<commit_before># DTASelect2PepXML
## Converter from DTASelect to pepXML 
This converter has been developed in order to obtain pepXML files from DTASelect output files, for the need of creating spectrum libraries using [SpectraST](http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST) software from results of ProLuCID + DTASelect workflow.

## How to obtain it
Go to [here](http://sealion.scripps.edu:8080/hudson/job/DTASelect2PepXML/lastSuccessfulBuild/artifact/target/dtaselect2pepxml.jar)

## How to use it
1. Download the jar file and save it to your computer.
2. In the command line, move to the folder where you downloaded the program and type ``java -jar dtaselect2pepxml.jar file [raw_file_extension] [enzyme_name]`` where:  
   - ```file``` is either a single pepXML or a folder. In case of being a folder, all files with ```txt``` extension will be considered as input files for the conversion. (**MANDATORY**)
   - ```raw_file_extension```  this optional parameter is present in order to specify the raw file type that eventually is going to be used in the creation of the library with  [SpectraST](http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST).  (OPTIONAL) 
   - ```enzyme_name```  this optional parameter is present in order to specify the enzyme in the pepXML file. The following values are allowed: 'Lys-N' ,'Lys-C/P' ,'Arg-C' ,'PepsinA' ,'Trypsin_Mod' ,'dualArgC_Cathep' ,'NoCleavage' ,'TrypChymo' ,'Chymotrypsin' ,'Trypsin' ,'Arg-C/P' ,'Trypsin/P' ,'dualArgC_Cathep/P' ,'Asp-N' ,'V8-DE' ,'Lys-C' ,'V8-E' ,'None'.  (OPTIONAL) 

**Example**:
```
java -jar dtaselect2pepxml.jar c:\users\salva\desktop\data\DTASelect-filter.txt 
```

## How to create the spectral library with [SpectraST](http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST)

1. Download and install SpectraST, included in [TPP](http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP)
2. Go to the folder bin inside of the TPP installation folder.
3. Follow the next steps: <commit_msg>Readme editing<commit_after># DTASelect2PepXML
## Converter from DTASelect to pepXML 
This converter has been developed in order to obtain pepXML files from DTASelect output files, for the need of creating spectrum libraries using [SpectraST](http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST) software from results of ProLuCID + DTASelect workflow.

## How to obtain it
Go to [here](http://sealion.scripps.edu:8080/hudson/job/DTASelect2PepXML/lastSuccessfulBuild/artifact/target/dtaselect2pepxml.jar) and download the jar file. It will contain all required dependencies, so you don't have to worry about it.

## How to use it
1. Download the jar file and save it to your computer.
2. In the command line, move to the folder where you downloaded the program and type ``java -jar dtaselect2pepxml.jar file [raw_file_extension] [enzyme_name]`` where:  
   - ```file``` is either a single pepXML or a folder. In case of being a folder, all files with ```txt``` extension will be considered as input files for the conversion. (**MANDATORY**)
   - ```raw_file_extension```  this optional parameter is present in order to specify the raw file type that eventually is going to be used in the creation of the library with  [SpectraST](http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST).  (OPTIONAL) 
   - ```enzyme_name```  this optional parameter is present in order to specify the enzyme in the pepXML file. The following values are allowed: 'Lys-N' ,'Lys-C/P' ,'Arg-C' ,'PepsinA' ,'Trypsin_Mod' ,'dualArgC_Cathep' ,'NoCleavage' ,'TrypChymo' ,'Chymotrypsin' ,'Trypsin' ,'Arg-C/P' ,'Trypsin/P' ,'dualArgC_Cathep/P' ,'Asp-N' ,'V8-DE' ,'Lys-C' ,'V8-E' ,'None'.  (OPTIONAL) 

**Example**:
```
java -jar dtaselect2pepxml.jar c:\users\salva\desktop\data\DTASelect-filter.txt 
```

## How to create the spectral library with [SpectraST](http://tools.proteomecenter.org/wiki/index.php?title=Software:SpectraST)

1. Download and install SpectraST, included in [TPP](http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP)
2. Go to the folder bin inside of the TPP installation folder.
3. Follow the next steps: 
{'fraction_non_alphanumeric': 0.11731044349070101, 'fraction_numerical': 0.007629947544110634, 'mean_word_length': 5.053391053391054, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 6}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 7, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '33797', 'n_tokens_mistral': 1428, 'n_tokens_neox': 1358, 'n_words': 462}