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Issue 2: Add ability to export saint data from command line
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Project Member Reported by rr.weinb...@gmail.com, Jan 25, 2011
Instead of going through the GUI of the website allow users to export the data they want from SAINT from a command line script.

The users need to supply:
1. The experiments Id
1. whether the experiment is a treatment ("T") or a control ("C")

There are additional features within the current php script to filter the results which we might also want to include in the script.

Additional feature:
Add command line option to take all experiments that are defined as control and collapse them to X number of controls (for example the user specifies 10 control samples but want to collapse them to only 2 controls by taking the 2 max counts for each protein across all 10 control samples)
Jan 26, 2011
Project Member #1 chocomoo...@gmail.com
For the inter.dat output file, the output columns are:

Column 1:	Sample ID (IP ID)

Column 2:	Saint Bait Name (Bait GeneName)
Column 3:	Prey Gene Name

Column 4:	Prey Peptide number

Is prey peptide number the number of unique peptides (Pep_num_uniqe in the Hits table), or simply the number of peptides (Pep_num).
Labels: -Type-Enhancement Type-Other
Jan 26, 2011
Project Member #2 rr.weinb...@gmail.com
From the Nature paper, Saint originally was using the number of unique peptides but the later method paper used the spectra count.

If possible it would be good to give the option of using either as there might be some that want to try to run it according to the specification in the nature paper.
Jan 27, 2011
Project Member #3 chocomoo...@gmail.com
Regarding the prey.dat output, I remember when we got together monday, I asked whether sequence data was available on the Prohits database (as opposed to having to scavenge the web for it).  I believe you guys mentioned it was available; however, I notice that the Protein_Sequence table for Prohits_Proteins is empty.  Is this table in fact used, or is the sequence data elsewhere in the database?
Labels: -Type-Other Type-Defect
Feb 1, 2011
Project Member #4 chocomoo...@gmail.com
Again regarding the prey.dat file (but actually, a more general question): what species/taxa are the prey proteins?  I am needing to know, as I am having issues mapping GI's to UniProtID for determining sequence length, however if I limit my species to say Human and Yeast, I am able to perform the mapping without having to do a workaround.
Labels: -Type-Defect Type-Other
Mar 29, 2011
Project Member #5 rr.weinb...@gmail.com
(No comment was entered for this change.)
Status: Fixed

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