Add --platypus option to PMDtools

[jfy133]

Is your feature request related to a problem? Please describe.

@pontussk suggests including the possibility for users to run PMDtools with the following flag --platypus. This is apparently used for mammals nDNA, as CpG cytosines are not affected by UDG treatment (and you can use it to see damage patterns still in UDG treatment, when using alongside --deamination!).

he also recommends including --first and --CpG

I will add those flags and maybe ask him to contribute some documentation (or 'recommendations' when to use those flags).

[jfy133]

Note --CpG is already implemented in

eager/main.nf

Line 1610 in da407f8

def treatment = params.pmd_udg_type ? (params.pmd_udg_type =='half' ? '--UDGhalf' : '--CpG') : '--UDGminus'

where it is always selected if UDG type is either 'full'. If UDG is set to 'half' the --UDGhalf parameter is used instead.

--deamination is already automatically added in with

eager/main.nf

Line 1623 in da407f8

samtools calmd -b $bam $fasta | samtools view -h - | pmdtools --deamination --range ${params.pmdtools_range} $treatment $snpcap -n ${params.pmdtools_max_reads} > "${bam.baseName}".cpg.range."${params.pmdtools_range}".txt

So I will just add --first and --platypus

[apeltzer]

Thanks for investigating this!

[TCLamnidis]

Preparing a PR that will be adding the option to include --platypus to the command.

I cannot get --first to work. It seems that the latest pmdtools release lacks some code changes that let this option work as intended (at least within my limited tests).

tagged release code:
https://github.com/pontussk/PMDtools/blob/0.60/pmdtools.0.60.py#L1074-L1082

vs
code at master (cc91fb8)
https://github.com/pontussk/PMDtools/blob/master/pmdtools.0.60.py#L1075-L1081

I suspect a new release will need to be pushed before --first can be implemented in eager.

[jfy133]

Can you make an issue on PMDtools to ask, and ref back here, so we can keep track of the convo?

[TCLamnidis]

pontussk/PMDtools#8

[pontussk]

Hi Thiseas, That is unfortunate that --first does not work. I can have a look at fixing this if you are able to send me any error messages. Best, Pontus

…

On Mon, 22 Mar 2021 at 14:09, Thiseas C. Lamnidis ***@***.***> wrote: pontussk/PMDtools#8 <pontussk/PMDtools#8> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#349 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABO76I65S2D5II4YNJN5ZZDTE5FQHANCNFSM4KSPAPZA> .

[TCLamnidis]

Using Conda

$ conda create --name pmdtools pmdtools -c bioconda`
$ conda activate pmdtools

pmdtools v0.50

$ samtools calmd -b JK2067_rmdup.bam hs37d5.fa | samtools view -h - | pmdtools --deamination --first --platypus --range 10 --CpG  -n 10000 > "JK2067".cpg.range."10".1st.txt`

Traceback (most recent call last):
  File "/projects1/users/lamnidis/miniconda3/envs/pmdtools/bin/pmdtools", line 1074, in <module>
    if n>0:
NameError: name 'n' is not defined
samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[E::bgzf_flush] File write failed (wrong size)
samtools calmd: failed to write to output file: Broken pipe
[E::bgzf_close] File write failed

Master branch (cc91fb8)

$ cd ~/Software/
$ git clone git@github.com:pontussk/PMDtools.git
$ python2 ~/Software/PMDtools/pmdtools.0.60.py --version

pmdtools.0.60.py v0.50

$ cd -
$ samtools calmd -b JK2067_rmdup.bam hs37d5.fa | samtools view -h - | python2 ~/Software/PMDtools/pmdtools.0.60.py --deamination --first --platypus --range 10 --CpG  -n 10000 > "JK2067".cpg.range."10".1st.github.txt

samtools view: writing to standard output failed: Broken pipe
samtools view: error closing standard output: -1
[bam_fillmd1] different MD for read 'K00233:65:HKTTVBBXX:6:2119:1387:28446': '30^T24' -> '30^N24'
[bam_fillmd1] different MD for read 'K00233:65:HKTTVBBXX:5:1112:4066:2070': '0A0C0T53' -> '0A0C0N53'

The latter command provides a valid output file, but the former does not.

$ ls -l 

-rw-r--r-- 1 lamnidis domain users 4.2K Mar 24 19:12 JK2067.cpg.range.10.1st.github.txt
-rw-r--r-- 1 lamnidis domain users    0 Mar 24 19:05 JK2067.cpg.range.10.1st.txt

I attach the bam and bai used above. Archive.zip

[apeltzer]

So the pipeline is able to do it, once the PMDTools tool / recipe is fixed this is runnable 👍🏻