\C no longer supported in regex

Yaqian Liu

unread,

Jun 14, 2019, 5:18:56 AM6/14/19

to ParseCNV

Dear Joseph Glessner:

Hi

I tried to run the example command:

perl ParseCNV.pl ExampleFiles/Cases.rawcnv ExampleFiles/Controls.rawcnv ExampleFiles/Cases.fam ExampleFiles/ChrSnp0Pos.map --out ./try

but got th following erro:

\C no longer supported in regex; marked by <-- HERE in m/(\ <-- HERE C)/ at PerlModules/URI/Escape.pm line 205.
Compilation failed in require at PerlModules/URI.pm line 22.
BEGIN failed--compilation aborted at PerlModules/URI.pm line 22.
Compilation failed in require at (eval 5) line 1.
Compilation failed in require at PerlModules/HTTP/Request.pm line 3.
Compilation failed in require at PerlModules/LWP/UserAgent.pm line 10.
BEGIN failed--compilation aborted at PerlModules/LWP/UserAgent.pm line 10.
Compilation failed in require at PerlModules/LWP/Simple.pm line 26.
BEGIN failed--compilation aborted at PerlModules/LWP/Simple.pm line 26.
Compilation failed in require at ParseCNV.pl line 381.
BEGIN failed--compilation aborted at ParseCNV.pl line 381.

Is there any update?

Thank you very much!

Yaqian

Joe Glessner

unread,

Jun 14, 2019, 8:24:00 AM6/14/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

It seems newer versions of perl do not allow this syntax.

If you edit PerlModules/URI/Escape.pm line 205 in the escape_char function:

Delete this:
return join '', @URI::Escape::escapes{$_[0] =~ /(\C)/g};
Add this:
my $dummy = substr($_[0], 0, 0);
if (utf8::is_utf8($_[0])) {
my $s = shift;
utf8::encode($s);
unshift(@_, $s);
}
return join '', @URI::Escape::escapes{split //, $_[0]};

If that still doesn't work, please provide the output to:

perl -v

Regards,

Joseph Glessner

--
You received this message because you are subscribed to the Google Groups "ParseCNV" group.
To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/b281633d-80b7-4e3b-acf8-d1ae441dfda7%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

Yaqian Liu

unread,

Jun 15, 2019, 9:37:32 PM6/15/19

to ParseCNV

Yes, lt can work now. Thank you very much!

在 2019年6月14日星期五 UTC+8下午8:24:00，Joe Glessner写道：

To unsubscribe from this group and stop receiving emails from it, send an email to pars...@googlegroups.com.

Yaqian Liu

unread,

Jun 15, 2019, 10:23:16 PM6/15/19

to ParseCNV

Sorry to bother you again. I got another problem.

I run the comman on my own data and got the warning:

WARNING: 3380 probes were found in rawcnv but not in map. These will be automatically defined as in temp/MissingSNPs.txt

but I checked the map file, all 3380 probes in MissingSNPs are in map.

Why did this happen?

在 2019年6月14日星期五 UTC+8下午8:24:00，Joe Glessner写道：

Hi Yaqian,

To unsubscribe from this group and stop receiving emails from it, send an email to pars...@googlegroups.com.

Yaqian Liu

unread,

Jun 16, 2019, 10:50:47 PM6/16/19

to ParseCNV

I have solved this, thank you.

But I want to know what the column 'PassFail' in CNVR_ALL_ReviewedCNVRs.txt means? I didn't find it in output fields description.

在 2019年6月16日星期日 UTC+8上午10:23:16，Yaqian Liu写道：

Joe Glessner

unread,

Jun 17, 2019, 10:49:10 AM6/17/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

The Pass/Fail column is an overall guidance based on the number of Red Flags observed at each significantly associated CNVR.

If >3 Red Flags are observed the CNVR is annotated Fail, otherwise it is Pass.

I recommend looking at the individual Red Flag values and making judgement based on that rather than the Pass/Fail alone, but that is a more recently added feature to make the results more readily interpretable and conform to the VCF specification.

Regards,

Joseph Glessner

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/b4f86cdf-a7ea-4dfc-aa96-1e7b517f8664%40googlegroups.com.

Yaqian Liu

unread,

Jun 18, 2019, 8:21:06 AM6/18/19

to ParseCNV

I see. Thank you for answering!

在 2019年6月17日星期一 UTC+8下午10:49:10，Joe Glessner写道：

Yaqian Liu

unread,

Jul 4, 2019, 10:28:32 AM7/4/19

to ParseCNV

Hi, Joseph Glessner:

I am trying to generate AllRes.pdf now, but failed, here's the command:

perl ParseCNV.pl ExampleFiles/Cases.rawcnv ExampleFiles/Controls.rawcnv ExampleFiles/Cases.fam ExampleFiles/ChrSnp0Pos.map --idToPath ExampleFiles/IDToPath.txt --probesBafLrr ExampleFiles/probesBafLrr.txt

and the log:

/usr/bin/bash
/home/yqliu/miniconda3/bin/R
/home/yqliu/bin/plink
/usr/bin/convert
NOTICE: --build set to hg18 by default. Please check you are clear and consistent with which build you are using and if not hg18, download build specific files to GeneRef folder as specified in README.txt under "GeneRef Folder download latest versions unix commands", then run ParseCNV again specifying --build option.
Running Command: perl ParseCNV.pl ExampleFiles/Cases.rawcnv ExampleFiles/Controls.rawcnv ExampleFiles/Cases.fam ExampleFiles/ChrSnp0Pos.map --idToPath ExampleFiles/IDToPath.txt --probesBafLrr ExampleFiles/probesBafLrr.txt
My Path ./
Unable to connect to web to check latest version
Run Started 10:11:42 PM on Jul 4 2019
Chromosomes found: chr1 
Average Inter Probe Distance: 1.000
Number of Probes:10
Done Initialization
Progress:100%
Results
-------
Cases:      5
Unaffected: 0
Controls:   4
Count Significant Deletion Probes Case Enrich:       1
Count Significant Duplication Probes Case Enrich:    1
Count Significant Deletion Probes Control Enrich:    0
Count Significant Duplication Probes Control Enrich: 0
GIFDel:0.378
GIFDup:0.134

scan_range2
-----------
CountCNVRsDel: 1
CountCNVRsDup: 1
CountCNVRsDel: 0
CountCNVRsDup: 0

scan_region
-----------
running Gene annotation deletions
running Gene annotation duplications

scan_DescPathway
----------------
Genes annotated with text description and pathway.
Genes annotated with text description and pathway.
Genes annotated with text description and pathway.
Genes annotated with text description and pathway.

scan_rangeJustPos2
------------------
CountCNVRsDel: 1
CountCNVRsDup: 1
CountCNVRsDel: 1
CountCNVRsDup: 1

vlookup SNP to Region ID
------------------------
del
dup
del
dup

countBarcodeOCCURENCE_V2
------------------------
del
dup
del
dup

vlookup Count Sig Regions
-------------------------
del
dup
del
dup

Sort by pvalue
--------------
running Sort deletion p
running Sort duplication p
running Sort deletion p
running Sort duplication p

Data-filter-advanced-unique records only
----------------------------------------
del
dup
del
dup

Create UCSC Custom Track For Review
-----------------------------------
case
state1,cn=0     4
state2,cn=1     1
state5,cn=3     5
state6,cn=4     1
control
state1,cn=0     1
state2,cn=1     1
state5,cn=3     1
state6,cn=4     1

NUMLines
--------
case
control

PercentSamples-AverageNumsnpLenComponentCalls
---------------------------------------------
Creating BAF/LRR Plots of two samples with associated CNV and one sample with CN=2 with flanking diploid data for each CNVR
WARNING: Assuming BAF LRR files not in the current working directory
Running: echo -e "Name\tChr\tPosition\tsample.B Allele Freq\tsample.Log R Ratio" > OutputFiles/Header5Col.txt
caseDel
Indexes: 0      1       2       4       3
Running: paste ExampleFiles/probesBafLrr.txt OutputFiles/Chr.txt OutputFiles/Pos.txt ExampleFiles/1_A.baflrr > 1_A.baflrr; cat OutputFiles/Header5Col.txt 1_A.baflrr > OutputFiles/tempintcsv.txt; sed 's/,/    /' OutputFiles/tempintcsv.txt > 1_A.baflrr
Running: perl ./PerlModules/visualize_cnv.pl -format plot -signal 1_A.baflrr OutputFiles/temp.txt
NOTICE: Signal values for 0 CNV region is found in 1_A.baflrr
ExampleFiles/1_A.baflrr.chr1.1.JPG
Indexes: 0      1       2       4       3
Running: paste ExampleFiles/probesBafLrr.txt OutputFiles/Chr.txt OutputFiles/Pos.txt ExampleFiles/2_A.baflrr > 2_A.baflrr; cat OutputFiles/Header5Col.txt 2_A.baflrr > OutputFiles/tempintcsv.txt; sed 's/,/    /' OutputFiles/tempintcsv.txt > 2_A.baflrr
Running: perl ./PerlModules/visualize_cnv.pl -format plot -signal 2_A.baflrr OutputFiles/temp.txt
NOTICE: Signal values for 0 CNV region is found in 2_A.baflrr
ExampleFiles/2_A.baflrr.chr1.1.JPG
Running: paste ExampleFiles/probesBafLrr.txt OutputFiles/Chr.txt OutputFiles/Pos.txt ExampleFiles/5_A.baflrr > 5_A.baflrr; cat OutputFiles/Header5Col.txt 5_A.baflrr > OutputFiles/tempintcsv.txt; sed 's/,/    /' OutputFiles/tempintcsv.txt > 5_A.baflrr
NOTICE: Signal values for 1 CNV region is found in 5_A.baflrr
NOTICE: Processing sample 5_A.baflrr CNV chr1:1-3 with copy number of 2 ...  written to 5_A.baflrr.chr1.1.JPG

Running: convert -font helvetica -draw "text 0,410 chr1.1-1" -pointsize 30 ExampleFiles/1_A.baflrr.chr1.1.JPG ExampleFiles/2_A.baflrr.chr1.1.JPG 5_A.baflrr.chr1.1.JPG +append OutputFiles/1.JPG
convert: unable to open image `ExampleFiles/1_A.baflrr.chr1.1.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
convert: unable to open image `ExampleFiles/2_A.baflrr.chr1.1.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
rm: cannot remove ?.xampleFiles/1_A.baflrr.chr1.1.JPG?. No such file or directory
rm: cannot remove ?.xampleFiles/2_A.baflrr.chr1.1.JPG?. No such file or directory
Running: rm 1_A.baflrr ExampleFiles/1_A.baflrr.chr1.1.JPG 2_A.baflrr ExampleFiles/2_A.baflrr.chr1.1.JPG 5_A.baflrr 5_A.baflrr.chr1.1.JPG 
caseDup
Indexes: 0      1       2       4       3
Running: paste ExampleFiles/probesBafLrr.txt OutputFiles/Chr.txt OutputFiles/Pos.txt ExampleFiles/1_A.baflrr > 1_A.baflrr; cat OutputFiles/Header5Col.txt 1_A.baflrr > OutputFiles/tempintcsv.txt; sed 's/,/    /' OutputFiles/tempintcsv.txt > 1_A.baflrr
Running: perl ./PerlModules/visualize_cnv.pl -format plot -signal 1_A.baflrr OutputFiles/temp.txt
NOTICE: Signal values for 0 CNV region is found in 1_A.baflrr
ExampleFiles/1_A.baflrr.chr1.5.JPG
Indexes: 0      1       2       4       3
Running: paste ExampleFiles/probesBafLrr.txt OutputFiles/Chr.txt OutputFiles/Pos.txt ExampleFiles/2_A.baflrr > 2_A.baflrr; cat OutputFiles/Header5Col.txt 2_A.baflrr > OutputFiles/tempintcsv.txt; sed 's/,/    /' OutputFiles/tempintcsv.txt > 2_A.baflrr
Running: perl ./PerlModules/visualize_cnv.pl -format plot -signal 2_A.baflrr OutputFiles/temp.txt
NOTICE: Signal values for 0 CNV region is found in 2_A.baflrr
ExampleFiles/2_A.baflrr.chr1.5.JPG
Running: paste ExampleFiles/probesBafLrr.txt OutputFiles/Chr.txt OutputFiles/Pos.txt ExampleFiles/5_A.baflrr > 5_A.baflrr; cat OutputFiles/Header5Col.txt 5_A.baflrr > OutputFiles/tempintcsv.txt; sed 's/,/    /' OutputFiles/tempintcsv.txt > 5_A.baflrr
NOTICE: Signal values for 1 CNV region is found in 5_A.baflrr
NOTICE: Processing sample 5_A.baflrr CNV chr1:5-7 with copy number of 2 ...  written to 5_A.baflrr.chr1.5.JPG

Running: convert -font helvetica -draw "text 0,410 chr1.7-7" -pointsize 30 ExampleFiles/1_A.baflrr.chr1.5.JPG ExampleFiles/2_A.baflrr.chr1.5.JPG 5_A.baflrr.chr1.5.JPG +append OutputFiles/2.JPG
convert: unable to open image `ExampleFiles/1_A.baflrr.chr1.5.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
convert: unable to open image `ExampleFiles/2_A.baflrr.chr1.5.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
rm: cannot remove ?.xampleFiles/1_A.baflrr.chr1.5.JPG?. No such file or directory
rm: cannot remove ?.xampleFiles/2_A.baflrr.chr1.5.JPG?. No such file or directory
Running: rm 1_A.baflrr ExampleFiles/1_A.baflrr.chr1.5.JPG 2_A.baflrr ExampleFiles/2_A.baflrr.chr1.5.JPG 5_A.baflrr 5_A.baflrr.chr1.5.JPG 
controlDel
controlDup
caseDel
caseDup
controlDel
controlDup
Running: convert OutputFiles/1.JPG OutputFiles/2.JPG -append OutputFiles/BAF_LRR_Plots_CNVRs_1.jpg
Running: rm OutputFiles/1.JPG OutputFiles/2.JPG 
Running: rm OutputFiles/temp.txt
Running: rm OutputFiles/Chr.txt OutputFiles/Pos.txt
Running: rm OutputFiles/Header5Col.txt OutputFiles/tempintcsv.txt

SpecificBafLrrAccessMany
------------------------
Done Initialization BafLrr
del
Indexes spec: 0 1       2       4       3
Indexes spec: 0 1       2       4       3
Indexes spec: 0 1       2       4       3
Indexes spec: 0 1       2       4       3
dup
Indexes spec: 0 1       2       4       3
Indexes spec: 0 1       2       4       3
Indexes spec: 0 1       2       4       3
Indexes spec: 0 1       2       4       3
del
dup
Make PDF image of BAF/LRR for significant association regions across all contributing case samples.
Error: cannot execute system command R CMD BATCH OutputFiles/.AllRes.R

Would you help me solve this?

Thank you again

在 2019年6月17日星期一 UTC+8下午10:49:10，Joe Glessner写道：

Hi Yaqian,

Joe Glessner

unread,

Jul 4, 2019, 11:28:40 AM7/4/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

Short answer: mkdir BafLrr/OutputFiles and run ParseCNV again.

Explanation:

This is one of the most complicated parts of ParseCNV.

Add the relatively recent folder restructuring and there ends up being issues.

First, make sure the Path column in the input file ExampleFiles/IDToPath.txt have the "ExampleFiles" prefix added. Do not copy baflrr raw signal files into the main ParseCNV directory where you are running the script.

SampleID Path

1_A.baflrr ExampleFiles/1_A.baflrr

2_A.baflrr ExampleFiles/2_A.baflrr

3_A.baflrr ExampleFiles/3_A.baflrr

4_A.baflrr ExampleFiles/4_A.baflrr

5_A.baflrr ExampleFiles/5_A.baflrr

Second, OutputFiles is generically added to the $out variable to improve folder structure. Of course, this is only good if the folder exists which it does not and the code doesn't check for that.

Line 5613 of ParseCNV after checking "BafLrr" directory exists, I added:

$dir = 'BafLrr/OutputFiles';
unless(-d $dir)
{
mkdir $dir or die;
}

Regards,

Joseph Glessner

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/cf6e6097-0b03-4dd8-bba2-e17e48ce663e%40googlegroups.com.

Yaqian Liu

unread,

Jul 4, 2019, 9:09:42 PM7/4/19

to ParseCNV

Yes, the second one worked.

But do these errors matter?

Running: convert -font helvetica -draw "text 0,410 chr1.1-1" -pointsize 30 ExampleFiles/1_A.baflrr.chr1.1.JPG ExampleFiles/2_A.baflrr.chr1.1.JPG 5_A.baflrr.chr1.1.JPG +append OutputFiles/1.JPG
convert: unable to open image `ExampleFiles/1_A.baflrr.chr1.1.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
convert: unable to open image `ExampleFiles/2_A.baflrr.chr1.1.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
rm: cannot remove ?.xampleFiles/1_A.baflrr.chr1.1.JPG?. No such file or directory

rm: cannot remove ?.xampleFiles/2_A.baflrr.chr1.1.JPG?. No such file or directory

Running: convert -font helvetica -draw "text 0,410 chr1.7-7" -pointsize 30 ExampleFiles/1_A.baflrr.chr1.5.JPG ExampleFiles/2_A.baflrr.chr1.5.JPG 5_A.baflrr.chr1.5.JPG +append OutputFiles/2.JPG
convert: unable to open image `ExampleFiles/1_A.baflrr.chr1.5.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
convert: unable to open image `ExampleFiles/2_A.baflrr.chr1.5.JPG': No such file or directory @ error/blob.c/OpenBlob/2642.
rm: cannot remove ?.xampleFiles/1_A.baflrr.chr1.5.JPG?. No such file or directory
rm: cannot remove ?.xampleFiles/2_A.baflrr.chr1.5.JPG?. No such file or directory

在 2019年7月4日星期四 UTC+8下午11:28:40，Joe Glessner写道：

Yaqian Liu

unread,

Jul 6, 2019, 2:59:12 AM7/6/19

to ParseCNV

I tried on my own data. It can generate AllRes.pdf, but image with BAF of each sample is empty.

TIM图片20190706144750.png

And LRRs of all significant CNVRs in AllRes.pdf are around 0. It seems all CNVRs are fake.

Is it because of the errors which are the same as those in the example log?

在 2019年7月4日星期四 UTC+8下午11:28:40，Joe Glessner写道：

Hi Yaqian,

Joe Glessner

unread,

Jul 7, 2019, 9:33:53 PM7/7/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

Line 5341 of ParseCNV.pl should change from:

$ComponentCNVCall[4]=$CallPath;
to:
$CallFile=$CallPath;
$CallFile=~s/.*\///;
$ComponentCNVCall[4]=$CallFile;

The ExampleFiles expected result images are attached for --idToPath ExampleFiles/IDToPath.txt --probesBafLrr ExampleFiles/probesBafLrr.txt

Regards,

Joseph Glessner

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/bf564e04-6c43-4fe2-986d-a6f85d63a461%40googlegroups.com.

BAF_LRR_Plots_CNVRs_1.jpg

AllRes.pdf

Yaqian Liu

unread,

Jul 8, 2019, 10:08:44 PM7/8/19

to ParseCNV

Hi Joseph Glessner,

I changed the perl file and run the ExampleFiles again. The result images are attached.

Then I run on my own data:

perl /home/yqliu/tools/ParseCNVRelease_20/ParseCNV.pl NBF10_case.rawcnv NBF10_control.rawcnv NBF10_case.fam allposition.map --build hg19 --idToPath IDToPath.txt --snpposfile SNP_pos.txt --probesBafLrr probesBAFLRR.txt --maxPInclusion 0.001

It still has no plot in BAF images no matter if I add --maxPInclusion. A part of the images is also attached.

Thank you,

Yaqian

在 2019年7月8日星期一 UTC+8上午9:33:53，Joe Glessner写道：

AllRes.pdf

BAF_LRR_Plots_CNVRs_1.jpg

mydata_BAFLRR.png

Yaqian Liu

unread,

Jul 8, 2019, 11:02:01 PM7/8/19

to ParseCNV

And another question, do I just need to list cases in idToPath file? or cases and controls?

在 2019年7月8日星期一 UTC+8上午9:33:53，Joe Glessner写道：

Hi Yaqian,

Joe Glessner

unread,

Jul 9, 2019, 9:43:03 AM7/9/19

to Yaqian Liu, ParseCNV

Sorry for these troubles.

First check if you have typical 5 column BafLrr signal files with the header. If so, you don't need to use "--probesBafLrr" at all, you just use "idToPath". You use "idToPath" if you have atypical (but ones I personally use) 2 column BafLrr signal files without the header.

So for the example simply run: (note no --probesBafLrr option used)

perl ParseCNV.pl ExampleFiles/Cases.rawcnv ExampleFiles/Controls.rawcnv ExampleFiles/Cases.fam ExampleFiles/ChrSnp0Pos.map --idToPath ExampleFiles/IDToPath.txt

The line I had you change last time should now be:

$ComponentCNVCall[4]=$CallPath;
if($ExampleBafLrrFile ne "")
{
$ComponentCNVCall[4]=$CallFile;
}

A little lower:

$myCnvCall=~s/$myCnvCallArray[4]/$key/;
$myCnvCall=~s/$myCnvCallArray[3]/state3,cn=2/;

should be:

$myCnvCallArray[4]=$CallPath;
if($ExampleBafLrrFile ne "")
{
$myCnvCallArray[4]=$key;
}
$myCnvCallArray[3]="state3,cn=2";
print TEMP "@myCnvCallArray";

Also.

$myJpg= $key.".".$ComponentCNVCall[0]; ## ComponentCNVCall[0] cleaned from above

Should be:

if($ExampleBafLrrFile ne "")
{
$myJpg= $key.".".$ComponentCNVCall[0]; ## ComponentCNVCall[0] cleaned from above
}
else
{
$myJpg= $CallPath.".".$ComponentCNVCall[0];
}

The expected output for the Example is attached along with a .txt version of the perl script in case it is hard to follow my code edits.

You just need to list cases in idToPath file.

Regards,

Joseph Glessner

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/0a173681-3ba0-40e8-82e4-72b1d5ed0000%40googlegroups.com.

ParseCNV.txt

BAF_LRR_Plots_CNVRs_1.jpg

Message has been deleted

Yaqian Liu

unread,

Jul 11, 2019, 10:45:45 PM7/11/19

to ParseCNV

Hi, Joseph Glessner

I changed the perl file and ran on the example again. It works. But when I tried on my own data, it still has no plot in BAF image.

My signal files have 3 columns: Name, LRR, BAF. So I ran the command:

perl /home/yqliu/tools/ParseCNVRelease_20/ParseCNV.pl NBF10_case.rawcnv NBF10_control.rawcnv NBF10_case.fam allposition.map --build hg19 --idToPath IDToPath.txt --probesBafLrr probesBAFLRR.txt --maxPInclude 0.001

Although the signal files have SNP name column, it will go wrong if I did't add --probesBafLrr probesBAFLRR.txt

Do you have any idea why this happen?

Thanks,

Yaqian

在 2019年7月9日星期二 UTC+8下午9:43:03，Joe Glessner写道：

Joe Glessner

unread,

Jul 12, 2019, 4:45:23 PM7/12/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

I think the issue is I did not consider the 3 column BAF LRR file (Name BAF LRR), only the 5 column BAF LRR file (Name Chr Position BAF LRR) or the 2 column BAF LRR file (BAF and LRR) with the --probesBafLrr definition file indicating the order of SNPs listed.

I will try to edit to accommodate the 3 column BAF LRR file.

Joseph Glessner

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/38f63202-a251-4437-ab2d-50aee3d1aa61%40googlegroups.com.

Joe Glessner

unread,

Jul 12, 2019, 6:36:51 PM7/12/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

print CHR "na\n";

print POS "na\n";
$InProbesBafLrrNotMap++;

should be:

if($chrLine[0] eq "Name")
{
print CHR "Chr\n";
print POS "Position\n";
$SecondHeader=1;
}
else
{
print CHR "na\n";
print POS "na\n";
$InProbesBafLrrNotMap++;
}

2 occurences of:
$command = "perl ".$MyDirectoryPathPrefix."PerlModules/visualize_cnv.pl -format plot -signal ".$CallPath." $out"."temp.txt";
this should be added before:
if($SecondHeader)
{

$c="sed '1d' $CallFile > a.txt; mv a.txt $CallFile";`$c`;
}

Then try again with --probesBafLrr option included.

The code with these edits attached as a .txt for reference.

ParseCNV_7-12-19.txt

Yaqian Liu

unread,

Jul 13, 2019, 9:02:14 PM7/13/19

to ParseCNV

Hi, Joe Glessner

Sorry to bother you again. It still has no plot in BAF image.

在 2019年7月13日星期六 UTC+8上午6:36:51，Joe Glessner写道：

Joe Glessner

unread,

Jul 14, 2019, 2:29:51 PM7/14/19

to Yaqian Liu, ParseCNV

Hi Yaqian,

No BAF plotted in BAF_LRR_Plots_CNVRs_1.jpg and/or AllRes.pdf?

After where you added:

$c="sed '1d' $CallFile > a.txt; mv a.txt $CallFile";`$c`;

Please add (in both instances):
$c="awk -F\"\\t\" '{print \$1\"\\t\"\$2\"\\t\"\$3}' $CallFile | sed 's/\\r//' | sort -k1,1 > a.txt";`$c`;
$c="awk -F\"\\t\" '{print \$4\"\\t\"\$5\"\\t\"\$6}' $CallFile | sed 's/\\r//' | sort -k1,1 > b.txt";`$c`;
$c="join a.txt b.txt -t \$'\\t' > $CallFile";`$c`;

$CallPath=$CallFile;

Given you had missing SNPs warning initially, I sense you have a mix of different microarray versions, so the probesBafLrr is not the same for all sample IDs (column 5 of .rawcnv). Therefore, the SNP to BAF/LRR and SNP to Chr/Position is double checked to make sure they line up properly. Formats "Name sample.B Allele Freq sample.Log R Ratio" and "Name sample.Log R Ratio sample.B Allele Freq" of the baflrr signal file are both supported.

Please provide the ParseCNV.log file if you continue to have troubles.

Regards,

Joe

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/6ed19679-8986-4e4e-b343-2e26a1c0eafb%40googlegroups.com.

ParseCNV_7-14-19.txt

Yaqian Liu

unread,

Jul 15, 2019, 9:04:40 AM7/15/19

to ParseCNV

Hi Joe,

It's no BAF plotted in BAF_LRR_Plots_CNVRs_1.jpg.

I only used Illumina Global Screening Array. Beifang and nanfang are samples from different places and their CNVs were called separately from different PFB files after QC. But I put all 700078 GSA SNPs in allposition.map. Is it because of this?

And the log file attached.

Thanks,

Yaqian
在 2019年7月15日星期一 UTC+8上午2:29:51，Joe Glessner写道：

ParseCNV.log

Yaqian Liu

unread,

Jul 15, 2019, 9:04:49 AM7/15/19

to ParseCNV

Hi Joe,

It's no BAF plotted in BAF_LRR_Plots_CNVRs_1.jpg.

I only used Illumina Global Screening Array. Beifang and nanfang are samples from different places and their CNVs were called separately from different PFB files after QC. But I put all 700078 GSA SNPs in allposition.map. Is it because of this?

And the log file attached.

Thanks,

Yaqian
在 2019年7月15日星期一 UTC+8上午2:29:51，Joe Glessner写道：

ParseCNV.log

Joe Glessner

unread,

Jul 15, 2019, 10:22:20 AM7/15/19

to Yaqian Liu, ParseCNV

Can you run:

perl /home/yqliu/tools/ParseCNVRelease_20/ParseCNV.pl NBF10_case.rawcnv NBF10_control.rawcnv NBF10_case.fam allposition.map --build hg19 --idToPath IDToPath.txt --probesBafLrr probesBAFLRR.txt --maxPInclude 0.001 > ParseCNVScreen.log 2>ParseCNVScreen_2.log

and

awk '{if(NR==2)print $2}' IDToPath.txt | sed 's/\r//' | xargs head

and send me the outputs?

Thanks,

Joe

To unsubscribe from this group and stop receiving emails from it, send an email to parsecnv+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/parsecnv/0e0a64e4-65cc-44a4-ab8f-85acec5e8942%40googlegroups.com.

Reply all

Reply to author

Forward