Path 'analyze' does not exist

[Anto007]

I'm sure this is a silly problem with my interpretation of the command-line from the manual but any suggestion would be appreciated here. I ran the below command-line from within the conda environment

pydamage --outdir pydamage_test analyze aligned.bam

and I got this error message: "Error: Invalid value for 'BAM': Path 'analyze' does not exist"

Oddly, doing pydamage aligned.bam generates output but then doing 'pydamage filter pydamage_results.csv' for the output returns the same kind of above error- "Path 'filter' does not exist". It might be also useful to mention in the manual what exact tool and command-lines were used to generate your bam input file. I'm trying to test now with your aligned.bam file that is available on this repository

[maxibor]

Hi @Anto007 ,
Which version of PyDamage are you using ?
The subcommand analyze only appeared from the version 0.6 (not yet released).

You can check the documentation for the current version (0.50beta) here: pydamage.readthedocs.io/en/0.50beta

[Anto007]

Ah I get it now; I'm using 0.50beta version and thank you for your response. This would mean that the filter option won't be available too correct? Also, can you let me know where I can find the pjd value in the output result csv from running the current version? I would appreciate it if you could share here the exact tools/command-lines that you used to generate the sorted and indexed input bam file. Super-interesting tool btw and thank you for bringing this out

[maxibor]

Hey @Anto007 ,
Thanks for your feedback !
What do you mean by the pjd value ?
The content of the csv file is described in the documentation linked above.
Sorting and indexing bam files is done with samtools:

samtools sort yourfile.bam > yourfile.sorted.bam
samtools index yourfile.sorted.bam

[Anto007]

Thanks for your response. By pjd value (sorry I didn't make this clear), I'm referring to the 'p<=0.6' mentioned on the legend of your preprint figure 6. The command-line (bowtie2?) that I was mainly looking for is the one that you used for read mapping to the metagenomic assembly so as to generate the bam file in the first place.

[maxibor]

Hey @Anto007 ,
To filter for , you can use the toolset of your liking (pandas, tidyverse, excel) and look for the damage_model_p column.

By the way, PyDamage 0.6 has been released, so you now have access to the analyze, filter, and cite subcommand !

The bowtie2 command line we used is the following:

bowtie2-build contigs.fa db_name
bowtie2 -x db_name -1 fwd.fastq -2 rev.fastq --very-sensitive -N 1 | samtools view -S -b -F 4 - | samtools sort - > result.sorted.bam

You can see more details here
Cheers,

Maxime

[Anto007]

Thanks for your response; I was just testing out PyDamage 0.6 from within a conda environment and I'm guessing there's a bug with the filter command? I'm of course aware that filtering can be done anywhere and nobody needs to depend on the pydamage -filter command per se :-) I get the error "FileNotFoundError: [Errno 2] No such file or directory: 'pydamage_results/pydamage_filtered_results.csv' when I run the below command-line from within the pydamage_results subdirectory:

pydamage filter -t 0.67 pydamage_results.csv

When I do head -n3 on pydamage_results.csv, I get the below and so main result file is not empty or anything

reference,predicted_accuracy,null_model_p0,null_model_p0_stdev,damage_model_p,damage_model_p_stdev,damage_model_pmin,damage_model_pmin_stdev,damage_model_pmax,damage_model_pmax_stdev,pvalue,qvalue,RMSE,nb_reads_aligned,coverage,reflen,CtoT-0,CtoT-1,CtoT-2,CtoT-3,CtoT-4,CtoT-5,CtoT-6,CtoT-7,CtoT-8,CtoT-9,CtoT-10,CtoT-11,CtoT-12,CtoT-13,CtoT-14,CtoT-15,CtoT-16,CtoT-17,CtoT-18,CtoT-19
NZ_JHCB02000018.1,1.0,0.013,0.002,0.462,0.098,0.009,0.001,0.043,0.005,0.0,0.0,0.005,3016,0.202,898379,0.042,0.028,0.029,0.007,0.005,0.012,0.013,0.003,0.01,0.002,0.01,0.014,0.015,0.01,0.006,0.01,0.007,0.014,0.008,0.01
NZ_JHCB02000014.1,1.0,0.014,0.002,0.403,0.091,0.009,0.002,0.047,0.005,0.0,0.0,0.005,3545,0.19,1114119,0.044,0.034,0.036,0.011,0.002,0.011,0.012,0.011,0.006,0.004,0.007,0.015,0.011,0.008,0.017,0.009,0.004,0.013,0.011,0.011

The same error "FileNotFoundError: [Errno 2] No such file or directory" when I specified the full path too: pydamage filter -t 0.67 /home/anto/Downloads/pydamage_test_output/pydamage_results.csv

[maxibor]

Hi @Anto007 ,
It's not a bug, it's a feature 😉
To be serious, it's nice to have users who think and use the program differently than I originally thought:
This happened because the default output directory is pydamage_results which you changed in the analyze subcommand by pydamage_test_output, but left to default for the filter subcommand, so it's trying to write in a directory that doesn't exist.

I'll make this more clear and flexible in the next release of PyDamage, thanks for the feedback !