update to include some dependency versions

Author: Jon Palmer

util/check_modules.py

@@ -1,12 +1,96 @@
 #!/usr/bin/env python
 
-import sys, pkg_resources
-import re
+import sys, os, re, pkg_resources, subprocess
 
 def mycmp(version1, version2):
     def normalize(v):
         return [int(x) for x in re.sub(r'(\.0+)*$','', v).split(".")]
     return cmp(normalize(version1), normalize(version2))
+    
+def check_version1(name):
+    try:
+        vers = subprocess.Popen([name, '-version'], stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
+        vers = vers.replace(': ', ' v')
+    except OSError as e:
+        if e.errno == os.errno.ENOENT:
+            return (name+': not installed')
+    return (vers)
+    
+def check_version2(name):
+    try:
+        if name == 'augustus':
+            vers = subprocess.Popen([name, '--version'], stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0].rstrip()
+        elif name == 'bamtools':
+            vers = subprocess.Popen([name, '--version'], stdout=subprocess.PIPE).communicate()[0].split('\n')[1]
+            vers = vers.replace('bamtools ', 'bamtools v')
+        elif name == 'gmap':
+            vers = subprocess.Popen([name, '--version'], stderr=subprocess.STDOUT, stdout=subprocess.PIPE).communicate()[0].split('\n')
+            for i in vers:
+                if i.startswith('GMAP'):
+                    vers = i
+                    break
+            vers = vers.split(' called')[0].replace('version', 'v')
+        else:
+            vers = subprocess.Popen([name, '--version'], stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
+        if 'exonerate' in vers:
+            vers = vers.replace('exonerate from ', '')
+        if 'AUGUSTUS' in vers:
+            vers = vers.split(' is ')[0].replace('(','v').replace(')', '')
+        vers = vers.replace('version ', 'v')
+    except OSError as e:
+        if e.errno == os.errno.ENOENT:
+            return (name+': not installed')
+    return (vers)
+    
+def check_version3(name):
+    try:
+        vers = subprocess.Popen([name, '-v'], stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
+        vers = vers.replace('version open-', 'v')
+    except OSError as e:
+        if e.errno == os.errno.ENOENT:
+            return (name+': not installed')
+    return (vers)
+
+def check_version4(name):
+    try:
+        vers = subprocess.Popen([name, 'version'], stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
+        vers = vers.replace('version ', 'v')
+        if name == 'ete3':
+            vers = 'ete3 v'+vers
+    except OSError as e:
+        if e.errno == os.errno.ENOENT:
+            return (name+': not installed')
+    return (vers)
+
+def check_version5(name):
+    try:
+        if name == 'gmes_petap.pl':
+            vers = subprocess.Popen([name], stdout=subprocess.PIPE).communicate()[0].split('\n')
+            for i in vers:
+                if i.startswith('GeneMark-ES'):
+                    vers = i
+            vers = vers.replace('version ', 'v')
+        elif name == 'blat':
+            vers = subprocess.Popen([name], stdout=subprocess.PIPE).communicate()[0].split('\n')[0]
+            vers = vers.split(' fast')[0]
+            vers = vers.split('Standalone ')[-1].replace('v. ', 'v')
+    except OSError as e:
+        if e.errno == os.errno.ENOENT:
+            return (name+': not installed')
+    return (vers)
+
+def check_version6(name):
+    try:
+        vers = subprocess.Popen([name, '-h'], stdout=subprocess.PIPE).communicate()[0].split('\n')
+        for i in vers:
+            if i.startswith('# HMMER'):
+                vers = i
+                break
+        vers = vers.split(';')[0].replace('# ', '')
+    except OSError as e:
+        if e.errno == os.errno.ENOENT:
+            return (name+': not installed')
+    return (vers)
 
 funannotate = ['numpy', 'pandas', 'matplotlib', 'scipy', 'scikit-learn', 'psutil', 'natsort', 'goatools', 'seaborn', 'biopython']
 min_versions = {'numpy': '1.10.0', 'pandas': '0.16.1', 'matplotlib': '1.5.0', 'scipy': '0.17.0', 'scikit-learn': '0.17.0', 'psutil': '4.0.0', 'natsort': '4.0.0', 'goatools': '0.6.4', 'seaborn': '0.7.0', 'biopython': '1.65'}
@@ -31,4 +115,24 @@ def normalize(v):
             print x,'=>',vers
     except pkg_resources.DistributionNotFound:
         print x,'=! ERROR. Not installed'
-print "-----------------------"
+print "-----------------------"
+print "External Dependencies:"
+print "-----------------------"
+
+programs1 = ['tblastn', 'blastp', 'blastn', 'makeblastdb', 'rmblastn'] #-version
+programs2 = ['exonerate', 'bedtools', 'bamtools', 'augustus', 'braker.pl', 'gmap'] #--version
+programs3 = ['RepeatModeler', 'RepeatMasker'] #-v
+programs4 = ['diamond', 'ete3'] #version
+programs5 = ['gmes_petap.pl', 'blat'] #no version option at all, a$$holes
+for i in programs1:
+    print check_version1(i)
+for i in programs2:
+    print check_version2(i)
+for i in programs3:
+    print check_version3(i)
+for i in programs4:
+    print check_version4(i)
+for i in programs5:
+    print check_version5(i)
+print check_version6('hmmsearch')
+