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        "description": "Welcome to Pypgen (v0.2.0) *BETA*\n---------------------------------\n\nPypgen provides various utilities for estimating standard genetic\ndiversity measures including Gst, G'st, G''st, and Jost's D from large\ngenomic datasets (Hedrick, 2005; Jost, 2008; Masatoshi Nei, 1973; Nei &\nChesser, 1983). Pypgen operates both on individual SNPs as\nwell as on user defined regions (e.g., five kilobase windows tiled\nacross each chromosome). For the windowed analyses pypgen estimates the\nmulti-locus versions of each estimator.\n\nFeatures:\n+++++++++\n\n-  Handles multiallelic SNP calls\n-  Allows a single VCF file to contain multiple populations\n-  Operates on standard `VCF (Variant Call\n   Format) <http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41>`_\n   formatted SNP calls\n-  Uses `bgziped <http://samtools.sourceforge.net/tabix.shtml>`_ input\n   for fast random access\n-  Takes advantage of multiple processor cores\n-  Calculates additional metrics:\n\n   -  snp count per window\n   -  mean read depth (+/- STDEV) per window\n   -  populations with fixed alleles per SNP\n   -  more as I think of them\n\nImportant Note:\n+++++++++++++++\n\nPYPGEN IS STILL IN ACTIVE DEVELOPMENT AND ALMOST CERTAINLY CONTAINS\nBUGS. If you find a bug please file a report in the `issues section <https://github.com/ngcrawford/pypgen/issues>`_ of\nthe github repository and I'll address it as soon as I can.\n\nEnclosed Scripts:\n+++++++++++++++++\n\n-  Sliding window analysis (vcf\\_sliding\\_window.py)\n-  Per SNP analysis (vcf\\_snpwise\\_fstats.py)\n\nDependancies:\n+++++++++++++\n\n-  OSX or Linux\n-  `Python 2.7 <http://www.python.org/download/releases/2.7/>`_\n-  `Numpy <http://www.numpy.org>`_\n-  `pysam <http://wwwfgu.anat.ox.ac.uk/+andreas/documentation/samtools/contents.html>`_\n   and `samtools <http://samtools.sourceforge.net/>`_\n\nInstallation:\n+++++++++++++\n\nFirst install `samtools <http://samtools.sourceforge.net/>`_. On OS X I recommend using `homebrew <http://mxcl.github.com/homebrew/>`_ to do this. Once you have samtools installed and available in terminal you can use either pip or setuptools to install the current release of pypgen:\n\n::\n\n        pip install pypgen\n\nor, \n\n::\n\n        easy_install pypgen\n\n\nAlternately, if you like to live on the edge, you can clone and install the current development version from github.\n\n::\n\n       pip install -e git+https://github.com/ngcrawford/pypgen.git\n\nDocumentation:\n++++++++++++++\n\nMore detailed documentation will be forthcoming, but in the meantime information about each script can be obtained by running:\n\n::\n\n        python [script name].py --help\n\nOutput: \n+++++++\n\nNote: this will probably change.\n\n**vcf\\_sliding\\_window.py:**\n\n-  *chrm* = Name of chromosome\n-  *start* = Starting position of window\n-  *stop* = Ending position of window\n-  *snp\\_count* = Total Number of SNPs in window\n-  *total\\_depth\\_mean* = Mean read depth across window\n-  *total\\_depth\\_stdev* = Standard deviation of read depth across\n   window\n-  *Pop1.sample\\_count.mean* = Mean number of samples per snp for 'Pop1'\n-  *Pop1.sample\\_count.stdev* = Standard deviation of samples per snp\n   for - 'Pop1'\n-  *Pop2.sample\\_count.mean* = Mean number of samples per snp for 'Pop2'\n-  *Pop2.sample\\_count.stdev* = Standard deviation of samples per snp\n   for 'Pop2'\n-  *Pop2.Pop1.D\\_est* = Multilocus Dest (Jost 2008)\n-  *Pop2.Pop1.G\\_double\\_prime\\_st\\_est* = (Meirmans & Hedrick 2011)\n-  *Pop2.Pop1.G\\_prime\\_st\\_est* = Standardized Gst (Hedrick 2005)\n-  *Pop2.Pop1.Gst\\_est* = Fst corrected for sample size and allowing for\n   multiallelic loci (Nei & Chesser 1983)\n-  cont...\n\n**vcf\\_snpwise\\_fstats.py:**\n\n-  *chrm* = Name of chromosome\n-  *pos* = Position of SNP\n-  *outgroups* = Number of samples\n-  *Pop1* = Population ID\n-  *Pop1.Pop2.D\\_est*\\ = Multilocus Dest (Jost 2008)\n-  *Pop1.Pop2.G\\_double\\_prime\\_st\\_est* = (Meirmans & Hedrick\n   2011)\n-  *Pop1.Pop2.G\\_prime\\_st\\_est* = Standardized Gst (Hedrick 2005)\n-  *Pop1.Pop2.Gst\\_est* = Fst corrected for sample size and\n   allowing for multiallelic loci (Nei & Chesser 1983)\n-  *Pop1.Pop2.Hs\\_est*\n-  *Pop1.Pop2.Ht\\_est*\n-  cont...,\n-  *Pop1\\_fixed* = If a sample is fixed at a particular allele this\n   flag is set to 1 (= \"True\" in binary).\n-  cont...",
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