Metadata-Version: 1.0
Name: BamTyper
Version: 0.2.1
Summary: Working with paired reads in BAM format
Home-page: http://pypi.python.org/pypi/BamTyper/
Author: Michael Imelfort
Author-email: mike@mikeimelfort.com
License: LICENSE.txt
Description:                                                                                
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        # Overview
        
        Ability to work out the orientation and insert size of a paired read data file
        Can estimate relative orientation and gap between pairs of contigs in the bam file (Useful for scaffolding) 
        
        # Installation
        
        use pip:
        
        ```sh
        $ pip install BamTyper
        ```
        # Usage
        ##As a library:
        ###Get the type of the reads:
            #!/usr/bin/env python
            from bamtyper.utilities import BamParser as BTBP
            BP = BTBP()
            bam_types = BP.getTypes(bamFiles)
        
            Where:
                bamFiles - a list of BAM filenames
            
            Returns:
                bam_types - a dict containing information about the insert size and 
                            relative orientation of reads in the bam file
                              { bam1 : (type, ins, stdev), ... }
                            Where:
                                type - orientation type:
                                    0 : OUT  : <--- --->
                                    1 : SAME : ---> --->
                                    2 : IN   : ---> <---
                                ins - estimated insert size (of original DNA fragment)
                                stdev - standard deviation of insert size      
        
        ###Get linking pairs:
            #!/usr/bin/env python
            from bamtyper.utilities import BamParser as BTBP
            BP = BTBP()
            (links, ref_lengths, coverages) = BP.getLinks(bamFiles, doCoverage=True)
            
            Where:
                bamFiles - a list of BAM filenames
            
            Returns:
                links - a dict containing information about links between two contigs
                          {c1: (c2, num_links, link_type, gap), ... }
                        Where:
                            num_links - Number of paired reads confirming the link
                            link_type - Relative orientation of the two contigs (Start and End)
                              SS, SE, ES, EE or ERROR
                            gap - Estimated gap between te two contigs
                            
                coverages - a dict containing the FRAGMENT coverage of each contig n the bam file(s)
                          {c1 : (cov1, cov2, ..., covN), ... }
                          
                ref_lengths - a dict containing the lengths of all contigs
                          {c1 : len, ... }
            
            Notes:
                bamtyper will automatically work out the orientation and insert size of the 
                reads in each bam file and base it's estimations of link_type and gap on this 
        
        ##On the command line:
        
            bamtyper type - Parse BAM files and determine reads type
            
                $ bamtyper type bamfile.bam
                
                Determining OT for BAM 'bamfile'
                Orientation: IN Insert: 301, Stdev: 29
         
            bamtyper links - Parse BAM files and get linking reads
        
            Usage 1:
        
                $ bamtyper links bamfile.bam 
        
              1.
                contig2 , [ contig1 , 39 , SE , 69 ]
                contig1 , [ contig2 , 39 , ES , 69 ]
                
                implies a layout which looks like:
                
                ---1--> 69bp ---2-->
        
              2.
                contig3 , [ contig2 , 3 , SS , 58 ]
                contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]
                contig1 , [ contig2 , 4 , EE , 45 ]
        
                implies a layout which looks like:
                
                ---1--> 45bp <--2--- 58bp ---3-->
        
            Usage 2: report FRAGMENT coverage too!
        
                $ bamtyper links bamfile1.bam bamfile2.bam -c
        
                contig3 , [ contig2 , 3 , SS , 58 ]
                contig2 , [ contig3 , 3 , SS , 58 ] , [ contig1 , 4 , EE , 45 ]
                contig1 , [ contig2 , 4 , EE , 45 ]
                contig3 0.6206 0.5234
                contig2 0.6558 0.0123
                contig1 0.6523 0.5634
        
                Where:
                    contig3 0.6206 0.5234
                    
                    Reports 0.6206 fragments per base in bamfile1 and 0.5234 in bamfile2
                    If these were 100bp reads then this would imply
                    coverages of 62x and 52x respectively
                    
        # Administration
        
        Project home page, info on the source tree, documentation, issues and how to contribute, see http://github.com/minillinim/BamTyper
        
        This software is currently unpublished.
        
        Copyright © 2012 Michael Imelfort. See LICENSE.txt for further details.
        
        
Platform: UNKNOWN
