Update the Readme files and Revision History

Author: alchemistmatt

PeptideToProteinMapper/bin/README.md

@@ -12,44 +12,47 @@ PeptideToProteinMapper.exe
  /I:PeptideInputFilePath /R:ProteinInputFilePath
  [/O:OutputDirectoryName] [/P:ParameterFilePath] [/F:FileFormatCode]
  [/N:InspectParameterFilePath] [/G] [/H] [/K] [/A]
- [/L[:LogFilePath]] [/LogDirectory:LogDirectoryPath] [/VerboseLog] [/Q]
+ [/L[:LogFilePath]] [/LogDir:LogDirectoryPath] [/VerboseLog] [/Q]
 ```
 
 The input file path can contain the wildcard character *. If a wildcard is
 present, the same protein input file path will be used for each of the peptide
 input files matched.
 
-The output directory name is optional. If omitted, the output files will be created
-in the same directory as the input file. If included, then a subdirectory is created
-with the name OutputDirectoryName.
+The output directory name is optional. If omitted, the output files will be
+created in the same directory as the input file. If included, then a subdirectory
+is created with the name OutputDirectoryName.
 
-The parameter file path is optional. If included, it should point to a valid XML parameter file.
+The parameter file path is optional. If included, it should point to a valid XML
+parameter file.
 
-Use /F to specify the peptide input file format code.  Options are:
-* 0=Auto Determine: Treated as /F:1 unless name ends in _inspect.txt, then /F:3
+Use `/F` to specify the peptide input file format code.  Options are:
+* 0=Auto Determine: Treated as `/F:1` unless name ends in _inspect.txt, then `/F:3`
 * 1=Peptide sequence in the 1st column (subsequent columns are ignored)
 * 2=Protein name in 1st column and peptide sequence 2nd column
 * 3=Inspect search results file (peptide sequence in the 3rd column)
 * 4=MS-GF+ search results file (peptide sequence in the column titled 'Peptide'; optionally scan number in the column titled 'Scan')
 * 5=SEQUEST, X!Tandem, Inspect, or MS-GF+ PHRP data file
 
-When processing an Inspect search results file, use /N to specify the Inspect parameter file used 
-(required for determining the mod names embedded in the identified peptides).
+When processing an Inspect search results file, use `/N` to specify the Inspect
+parameter file used (required for determining the mod names embedded in the
+identified peptides).
 
-Use /G to ignore I/L differences when finding peptides in proteins or computing coverage
+Use `/G` to ignore I/L differences when finding peptides in proteins or computing coverage
 
-Use /H to suppress (hide) the protein sequence in the _coverage.txt file
+Use `/H` to suppress (hide) the protein sequence in the _coverage.txt file
 
-Use /K to skip the protein coverage computation steps (enabling faster processing)
+Use `/K` to skip the protein coverage computation steps (enabling faster processing)
 
-Use /A to create a copy of the source file, but with a new column listing the mapped protein for each peptide.
-If a peptide maps to multiple proteins, then multiple lines will be listed.
+Use `/A` to create a copy of the source file, but with a new column listing the
+mapped protein for each peptide. If a peptide maps to multiple proteins, then
+multiple lines will be listed
 
-Use /L to create a log file, optionally specifying the file name
+Use `/L` to create a log file, optionally specifying the file name
 
-Use /LogDirectory to define the directory in which the log file should be created
+Use `/LogDir` to define the directory in which the log file should be created
 
-Use /VerboseLog to create a detailed log file
+Use `/VerboseLog` to create a detailed log file
 
 ## Contacts
 

README.md

@@ -11,8 +11,28 @@ A graphical user interface (GUI) is provided to allow the user to select the inp
 The results browser displays the protein sequences, highlighting the residues that were present 
 in the peptide input file, and providing sequence coverage stats for each protein.
 
+## Example files:
+
+Input files:
+* [BSA_P171_QID1638_TestPeptides.txt](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestPeptides.txt)
+* [BSA_P171_QID1638_TestPeptides_SequenceOnly.txt](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestPeptides_SequenceOnly.txt)
+* [BSA_P171_QID1638_TestProteins.fasta](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestProteins.fasta)
+
+Output files:
+* [BSA_P171_QID1638_TestPeptides_coverage.txt](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestPeptides_coverage.txt)
+* [BSA_P171_QID1638_TestPeptides_ProteinToPeptideMapping.txt](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestPeptides_ProteinToPeptideMapping.txt)
+* [BSA_P171_QID1638_TestPeptides_SequenceOnly_coverage.txt](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestPeptides_SequenceOnly_coverage.txt)
+* [BSA_P171_QID1638_TestPeptides_SequenceOnly_ProteinToPeptideMapping.txt](https://github.com/PNNL-Comp-Mass-Spec/protein-coverage-summarizer/blob/master/bin/BSA_P171_QID1638_TestPeptides_SequenceOnly_ProteinToPeptideMapping.txt)
+
+
 ## Console Version Syntax
 
+There are two options for computing protein coverage and peptide to protein mapping from the command line:
+* ProteinCoverageSummarizerGUI.exe
+* PeptideToProteinMapper.exe
+
+### Console Arguments for ProteinCoverageSummarizerGUI.exe
+
 ```
 ProteinCoverageSummarizerGUI.exe
   /I:PeptideInputFilePath /R:ProteinInputFilePath [/O:OutputDirectoryName]
@@ -21,7 +41,8 @@ ProteinCoverageSummarizerGUI.exe
 
 The input file path can contain the wildcard character *. If a wildcard is
 present, the same protein input file path will be used for each of the peptide
-input files matched.
+input files matched. If the input file has one column of data, it is assumed to be Peptide Sequence.
+If two columns of data (separated by a tab character), it is assumed to be Protein Name then Peptide Sequence.
 
 The output directory name is optional. If omitted, the output files will be created
 in the same directory as the input file. If included, a subdirectory is created with
@@ -30,17 +51,72 @@ the name OutputDirectoryName.
 The parameter file path is optional. If included, it should point to a valid XML
 parameter file.
 
-Use /G to ignore I/L differences when finding peptides in proteins or computing coverage.
+Use `/G` to ignore I/L differences when finding peptides in proteins or computing coverage.
+
+Use `/H` to suppress (hide) the protein sequence in the _coverage.txt file.
+
+Use `/M` to enable the creation of a protein to peptide mapping file.
+
+Use `/K` to skip protein coverage computation steps
+
+Use `/Debug` to keep the console open to see additional debug messages
+
+Use `/KeepDB` to keep the SQLite database after processing (by default it is deleted)
+
+
+### Console Arguments for PeptideToProteinMapper.exe
+
+The PeptideToProteinMapper reads in a text file containing peptide sequences then 
+searches the specified .fasta or text file containing protein names and sequences 
+to find the proteins that contain each peptide.  The program will also compute 
+the sequence coverage percent for each protein (though this can be disable using /K).
+
+```
+PeptideToProteinMapper.exe
+ /I:PeptideInputFilePath /R:ProteinInputFilePath
+ [/O:OutputDirectoryName] [/P:ParameterFilePath] [/F:FileFormatCode]
+ [/N:InspectParameterFilePath] [/G] [/H] [/K] [/A]
+ [/L[:LogFilePath]] [/LogDir:LogDirectoryPath] [/VerboseLog] [/Q]
+```
+
+The input file path can contain the wildcard character *. If a wildcard is
+present, the same protein input file path will be used for each of the peptide
+input files matched.
+
+The output directory name is optional. If omitted, the output files will be
+created in the same directory as the input file. If included, then a subdirectory
+is created with the name OutputDirectoryName.
+
+The parameter file path is optional. If included, it should point to a valid XML
+parameter file.
+
+Use `/F` to specify the peptide input file format code.  Options are:
+* 0=Auto Determine: Treated as `/F:1` unless name ends in _inspect.txt, then `/F:3`
+* 1=Peptide sequence in the 1st column (subsequent columns are ignored)
+* 2=Protein name in 1st column and peptide sequence 2nd column
+* 3=Inspect search results file (peptide sequence in the 3rd column)
+* 4=MS-GF+ search results file (peptide sequence in the column titled 'Peptide'; optionally scan number in the column titled 'Scan')
+* 5=SEQUEST, X!Tandem, Inspect, or MS-GF+ PHRP data file
+
+When processing an Inspect search results file, use `/N` to specify the Inspect
+parameter file used (required for determining the mod names embedded in the
+identified peptides).
+
+Use `/G` to ignore I/L differences when finding peptides in proteins or computing coverage
+
+Use `/H` to suppress (hide) the protein sequence in the _coverage.txt file
 
-Use /H to suppress (hide) the protein sequence in the _coverage.txt file.
+Use `/K` to skip the protein coverage computation steps (enabling faster processing)
 
-Use /M to enable the creation of a protein to peptide mapping file.
+Use `/A` to create a copy of the source file, but with a new column listing the
+mapped protein for each peptide. If a peptide maps to multiple proteins, then
+multiple lines will be listed
 
-Use /K to skip protein coverage computation steps
+Use `/L` to create a log file, optionally specifying the file name
 
-Use /Debug to keep the console open to see additional debug messages
+Use `/LogDir` to define the directory in which the log file should be created
 
-Use /KeepDB to keep the SQLite database after processing (by default it is deleted)
+Use `/VerboseLog` to create a detailed log file
 
 ## Contacts
 

RevisionHistory.txt

@@ -1,5 +1,8 @@
 Protein Coverage Summarizer Change Log
 
+Version 1.3.7026; March 28, 2019
+	- Check for closed or broken SQLite connection
+
 Version 1.3.7020; March 22, 2019
 	- Replaced SharedVBNetRoutines.dll with PRISMWin-library