Recent changes to Preparing data

Preparing data modified by Thomas Abeel

Thomas Abeel — Tue, 01 Apr 2014 16:11:25 -0000

--- v12
+++ v13
@@ -1,4 +1,4 @@
-TripleV requires your data to be formatted in a custom file format. The [VizFileCreatorPackage](http://sourceforge.net/projects/triplev/files/VizFileCreatorPackage.zip/download) has all tools to get started and convert commons genomics file formats into the required format. At the bare minimum you need to load in a multiple alignment file that includes the reference sequence and a separate file called reference.txt
+TripleV requires your data to be formatted in a custom file format. The VizFileCreatorPackage that is included with the download package has all tools to get started and convert commons genomics file formats into the required format. At the bare minimum you need to load in a multiple alignment file that includes the reference sequence and a separate file called reference.txt

 This package was tested and designed to run on Unix-like system.

@@ -6,8 +6,7 @@

 Step-by-step instructions
 ===
-1. Start by downloading the [VizFileCreatorPackage](http://sourceforge.net/projects/triplev/files/VizFileCreatorPackage.zip/download)
-* Unzip VizFileCreatorPackage.zip in a unix directory.
+1. Unzip VizFileCreatorPackage.zip in a unix directory.
 * Modify the text file muscle_path.txt to specify the path of where your local version of muscle is located. (supported using muscle version 3.8 and above). Muscle needs to be [downloaded separately](http://www.drive5.com/muscle/) from the authors.
 * Run the config program (perl config.pl) that will create the functional version of the final script, called “createVizFile.pl”, and will show up in the same directory.
 * Run this configured script, "createVizFile.pl" with your input files.

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:51:49 -0000

--- v11
+++ v12
@@ -1,6 +1,8 @@
 TripleV requires your data to be formatted in a custom file format. The [VizFileCreatorPackage](http://sourceforge.net/projects/triplev/files/VizFileCreatorPackage.zip/download) has all tools to get started and convert commons genomics file formats into the required format. At the bare minimum you need to load in a multiple alignment file that includes the reference sequence and a separate file called reference.txt

 This package was tested and designed to run on Unix-like system.
+
+The [TripleV file format description] gives an in-depth description how the custom file format works.

 Step-by-step instructions
 ===

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:46:28 -0000

--- v10
+++ v11
@@ -39,7 +39,7 @@

 File type | Example file
 --- | --- 
-Reference Files | 
+Reference Files | references.txt
 Alignment Files (DNA) | 9213_all_nuc_aligned_DNA.fas
 Alignment Files (AA) | none
 Variant Files (DNA) | 9213_165_ntfreq.txt

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:45:03 -0000

--- v9
+++ v10
@@ -41,11 +41,10 @@
 --- | --- 
 Reference Files | 
 Alignment Files (DNA) | 9213_all_nuc_aligned_DNA.fas
-Alignment Files (AA) | 
+Alignment Files (AA) | none
 Variant Files (DNA) | 9213_165_ntfreq.txt
 Variant Files (AA) | 9213_final_cleaned_9213_165_codonfreq.xls
 Gene List Files | 9213_0_genelist.txt
 Muscle Path | muscle_path.txt
-Epitope Files | 
+Epitope Files | epitopes.fasta
 Metadata Files | 9213_metadata.txt
-

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:43:50 -0000

--- v8
+++ v9
@@ -24,7 +24,7 @@
 --- | --- | --- | ---
 Reference Files | 'txt' | references.txt
 Alignment Files (DNA) | 'fa', 'fas', 'fsa', 'fasta', 'fna','frn', 'mfa', 'afa', 'aln', 'dna' |  \*DNA*
-Alignment Files (AA) | 'fa', 'fas', 'fsa', 'fasta', 'faa', 'frn', 'mfa', 'afa', 'aln', 'pep' | *AA*
+Alignment Files (AA) | 'fa', 'fas', 'fsa', 'fasta', 'faa', 'frn', 'mfa', 'afa', 'aln', 'pep' | \*AA*
 Variant Files (DNA) | 'txt' | *ntfreq.txt | These include the output files from vPhaser and vProfiler.
 Variant Files (AA) | 'txt', 'xls' | *codonfreq.txt or *codonfreq.xls
 Gene List Files | 'txt' | *genelist.txt
@@ -33,5 +33,19 @@
 Metadata Files | 'txt' | metadata.txt

+Example files
+---
+These files are included in the VizFileCreatorPackage you downloaded.

+File type | Example file
+--- | --- 
+Reference Files | 
+Alignment Files (DNA) | 9213_all_nuc_aligned_DNA.fas
+Alignment Files (AA) | 
+Variant Files (DNA) | 9213_165_ntfreq.txt
+Variant Files (AA) | 9213_final_cleaned_9213_165_codonfreq.xls
+Gene List Files | 9213_0_genelist.txt
+Muscle Path | muscle_path.txt
+Epitope Files | 
+Metadata Files | 9213_metadata.txt

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:39:37 -0000

--- v7
+++ v8
@@ -23,7 +23,7 @@
 File type | Permitted extensions | Files name expression | Notes
 --- | --- | --- | ---
 Reference Files | 'txt' | references.txt
-Alignment Files (DNA) | 'fa', 'fas', 'fsa', 'fasta', 'fna','frn', 'mfa', 'afa', 'aln', 'dna' |  *DNA*
+Alignment Files (DNA) | 'fa', 'fas', 'fsa', 'fasta', 'fna','frn', 'mfa', 'afa', 'aln', 'dna' |  \*DNA*
 Alignment Files (AA) | 'fa', 'fas', 'fsa', 'fasta', 'faa', 'frn', 'mfa', 'afa', 'aln', 'pep' | *AA*
 Variant Files (DNA) | 'txt' | *ntfreq.txt | These include the output files from vPhaser and vProfiler.
 Variant Files (AA) | 'txt', 'xls' | *codonfreq.txt or *codonfreq.xls

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:38:55 -0000

--- v6
+++ v7
@@ -21,7 +21,7 @@
 The following three file types must be designated as shown below in the regular expression column.  These are not case sensitive.  For example, the valid name for the reference file can be references.txt, REFERENCES.TXT, or even ReFeReNcEs.TxT.  The sampleID in the reference file must match exactly with the sampleID in the alignments, genelist annotations, variants files, etc.

 File type | Permitted extensions | Files name expression | Notes
---- | ---
+--- | --- | --- | ---
 Reference Files | 'txt' | references.txt
 Alignment Files (DNA) | 'fa', 'fas', 'fsa', 'fasta', 'fna','frn', 'mfa', 'afa', 'aln', 'dna' |  *DNA*
 Alignment Files (AA) | 'fa', 'fas', 'fsa', 'fasta', 'faa', 'frn', 'mfa', 'afa', 'aln', 'pep' | *AA*

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 17:38:35 -0000

--- v5
+++ v6
@@ -14,3 +14,24 @@

 Detailed information
 ===
+File extensions and names
+---
+File extensions (what comes after the dot in a file name; e.g. ".txt") that must be used to designate the appropriate file types
+
+The following three file types must be designated as shown below in the regular expression column.  These are not case sensitive.  For example, the valid name for the reference file can be references.txt, REFERENCES.TXT, or even ReFeReNcEs.TxT.  The sampleID in the reference file must match exactly with the sampleID in the alignments, genelist annotations, variants files, etc.
+
+File type | Permitted extensions | Files name expression | Notes
+--- | ---
+Reference Files | 'txt' | references.txt
+Alignment Files (DNA) | 'fa', 'fas', 'fsa', 'fasta', 'fna','frn', 'mfa', 'afa', 'aln', 'dna' |  *DNA*
+Alignment Files (AA) | 'fa', 'fas', 'fsa', 'fasta', 'faa', 'frn', 'mfa', 'afa', 'aln', 'pep' | *AA*
+Variant Files (DNA) | 'txt' | *ntfreq.txt | These include the output files from vPhaser and vProfiler.
+Variant Files (AA) | 'txt', 'xls' | *codonfreq.txt or *codonfreq.xls
+Gene List Files | 'txt' | *genelist.txt
+Muscle Path | 'txt' | muscle_path.txt | Due to the way that genomes containing genes with introns are spliced, it’s extremely difficult to use a user’s protein alignment since this will not match up perfectly with the variant file data.  Therefore, we need to perform an alignment from the existing nucleotide data.
+Epitope Files | 'fasta', 'fas', 'fa' | *EPITOPES.FASTA |The epitope file is just a fasta file with a small number of amino acids that make up the peptide.  We actively map all of the short protein fragments to the translated polypeptide.  Note, a single peptide may map to multiple places if it can be perfectly aligned without any gaps to the reference in more than one locus. 
+Metadata Files | 'txt' | metadata.txt
+
+
+
+

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 16:40:19 -0000

--- v4
+++ v5
@@ -3,10 +3,14 @@
 This package was tested and designed to run on Unix-like system.

 Step-by-step instructions
----
+===
 1. Start by downloading the [VizFileCreatorPackage](http://sourceforge.net/projects/triplev/files/VizFileCreatorPackage.zip/download)
 * Unzip VizFileCreatorPackage.zip in a unix directory.
 * Modify the text file muscle_path.txt to specify the path of where your local version of muscle is located. (supported using muscle version 3.8 and above). Muscle needs to be [downloaded separately](http://www.drive5.com/muscle/) from the authors.
 * Run the config program (perl config.pl) that will create the functional version of the final script, called “createVizFile.pl”, and will show up in the same directory.
 * Run this configured script, "createVizFile.pl" with your input files. 
 * Finally, if all goes well this will create a file called "ViralViewerDataFile.viz" that can then be loaded into TripleV.
+
+
+Detailed information
+===

Preparing data modified by Thomas Abeel

Thomas Abeel — Mon, 31 Mar 2014 16:39:29 -0000

--- v3
+++ v4
@@ -3,8 +3,10 @@
 This package was tested and designed to run on Unix-like system.

 Step-by-step instructions
+---
 1. Start by downloading the [VizFileCreatorPackage](http://sourceforge.net/projects/triplev/files/VizFileCreatorPackage.zip/download)
-+ Unzip VizFileCreatorPackage.zip in a unix directory.
-+ Modify the text file muscle_path.txt to specify the path of where your local version of muscle is located. (supported using muscle version 3.8 and above)
-+ Run the config program (perl config.pl) that will create the functional version of the final script, called “createVizFile.pl”, and will show up in the same directory.
-+ Run this configured script, "createVizFile.pl" with your input files.  I've included a command log of this exact process called "logfile.txt" if you want to see the expected outputs. Finally, if all goes well this will create a file called "ViralViewerDataFile.viz" that can then be loaded into ViralViewer.
+* Unzip VizFileCreatorPackage.zip in a unix directory.
+* Modify the text file muscle_path.txt to specify the path of where your local version of muscle is located. (supported using muscle version 3.8 and above). Muscle needs to be [downloaded separately](http://www.drive5.com/muscle/) from the authors.
+* Run the config program (perl config.pl) that will create the functional version of the final script, called “createVizFile.pl”, and will show up in the same directory.
+* Run this configured script, "createVizFile.pl" with your input files. 
+* Finally, if all goes well this will create a file called "ViralViewerDataFile.viz" that can then be loaded into TripleV.