From f3973fe556fd8542e2ee6020be9e07619e5368a8 Mon Sep 17 00:00:00 2001
From: Ali Ghaffaari <ali.ghaffaari@gmail.com>
Date: Thu, 7 Jun 2018 23:10:39 +0200
Subject: [PATCH 1/3] Add ksnper script

---
 vcfy/ksnper.py | 120 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 120 insertions(+)
 create mode 100644 vcfy/ksnper.py

diff --git a/vcfy/ksnper.py b/vcfy/ksnper.py
new file mode 100644
index 0000000..e4c4dce
--- /dev/null
+++ b/vcfy/ksnper.py
@@ -0,0 +1,120 @@
+# coding=utf-8
+
+"""
+    vcfy.ksnper
+    ~~~~~~~~~~~
+
+    Report the number of SNPs in all k-mers.
+
+    :copyright: (c) 2018 by Ali Ghaffaari.
+    :license: MIT, see LICENSE for more details.
+"""
+
+import csv
+
+import click
+import vcf
+from Bio import SeqIO
+from BitVector import BitVector
+
+
+def reflen(ref_file):
+    """Get the length of reference genome sequence length.
+
+    Args:
+        ref_file : file-like object or str
+            The reference genome file or file path.
+    """
+    return len(next(SeqIO.parse(ref_file, 'fasta')).seq)
+
+
+def compute_snpbv(vcf_reader, length):
+    """Compute SNP bitvector. The SNP bitvector is a bitvector of the length of
+    the reference genome where SNP loci are set.
+
+    Args:
+        vcf_reader : vcf.Reader
+            VCF reader.
+        length : int
+            The length of reference genome.
+
+    Return:
+        A BitVector.BitVector instance of size `length` where all SNP loci are
+        set.
+    """
+    cnt = BitVector(size=length)
+    for record in vcf_reader:
+        cnt[record.POS-1] = 1
+    return cnt
+
+
+def ksnpcounts(snpbv, k):
+    """Generate number of SNPs in all k-mers in the reference genome.
+
+    Args:
+        snpbv : BitVector.BitVector
+            The SNP bitvector.
+        k : int
+            The length of the k-mer.
+
+    Return:
+        The number of SNPs in a k-mer. It yields this for all k-mers in the
+        reference genome.
+    """
+    kcount = 0
+    for i in range(k):
+        kcount += snpbv[i]
+    yield kcount
+    for i in range(k, len(snpbv)):
+        kcount += snpbv[i]
+        kcount -= snpbv[i-k]
+        yield kcount
+
+
+def write_csv(output, vcf_file, ref_file, k, dialect='unix'):
+    """Write CSV file.
+
+    Args:
+        output : file-like object
+            The output CSV file.
+        vcf_file : file-like object or str
+            The input VCF file or file path.
+        ref_file : file-like object or str
+            The input reference genome. If it is set to `None`, the reference
+            genome path will be inferred from VCF metadata (header).
+        k : int
+            The length of the k-mer.
+        dialect : str
+            This string specifies the dialect of the output CSV file.
+    """
+    csv_writer = csv.DictWriter(output,
+                                fieldnames=['k', 'count'],
+                                dialect=dialect,
+                                quoting=csv.QUOTE_NONE)
+    csv_writer.writeheader()
+
+    vcf_reader = vcf.Reader(vcf_file)
+    if ref_file is None:
+        ref_file = open(vcf_reader.metadata['reference'], 'r')
+    bv = compute_snpbv(vcf_reader, reflen(ref_file))
+    for count in ksnpcounts(bv, k):
+        csv_writer.writerow(dict(k=k, count=count))
+
+
+@click.command()
+@click.argument('vcf', type=click.File('r'), default="-")
+@click.option('-o', '--output', type=click.File('w'), default="-",
+              help="Write to this file instead of standard output.")
+@click.option('-r', '--reference', type=click.File('r'), default=None,
+              help=("Reference genome FASTA file. It will be inferred from VCF "
+                    "header, if not specified."))
+@click.option('-k', type=int, required=True, help="The value of k.")
+@click.option('-d', '--dialect', type=click.Choice(csv.list_dialects()),
+              default='unix', show_default=True,
+              help="Use this CSV dialect.")
+def cli(**kwargs):
+    write_csv(kwargs.pop('output'),
+              kwargs.pop('vcf'),
+              kwargs.pop('reference'),
+              kwargs.pop('k'),
+              kwargs.pop('dialect'))

From afec230f98a5689a5a3c9ef2818a7e5d8ca2722f Mon Sep 17 00:00:00 2001
From: Ali Ghaffaari <ali.ghaffaari@gmail.com>
Date: Thu, 7 Jun 2018 23:11:39 +0200
Subject: [PATCH 2/3] Update package setup

- Add new script dependencies.
- Add `ksnper` to the list of console scripts.
---
 vcfy/release.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/vcfy/release.py b/vcfy/release.py
index d917e99..23609e3 100644
--- a/vcfy/release.py
+++ b/vcfy/release.py
@@ -71,6 +71,7 @@
     'PyVCF>=0.6.8',
     'biopython>=1.71',
     'numpy>=1.14.3',
+    'BitVector>=3.4.8',
     'click>=6.7',
 ]
 __tests_require__ = []
@@ -81,4 +82,5 @@
 __entry_points__ = '''
 [console_scripts]
 vcfy=vcfy.cli:cli
+ksnper=vcfy.ksnper:cli
 '''

From d7b9e884c26bf09a95d44adedc9a76503f3b931b Mon Sep 17 00:00:00 2001
From: Ali Ghaffaari <ali.ghaffaari@gmail.com>
Date: Thu, 7 Jun 2018 23:15:52 +0200
Subject: [PATCH 3/3] Bump to version number v0.0.5

---
 vcfy/release.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vcfy/release.py b/vcfy/release.py
index 23609e3..0632bae 100644
--- a/vcfy/release.py
+++ b/vcfy/release.py
@@ -38,7 +38,7 @@
 __license__ = 'MIT'
 
 # Release
-__version__ = '0.0.4'
+__version__ = '0.0.5'
 __status__ = DS_PREALPHA
 
 # Package data