[biomodal]

Hey Aakash,

Great plugin, however, my colleague thinks he has found a bug:

In the MD file, we have the backslash near the end of the line:

https://drive.google.com/file/d/1ClhoE3wCq-rCtfzY3kXFk9xDbNjUm0R2/view?usp=sharing

However, when pulled through to WP, the backslash has disappeared:

https://drive.google.com/file/d/1jGlRn-mPn-Dni8bdbETjfzDAURPDMw8w/view?usp=sharing

Any chance we can get this resolved, please?

[Aakash Chakravarthy]

Hi biomodal,

1) Can you please share the full file content for me to test?

2) Can you please try the same content on the markdown reader here – https://parsedown.org/extra/? GIW uses the same library for HTML conversion. Let me know if it parsing is correct here.

Thanks,
Aakash

[biomodal]

Sure, this is the code block from GitHub:

`
library(data.table)
library(tidyverse)
library(methylKit)

# 5mC
fread(“~/CEG1485-EL01-D1115-005.genome.GRCh38Decoy_primary_assembly.dedup.duet-evoC.CG_quant.CXreport.txt.gz”,
col.names =c(‘contig’, ‘coordinate’, ‘strand’, ‘mC’, ‘hmC’, ‘C’, ‘context’, ‘trinucleotide’, ‘coverage’) )%>%
## Chromosome Position Strand Count methylated. Count unmethylated. C-context Trinucleotide context
select(contig, coordinate, strand, mC, C, context, trinucleotide)%>%
fwrite(“~/CEG1485-EL01-D1115-005.genome.GRCh38Decoy_primary_assembly.dedup.duet-evoC.CG_quant.CXreport_reformatted_mC.txt.gz”,quote = FALSE,col.names = FALSE,row.names = FALSE,sep=”\t”)

#. 5hmC
fread(“~/CEG1485-EL01-D1115-005.genome.GRCh38Decoy_primary_assembly.dedup.duet-evoC.CG_quant.CXreport.txt.gz”,
col.names =c(‘contig’, ‘coordinate’, ‘strand’, ‘mC’, ‘hmC’, ‘C’, ‘context’, ‘trinucleotide’, ‘coverage’) )%>%
## Chromosome Position Strand Count methylated. Count unmethylated. C-context Trinucleotide context
select(contig, coordinate, strand, hmC, C, context, trinucleotide)%>%
fwrite(“~/CEG1485-EL01-D1115-005.genome.GRCh38Decoy_primary_assembly.dedup.duet-evoC.CG_quant.CXreport_reformatted_hmC.txt.gz”,quote = FALSE,col.names = FALSE,row.names = FALSE,sep=”\t”)

##Read the reformatted files in methylkit
myobj<-methRead(list(‘~/CEG1485-EL01-D1115-005.genome.GRCh38Decoy_primary_assembly.dedup.duet-evoC.CG_quant.CXreport_reformatted_mC.txt.gz’,
‘~/CEG1485-EL01-D1115-005.genome.GRCh38Decoy_primary_assembly.dedup.duet-evoC.CG_quant.CXreport_reformatted_hmC.txt.gz’),
sample.id=list(“mC”,”hmC”),
assembly=”hg38″,
treatment=c(0,0),
context=”CpG”,
mincov = 10,
pipeline=’bismarkCytosineReport’
)
#Make the plots
getMethylationStats(myobj[[1]],plot=TRUE,both.strands=FALSE)
getMethylationStats(myobj[[2]],plot=TRUE,both.strands=FALSE)
`

And when I drop that code into the parsedown link you sent, the backslashes appear to be there:

[Aakash Chakravarthy]

Hi @biomodal,

Can you please make the below change in plugin editor?

1) Deactivate Git it write plugin
2) Go to plugin editor and select the file git-it-write/includes/publisher.php
3) Insert the below code at line no. 137

$content = wp_slash( $content );

4) Save and activate the plugin.
5) Delete the post and pull the repository again and confirm if the slash is retained.

If things work as expected, I’ll ensure this change is published in the next version of the plugin.

Thanks,
Aakash

[biomodal]

This worked. Thank you very much!

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