option to specify output directory

[vivekbhr]

Dear Felix

Thanks for the useful tool. I am trying to add SNPsplit into an RNAseq pipeline but the lack of option to specify output directory of the allele-sorted files is creating a trouble.. It would be good to add this parameter in SNPsplit..

Also the documentation doesn't mention which file names/prefix/suffix to expect from the output files in case of single/dual hybrid genome preparation.. I figured this out in my case but would be good to have it in the docs..

Thanks Vivek

[FelixKrueger]

Hi Vivek,

It shouldn't be too difficult to add output directory handling to the SNPsplit, I can try to look into this next week.

I'll also try to to update the documentation so that it is more obvious what you have to expect.

Best, Felix

[FelixKrueger]

Hi Vivek,

I have tried to add an option -o/--output_dir <dir> to SNPsplit (and also to tag2sort) in this commit 7fef3bf6ef131a2e7184b4a165b2761cd312181d. Can you clone the latest development version and let me know if it works in your hands?

[vivekbhr]

sure.. Let me test that and get back to you..

[FelixKrueger]

Right, I had to change how the current working directory is passed on to tag2sort. It should work now, apologies.

[vivekbhr]

If I read file input_dir/file.bam and write to dir output_dir, It tries to create the file output_dir/input_dir/<filename>*SNPsplit.report.txt and fails

[FelixKrueger]

File path handling is hard... I have tried to fix this (new) problem now (here 0f705aad1c5f1ebb3803d8ab22f9938576a2b5ab). Please clone and try again. Cheers, Felix

[vivekbhr]

This time it works..

[vivekbhr]

since snpsplit outputs more than one log files, i think it would be also good to put them in a separate log directory (maybe inside the output dir itself) so that the output dir is a bit cleaner.

[FelixKrueger]

I believe specifying an output dir will also write the reports to that output directory. Does it not?

[vivekbhr]

yes indeed..! I was just suggesting to write to output_dir/log

[FelixKrueger]

Ahh, I see. To be honest I am fan of keeping things simple (and in the same folder), can't you just do

mv *report.txt log/

once the run(s) have completed?

[vivekbhr]

Sure. I would continue this way.. :)

[vivekbhr]

Hey Felix

Just found that while running SNPsplit with --output_dir , tag2sort fails to find the allele_flagged.bam file, since it still expects it to be in the input_dir, while the file is actually created in output_dir. couldn't detect this earlier since SNPsplit finished successfully, but later I found that genome_1 and genome_2 bam files were empty.

Best, Vivek

[FelixKrueger]

Hmm, this should not happen as I have also changed tag2sort in this commit: 7fef3bf6ef131a2e7184b4a165b2761cd312181d. Did you clone the entire repository or just update SNPsplit itself? Can you try updating everything, and if it still fails post the entire command that failed?

[vivekbhr]

I was doing a git pull on the repo that I had cloned earlier. Today I removed and did a fresh clone of the master branch and repeated, got the empty files again.

Here's an example with a test file (129/CAST genome)..

~/programs/SNPsplit/SNPsplit --paired --snp_file ../../snp_genome/all_CAST_EiJ_SNPs_129S1_SvImJ_reference.based_on_GRCm38.txt -o test filtered_bam/MouseIgG_control.filtered.sortedByName.bam

Output reports are attached. MouseIgG_control.filtered.sortedByName.SNPsplit_report.txt MouseIgG_control.filtered.sortedByName.SNPsplit_sort.txt

And this was the error:

[E::hts_open_format] fail to open file 'MouseIgG_control.filtered.sortedByName.allele_flagged.bam'                                                                        
samtools view: failed to open "MouseIgG_control.filtered.sortedByName.allele_flagged.bam" for reading: No such file or directory 

[FelixKrueger]

Hi Vivek,

Thanks for the details. I am currently still travelling but I will take a look at this next week. Cheers, Felix

[FelixKrueger]

Hi Vivek,

it turns out that it was working only in single-end mode, but have now added it for paired-end and Hi-C mode as well. Sorry for that, please clone and try again. Felix

[vivekbhr]

Seems to be working.. Thanks :)