Unfixed pipeline: format_trans.pl returns empty file on .ppe file

[weiju]

Hi, we are having trouble getting results out of the Unfixed pipeline. One problem seems to be that the Perl script format_trans.pl returns an empty file. As I understand the PPE file is created from PE_IS_filt.pl from a .varscan file and this actually generates a file.

I am not particularly fluent with Perl, but as I understand it, it rearranges the file structure.

To me, this section if($=~m/^Chrom/){ }else{ @a=split "\t",$;

will only process the lines that don't begin with "Chrom", however, our PPE file looks like this:

============= PPE FILE Chrom Position Ref Var Cons:Cov:Reads1:Reads2:Freq:P-value StrandFilter:R1+:R1-:R2+:R2-:pval SamplesRef SamplesHet SamplesHom SamplesNC Cons:Cov:Reads1:Reads2:Freq:P-value Chromosome 293 T C Y:115:113:2:1.74%:9.8E-1 Pass:1.0:56:57:2:0:2.5217E-1 0 1 0 0 Y:115:113:2:1.74%:9.8E-1 Chromosome 294 C A M:114:112:2:1.75%:9.8E-1 Pass:1.0:57:55:2:0:2.6564E-1 0 1 0 0 M:114:112:2:1.75%:9.8E-1 .... =========== PPE FILE END

So every line starts with Chrom. My assumption is that the PPE/VARSCAN file is not in the format that format_trans.pl expects ?

Any thoughts about this are appreciated, I think all the subsequent pipeline steps are affected by this

Thanks !

[weiju]

I am able to proceed here by

changing

if($=~m/^Chrom/){

to

if($=~m/^Chrom\t/){

[MtbEvolution]

Excellent!

Thanks for the update! Let me know if there is any other question.

On Dec 15, 2023, at 13:31, Wei-ju Wu @.**@.>> wrote:

I am able to proceed here by

changing

if($=~m/^Chrom/){

to

if($=~m/^Chrom\t/){

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