add dependency checks to setup

setup.py

@@ -1,5 +1,89 @@
 from setuptools import setup, find_packages
 
+import sys
+import subprocess
+
+
+def check_bwa():
+    p = subprocess.Popen(['bwa'], stderr=subprocess.PIPE)
+    for line in p.stderr:
+        if line.startswith('Version:'):
+            major, minor, sub = line.strip().split()[1].split('.')
+            sub = sub.split('-')[0]
+            if int(major) >= 0 and int(minor) >= 7 and int(sub) >= 12:
+                return True
+    return False
+
+
+def check_samtools():
+    p = subprocess.Popen(['samtools'], stderr=subprocess.PIPE)
+    for line in p.stderr:
+        if line.startswith('Version:'):
+            major, minor = line.strip().split()[1].split('.')[:2]
+            minor = minor.split('-')[0]
+            if int(major) >= 1 and int(minor) >= 2:
+                return True
+    return False
+
+
+def check_bcftools():
+    p = subprocess.Popen(['bcftools'], stderr=subprocess.PIPE)
+    for line in p.stderr: 
+        if line.startswith('Version:'):
+            major, minor = line.strip().split()[1].split('.')[:2]
+            minor = minor.split('-')[0]
+            if int(major) >= 1 and int(minor) >= 2:
+                return True
+    return False
+
+
+def check_wgsim():
+    p = subprocess.Popen(['wgsim'], stderr=subprocess.PIPE)
+    for line in p.stderr:
+        if line.startswith('Version:'):
+            major, minor = line.strip().split()[1].split('.')[:2]
+            minor = minor.split('-')[0]
+            if int(major) >= 0 and int(minor) >= 2:
+                return True
+    return False
+
+
+def check_velvet():
+    p = subprocess.Popen(['velvetg'], stdout=subprocess.PIPE)
+    for line in p.stdout: 
+        if line.startswith('Version'):
+            major, minor = line.strip().split()[1].split('.')[:2]
+            minor = minor.split('-')[0]
+            if int(major) >= 1 and int(minor) >= 2:
+                return True
+    return False
+
+
+def check_exonerate():
+    p = subprocess.Popen(['exonerate'], stdout=subprocess.PIPE)
+    for line in p.stdout:
+        if line.startswith('exonerate from exonerate'):
+            major, minor = line.strip().split()[-1].split('.')[:2]
+            minor = minor.split('-')[0]
+            if int(major) >= 2 and int(minor) >= 2:
+                return True
+    return False
+
+
+def check_python():
+    return sys.hexversion >= 0x20702f0
+
+
+if __name__ == '__main__':
+    if not check_python(): sys.exit('Dependency problem: python >= 2.7.2 is required')
+    if not check_bwa(): sys.exit('Dependency problem: bwa >= 0.7.12 not found')
+    if not check_samtools(): sys.exit('Dependency problem: samtools >= 1.2 not found')
+    if not check_bcftools(): sys.exit('Dependency problem: bcftools >= 1.2 not found')
+    if not check_wgsim(): sys.exit('Dependency problem: wgsim not found (required for addsv)')
+    if not check_velvet(): sys.exit('Dependency problem: velvet >= 1.2 not found (required for addsv)')
+    if not check_exonerate(): sys.exit('Dependency problem: exonerate >= 2.2 not found (required for addsv)')
+
+
 setup(name='bamsurgeon',
 	version='1.0',
 	author='Adam Ewing',
@@ -25,4 +109,7 @@
 		'scripts/seperation.py',
         'scripts/match_fasta_to_bam.py'],
 	packages=find_packages(),
+    install_requires = [
+        'pysam>=0.8.1',
+    ],
 	)