Re: [spctools-discuss] Re: Output sequence coverage info

['Luis Mendoza' via spctools-discuss]

Sure thing.

And to answer your original question: there is a command-line tool in TPP
called batchcoverage (look in the bin/ directory) that calculates this
residue coverage -- and is the one used by ProteinProphet to populate that
attribute in protXML.

It needs an input file of the form:
>PROTEIN_1
PEPTIDE
ANOTHERONE
ANDTHISONE
>PROTEIN_2
ELVIS
WASHERE
>PROTEIN_3
...

And you run it by providing a reference fasta file location and output file
name, like this:
batchcoverage   

The output file will contain a 2-column list of   values.

Hope this helps, and stay tuned for updates!
--Luis



On Tue, Mar 28, 2023 at 3:59 PM Yasir Ahmed  wrote:

> Thanks Luis, that's helpful. For now I'll just use an older version of TPP
> to get the coverage values.
>
> Cheers,
> Yasir
>
> On Tuesday, March 28, 2023 at 6:46:58 PM UTC-4 Luis Mendoza wrote:
>
>> Hello Yasir,
>>
>> We have recently identified a bug in ProteinProphet that mis-reports the
>> coverage as zero for all proteins.  This affects TPP versions 6.1.0 and
>> 6.2.0.  We will be releasing an update soon that corrects this and other
>> bugs.
>>
>> Even then, the value that is reported in protXML is the ratio of observed
>> amino acids to total.  There is no simple way to get the coverage based on
>> the digestible portion of the protein, though we could think about adding
>> that as a feature.
>>
>> Let me know if you would like to get a preview version of just
>> ProteinProphet in advance of our release and I can post that separately,
>> just specify if you use Linux or Windows.  Alternatively, if you have a
>> pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the
>> coverage values reported.
>>
>> Cheers,
>> --Luis
>>
>>
>> On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed  wrote:
>>
>>> I guess I have another question about coverage: using ProtXMLViewer
>>> (which is similar to the output from ProteinProphet), the coverage values
>>> are almost always zero. For example, the example I show above has Obs/Dig
>>> of 82%, but is showing percent coverage to be zero in the ProteinProphet
>>> output. Any idea why? And can one get those Obs/Dig values?
>>>
>>> On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote:
>>>
 Never mind, got it with ProtXMLViewer.pl (duh).

 On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:

> Greetings Friends,
>
> Is there a command line tool within the TPP that can output sequence
> residue coverage percentages (Obs/Tot)? I can get those for individual
> proteins using the ProtXMLViewer GUI (see attached image), but would like
> to do this for every protein in my database.
>
> Cheers,
> Yasir
>
> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]
>
 --
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>>> .
>>>
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Re: [spctools-discuss] Re: Output sequence coverage info

[Yasir Ahmed]

Thanks Luis, that's helpful. For now I'll just use an older version of TPP 
to get the coverage values.

Cheers,
Yasir

On Tuesday, March 28, 2023 at 6:46:58 PM UTC-4 Luis Mendoza wrote:

> Hello Yasir,
>
> We have recently identified a bug in ProteinProphet that mis-reports the 
> coverage as zero for all proteins.  This affects TPP versions 6.1.0 and 
> 6.2.0.  We will be releasing an update soon that corrects this and other 
> bugs.
>
> Even then, the value that is reported in protXML is the ratio of observed 
> amino acids to total.  There is no simple way to get the coverage based on 
> the digestible portion of the protein, though we could think about adding 
> that as a feature.
>
> Let me know if you would like to get a preview version of just 
> ProteinProphet in advance of our release and I can post that separately, 
> just specify if you use Linux or Windows.  Alternatively, if you have a 
> pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the 
> coverage values reported.
>
> Cheers,
> --Luis
>
>
> On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed  wrote:
>
>> I guess I have another question about coverage: using ProtXMLViewer 
>> (which is similar to the output from ProteinProphet), the coverage values 
>> are almost always zero. For example, the example I show above has Obs/Dig 
>> of 82%, but is showing percent coverage to be zero in the ProteinProphet 
>> output. Any idea why? And can one get those Obs/Dig values?
>>
>> On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote:
>>
>>> Never mind, got it with ProtXMLViewer.pl (duh). 
>>>
>>> On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:
>>>
 Greetings Friends,

 Is there a command line tool within the TPP that can output sequence 
 residue coverage percentages (Obs/Tot)? I can get those for individual 
 proteins using the ProtXMLViewer GUI (see attached image), but would like 
 to do this for every protein in my database.

 Cheers,
 Yasir

 [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]

>>> -- 
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>> "spctools-discuss" group.
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>>  
>> 
>> .
>>
>

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Re: [spctools-discuss] Re: Output sequence coverage info

['Luis Mendoza' via spctools-discuss]

Hello Yasir,

We have recently identified a bug in ProteinProphet that mis-reports the
coverage as zero for all proteins.  This affects TPP versions 6.1.0 and
6.2.0.  We will be releasing an update soon that corrects this and other
bugs.

Even then, the value that is reported in protXML is the ratio of observed
amino acids to total.  There is no simple way to get the coverage based on
the digestible portion of the protein, though we could think about adding
that as a feature.

Let me know if you would like to get a preview version of just
ProteinProphet in advance of our release and I can post that separately,
just specify if you use Linux or Windows.  Alternatively, if you have a
pre-6.1.0 version of TPP installed, you can run ProteinProphet and get the
coverage values reported.

Cheers,
--Luis


On Tue, Mar 28, 2023 at 2:50 PM Yasir Ahmed  wrote:

> I guess I have another question about coverage: using ProtXMLViewer (which
> is similar to the output from ProteinProphet), the coverage values are
> almost always zero. For example, the example I show above has Obs/Dig of
> 82%, but is showing percent coverage to be zero in the ProteinProphet
> output. Any idea why? And can one get those Obs/Dig values?
>
> On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote:
>
>> Never mind, got it with ProtXMLViewer.pl (duh).
>>
>> On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:
>>
>>> Greetings Friends,
>>>
>>> Is there a command line tool within the TPP that can output sequence
>>> residue coverage percentages (Obs/Tot)? I can get those for individual
>>> proteins using the ProtXMLViewer GUI (see attached image), but would like
>>> to do this for every protein in my database.
>>>
>>> Cheers,
>>> Yasir
>>>
>>> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]
>>>
>> --
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> 
> .
>

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[spctools-discuss] Re: Output sequence coverage info

[Yasir Ahmed]

I guess I have another question about coverage: using ProtXMLViewer (which 
is similar to the output from ProteinProphet), the coverage values are 
almost always zero. For example, the example I show above has Obs/Dig of 
82%, but is showing percent coverage to be zero in the ProteinProphet 
output. Any idea why? And can one get those Obs/Dig values?

On Tuesday, March 28, 2023 at 5:23:06 PM UTC-4 Yasir Ahmed wrote:

> Never mind, got it with ProtXMLViewer.pl (duh). 
>
> On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:
>
>> Greetings Friends,
>>
>> Is there a command line tool within the TPP that can output sequence 
>> residue coverage percentages (Obs/Tot)? I can get those for individual 
>> proteins using the ProtXMLViewer GUI (see attached image), but would like 
>> to do this for every protein in my database.
>>
>> Cheers,
>> Yasir
>>
>> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]
>>
>

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[spctools-discuss] Re: Output sequence coverage info

[Yasir Ahmed]

Never mind, got it with ProtXMLViewer.pl (duh). 

On Tuesday, March 28, 2023 at 5:03:14 PM UTC-4 Yasir Ahmed wrote:

> Greetings Friends,
>
> Is there a command line tool within the TPP that can output sequence 
> residue coverage percentages (Obs/Tot)? I can get those for individual 
> proteins using the ProtXMLViewer GUI (see attached image), but would like 
> to do this for every protein in my database.
>
> Cheers,
> Yasir
>
> [image: Screen Shot 2023-03-28 at 4.29.18 PM.png]
>

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