Metadata-Version: 2.1
Name: pepaln
Version: 0.0.8
Summary: Peptide Matcher 
Home-page: UNKNOWN
Author: Istvan Albert
Author-email: istvan.albert@gmail.com
License: UNKNOWN
Description: 
        ## PepMatch: Peptide Matching
        
        This Python package is designed match short peptide sequences to a FASTA file then produce alignment outputs in various formats.
        
        ## What does this package do?
        
        A collaborator asked me to align short peptides from a Mass Spec experiment to a sequence, then show him an image that displays in an easy to see format
        where does each peptide align and which regions are not covered.
        
        For example, for an input that looks like:
        
            VL LS LSP LSPAD PA NVKAA NVK VKA AA
            
        And a sequence:
        
            VLSPADKTNVKAAWGK
        
        They wanted to see it aligned like so :
        
            VLSPADKTNVKAAWG
                  **      
            VL PA   NVKAA  
             LS     NVK    
             LSP     VKA     
             LSPAD     AA     
             
        The `*` above indicates regions that are not covered. In addition they wanted to display different peptides with colors as well.
        
        I was unable to locate a tool that fulfills this need, hence this package.     
        
        ## Input data
        
        The input consists of a tab delimited format with at least three columns:
        
            Peptide     F145I/Dd2Dd2    Mass_Spec_Mode
            VG;GV          3.493           POS
            PA             2.454           POS
            SP             4.701           NEG
        
        Where:
        
        1. The first column lists the peptide sequence (multiple sequences may be listed separated with a semicolon `;`).
        2. The second column lists a value 
        3. The third column indicates the ionization mode
        
        The reference fasta file may contain more than one target sequence.
        
            >ha
            VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPN
            >hb
            VHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLGAFSDGLAHL
            
        ## Outputs
        
        
        ### Text output:
        
            >ha (Mode=POS)
            VLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNAVAHVDDMPN
                         **                    *   *         *                            
            VL PA   NVKAA  KVGA AGEYG  AL RMF   PTT TYF HFD   GSAQV   GKKV DAL  AV      PN
             LS  DKTNVK    KVGAHA EY    LE   LS      YFPH DL    AQVKG GKKVADA TNAVAHVDDM  
             LSP     VKA    VGA  GEYGA                FPH DLS    QV     KVA AL  AVAH      
             LSPAD     AA    GAHA   GAEA               PHF LS    QVK     VA ALTNA AHV     
               PADK           AHAG                     PHFD       VKGH       LT  VA       
                               HAGEYG                   HFDL       KGHGKKVA      VAH      
         
        
        ### PDF output 
        
        The peptides are colored by their value field:
        
        ![](http://ialbert.me/static/images/output.png)
        
        ### GFF output:
            
            ha	VL	.	1	2	.	2.433	.	Mode=POS
            ha	LS	.	2	3	.	4.806	.	Mode=POS
            ha	LSP	.	2	4	.	2.522	.	Mode=POS
            ha	LSPAD	.	2	6	.	1.613	.	Mode=POS
            ha	PA	.	4	5	.	2.2	.	Mode=POS
            ha	PADK	.	4	7	.	1.548	.	Mode=POS
            ha	DKTNVK	.	6	11	.	1.845	.	Mode=POS
            ha	NVKAA	.	9	13	.	3.012	.	Mode=POS
            ha	VKA	.	10	12	.	3.986	.	Mode=POS
            ...
            
        ## Installation
        
            pip install pepmatch
            
        ## Usage
        
        	python -m pepmatch -m mass_spec.txt -r reference.fa
        
        Generates the files called `output.gff`, `output.txt` and `output.pdf`
        
        ## Help
        
            $ python -m pepmatch -h
            usage: __main__.py [-h] [-m MASS] [-r REF] [-p output.pdf] [-t output.txt]
                               [-g output.gff]
            
            optional arguments:
              -h, --help            show this help message and exit
              -m MASS, --mass MASS  Mass-spec result file containing peptide sequences.
              -r REF, --ref REF     Reference file to match the peptides against.
              -p output.pdf, --pdf output.pdf
                                    Output file for pdf file
              -t output.txt, --txt output.txt
                                    Output file for text alignments
              -g output.gff, --gff output.gff
                                    Output file as GFF data
                                    
        
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
