Support for CGmap inputs

[harish0201]

Hi Dave!

I have recently come across cgmaptools which is a host of tools that can be used to call methylation and other analysis like allele specific methylation, snv calling etc.

The cgmap output can be derived from either post-processing the aligned bams or is one of the outputs from BS-Seeker.

The format as such looks like this:

chr1 G 3000851 CHH CC 0.1 1 10
chr1 C 3001624 CHG CA 0.0 0 9
chr1 C 3001631 CG CG 1.0 5 5
chr1 G 3001632 CG CG 0.9 9 10

Where the headers are:

Chromosome Reference_Nucleotide Position Context_Type Context Methylation_Status Methylated_Cyto_Counts Total_Cyto_Counts

The format as such seems to be similar to Bismark's format 5 as per the Readme.

Would it be possible for you to support it?

[hhg7]

Hi @harish0201

sure, I'll get working on that for the next version, I'll update you soon!

[hhg7]

Hi @harish0201

I updated Defiant so it now reads CGmap input. Please let me know if it works for you.

[harish0201]

Alright! Thanks for the update.

I'll check it now.

[harish0201]

Hi Dave!

I'm working on the inputs, but they seem to crash on the wheat genome, I'll parse them out chromosome wise and get back to you. It seems to give me a CRC error on gzipped files though gunzipping them seems to work.

[hhg7]

Hi Harish,

Defiant only reads regular ASCII files. I've considered making it to read gz, but I don't know how yet. Please let me know how everything works out.

[harish0201]

Will do!

In the mean time, may be trying to use the system calls (zcat or pigz -c) should be better in order to read compressed files!

However, I'm facing no issues running on the unzipped files though, so it's all good :)

Edit: Duplicate Comment

[hhg7]

Did everything work out? I'd like to close the issue.

[harish0201]

Yup, it seems to have the trick! Sorry I was travelling a bit, so I wasn't able to do. it.

BTW, would you be at the PAG? I would to have a chat with you.

[hhg7]

@harish0201 unfortunately, no, but I would have applied had I known about the conference.

[hhg7]

My email is dec986@gmail.com if you have any questions, or would like to chat.