_chr)
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 184, in scanbam
amp_results[amp_name] = scanamplicon(amplicon_iter, mut_dict)
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 134, in scanamplicon
(t_pos, t_read) = test_read(R, mut_dict)
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 82, in test_read
found_site = [p for p,m in mut_dict.items() if read.reference_start <= (p-1) <= (read.reference_end-len(m))]
File "/home/evan/anaconda3/envs/cojac/bin/cooc-mutbamscan", line 82, in
found_site = [p for p,m in mut_dict.items() if read.reference_start <= (p-1) <= (read.reference_end-len(m))]
TypeError: unsupported operand type(s) for -: 'NoneType' and 'int'

All the best,
Evan

configurable amplicon list

add code that:

uses a BED file describin amplicon
recomputes list of cooccuring mutation

Issue with MutationOccurrenceVisualization notebook

When I run JupyterLab's notebook MutationOccurrenceVisualization I get this error:

ValueError                                Traceback (most recent call last)
<ipython-input-19-5431d1030684> in <module>
      5         print(sample, amplicon, amplicon_data)
      6 
----> 7         max_entry = max(amplicon_data['sites'])  # corresponds to all mutations
      8 
      9         if max_entry not in amplicon_data['muts']:

ValueError: max() arg is an empty sequence

I don´t kwon how to solve this isseu.
This is my data, which I have obtained after running V-pipe and getting the cooc-test.json file.

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