Re: [galaxy-dev] patch for vcf QUAL field with missing value "." in lib/galaxy/visualization/tracks/data_providers.py

2012-08-23 Thread Jeremy Goecks 
Committed in -central changeset 146d0f4c29de

Thanks much Jim,
J.

On Aug 22, 2012, at 4:09 PM, Jim Johnson wrote:

> The VCF format ( 
> http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
>  )
> specifies "." to represent missing values.
> 
> lib/galaxy/visualization/tracks/data_providers.py  throws an float conversion 
> error when the qual field of  a vcf file has the missing value:  "."
> 
> This can be remedied with the following patch,  trackster handles the "None"  
> value when displaying the variant.
> 
> diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py
> --- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49 
> 2012 -0500
> +++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46 
> 2012 -0500
> @@ -634,7 +634,7 @@
> # TODO? VCF does not have strand, so default to 
> positive.
> "+",
> new_seq,
> -float( feature[5] ) ]
> +None if feature[5] == '.' else float( feature[5] 
> ) ]
> rval.append(payload)
> 
> return { 'data': rval, 'message': message }
> 


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[galaxy-dev] patch for vcf QUAL field with missing value "." in lib/galaxy/visualization/tracks/data_providers.py

2012-08-22 Thread Jim Johnson 

The VCF format ( 
http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41
 )
specifies "." to represent missing values.

lib/galaxy/visualization/tracks/data_providers.py  throws an float conversion error when 
the qual field of  a vcf file has the missing value:  "."

This can be remedied with the following patch,  trackster handles the "None"  
value when displaying the variant.

diff -r eb542e228a0f lib/galaxy/visualization/tracks/data_providers.py
--- a/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:56:49 
2012 -0500
+++ b/lib/galaxy/visualization/tracks/data_providers.py Wed Aug 22 14:58:46 
2012 -0500
@@ -634,7 +634,7 @@
 # TODO? VCF does not have strand, so default to 
positive.
 "+",
 new_seq,
-float( feature[5] ) ]
+None if feature[5] == '.' else float( feature[5] ) 
]
 rval.append(payload)

 return { 'data': rval, 'message': message }

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