changeset 2:a0c85f2d74a5 draft

planemo upload for repository https://github.com/sanbi-sa/tools-sanbi-uwc commit 9612f06b8c60520dc0a047ec072ced317c7796e4

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pyqver2.py	Wed Feb 01 08:45:12 2017 -0500
@@ -0,0 +1,366 @@
+#!/usr/bin/env python
+
+import compiler
+import platform
+import sys
+
+StandardModules = {
+    "__future__":       (2, 1),
+    "abc":              (2, 6),
+    "argparse":         (2, 7),
+    "ast":              (2, 6),
+    "atexit":           (2, 0),
+    "bz2":              (2, 3),
+    "cgitb":            (2, 2),
+    "collections":      (2, 4),
+    "contextlib":       (2, 5),
+    "cookielib":        (2, 4),
+    "cProfile":         (2, 5),
+    "csv":              (2, 3),
+    "ctypes":           (2, 5),
+    "datetime":         (2, 3),
+    "decimal":          (2, 4),
+    "difflib":          (2, 1),
+    "DocXMLRPCServer":  (2, 3),
+    "dummy_thread":     (2, 3),
+    "dummy_threading":  (2, 3),
+    "email":            (2, 2),
+    "fractions":        (2, 6),
+    "functools":        (2, 5),
+    "future_builtins":  (2, 6),
+    "hashlib":          (2, 5),
+    "heapq":            (2, 3),
+    "hmac":             (2, 2),
+    "hotshot":          (2, 2),
+    "HTMLParser":       (2, 2),
+    "importlib":        (2, 7),
+    "inspect":          (2, 1),
+    "io":               (2, 6),
+    "itertools":        (2, 3),
+    "json":             (2, 6),
+    "logging":          (2, 3),
+    "modulefinder":     (2, 3),
+    "msilib":           (2, 5),
+    "multiprocessing":  (2, 6),
+    "netrc":            (1, 5, 2),
+    "numbers":          (2, 6),
+    "optparse":         (2, 3),
+    "ossaudiodev":      (2, 3),
+    "pickletools":      (2, 3),
+    "pkgutil":          (2, 3),
+    "platform":         (2, 3),
+    "pydoc":            (2, 1),
+    "runpy":            (2, 5),
+    "sets":             (2, 3),
+    "shlex":            (1, 5, 2),
+    "SimpleXMLRPCServer": (2, 2),
+    "spwd":             (2, 5),
+    "sqlite3":          (2, 5),
+    "ssl":              (2, 6),
+    "stringprep":       (2, 3),
+    "subprocess":       (2, 4),
+    "sysconfig":        (2, 7),
+    "tarfile":          (2, 3),
+    "textwrap":         (2, 3),
+    "timeit":           (2, 3),
+    "unittest":         (2, 1),
+    "uuid":             (2, 5),
+    "warnings":         (2, 1),
+    "weakref":          (2, 1),
+    "winsound":         (1, 5, 2),
+    "wsgiref":          (2, 5),
+    "xml.dom":          (2, 0),
+    "xml.dom.minidom":  (2, 0),
+    "xml.dom.pulldom":  (2, 0),
+    "xml.etree.ElementTree": (2, 5),
+    "xml.parsers.expat":(2, 0),
+    "xml.sax":          (2, 0),
+    "xml.sax.handler":  (2, 0),
+    "xml.sax.saxutils": (2, 0),
+    "xml.sax.xmlreader":(2, 0),
+    "xmlrpclib":        (2, 2),
+    "zipfile":          (1, 6),
+    "zipimport":        (2, 3),
+    "_ast":             (2, 5),
+    "_winreg":          (2, 0),
+}
+
+Functions = {
+    "all":                      (2, 5),
+    "any":                      (2, 5),
+    "collections.Counter":      (2, 7),
+    "collections.defaultdict":  (2, 5),
+    "collections.OrderedDict":  (2, 7),
+    "enumerate":                (2, 3),
+    "frozenset":                (2, 4),
+    "itertools.compress":       (2, 7),
+    "math.erf":                 (2, 7),
+    "math.erfc":                (2, 7),
+    "math.expm1":               (2, 7),
+    "math.gamma":               (2, 7),
+    "math.lgamma":              (2, 7),
+    "memoryview":               (2, 7),
+    "next":                     (2, 6),
+    "os.getresgid":             (2, 7),
+    "os.getresuid":             (2, 7),
+    "os.initgroups":            (2, 7),
+    "os.setresgid":             (2, 7),
+    "os.setresuid":             (2, 7),
+    "reversed":                 (2, 4),
+    "set":                      (2, 4),
+    "subprocess.check_call":    (2, 5),
+    "subprocess.check_output":  (2, 7),
+    "sum":                      (2, 3),
+    "symtable.is_declared_global": (2, 7),
+    "weakref.WeakSet":          (2, 7),
+}
+
+Identifiers = {
+    "False":        (2, 2),
+    "True":         (2, 2),
+}
+
+def uniq(a):
+    if len(a) == 0:
+        return []
+    else:
+        return [a[0]] + uniq([x for x in a if x != a[0]])
+
+class NodeChecker(object):
+    def __init__(self):
+        self.vers = dict()
+        self.vers[(2,0)] = []
+    def add(self, node, ver, msg):
+        if ver not in self.vers:
+            self.vers[ver] = []
+        self.vers[ver].append((node.lineno, msg))
+    def default(self, node):
+        for child in node.getChildNodes():
+            self.visit(child)
+    def visitCallFunc(self, node):
+        def rollup(n):
+            if isinstance(n, compiler.ast.Name):
+                return n.name
+            elif isinstance(n, compiler.ast.Getattr):
+                r = rollup(n.expr)
+                if r:
+                    return r + "." + n.attrname
+        name = rollup(node.node)
+        if name:
+            v = Functions.get(name)
+            if v is not None:
+                self.add(node, v, name)
+        self.default(node)
+    def visitClass(self, node):
+        if node.bases:
+            self.add(node, (2,2), "new-style class")
+        if node.decorators:
+            self.add(node, (2,6), "class decorator")
+        self.default(node)
+    def visitDictComp(self, node):
+        self.add(node, (2,7), "dictionary comprehension")
+        self.default(node)
+    def visitFloorDiv(self, node):
+        self.add(node, (2,2), "// operator")
+        self.default(node)
+    def visitFrom(self, node):
+        v = StandardModules.get(node.modname)
+        if v is not None:
+            self.add(node, v, node.modname)
+        for n in node.names:
+            name = node.modname + "." + n[0]
+            v = Functions.get(name)
+            if v is not None:
+                self.add(node, v, name)
+    def visitFunction(self, node):
+        if node.decorators:
+            self.add(node, (2,4), "function decorator")
+        self.default(node)
+    def visitGenExpr(self, node):
+        self.add(node, (2,4), "generator expression")
+        self.default(node)
+    def visitGetattr(self, node):
+        if (isinstance(node.expr, compiler.ast.Const)
+            and isinstance(node.expr.value, str)
+            and node.attrname == "format"):
+            self.add(node, (2,6), "string literal .format()")
+        self.default(node)
+    def visitIfExp(self, node):
+        self.add(node, (2,5), "inline if expression")
+        self.default(node)
+    def visitImport(self, node):
+        for n in node.names:
+            v = StandardModules.get(n[0])
+            if v is not None:
+                self.add(node, v, n[0])
+        self.default(node)
+    def visitName(self, node):
+        v = Identifiers.get(node.name)
+        if v is not None:
+            self.add(node, v, node.name)
+        self.default(node)
+    def visitSet(self, node):
+        self.add(node, (2,7), "set literal")
+        self.default(node)
+    def visitSetComp(self, node):
+        self.add(node, (2,7), "set comprehension")
+        self.default(node)
+    def visitTryFinally(self, node):
+        # try/finally with a suite generates a Stmt node as the body,
+        # but try/except/finally generates a TryExcept as the body
+        if isinstance(node.body, compiler.ast.TryExcept):
+            self.add(node, (2,5), "try/except/finally")
+        self.default(node)
+    def visitWith(self, node):
+        if isinstance(node.body, compiler.ast.With):
+            self.add(node, (2,7), "with statement with multiple contexts")
+        else:
+            self.add(node, (2,5), "with statement")
+        self.default(node)
+    def visitYield(self, node):
+        self.add(node, (2,2), "yield expression")
+        self.default(node)
+
+def get_versions(source):
+    """Return information about the Python versions required for specific features.
+
+    The return value is a dictionary with keys as a version number as a tuple
+    (for example Python 2.6 is (2,6)) and the value are a list of features that
+    require the indicated Python version.
+    """
+    tree = compiler.parse(source)
+    checker = compiler.walk(tree, NodeChecker())
+    return checker.vers
+
+def v27(source):
+    if sys.version_info >= (2, 7):
+        return qver(source)
+    else:
+        print >>sys.stderr, "Not all features tested, run --test with Python 2.7"
+        return (2, 7)
+
+def qver(source):
+    """Return the minimum Python version required to run a particular bit of code.
+
+    >>> qver('print "hello world"')
+    (2, 0)
+    >>> qver('class test(object): pass')
+    (2, 2)
+    >>> qver('yield 1')
+    (2, 2)
+    >>> qver('a // b')
+    (2, 2)
+    >>> qver('True')
+    (2, 2)
+    >>> qver('enumerate(a)')
+    (2, 3)
+    >>> qver('total = sum')
+    (2, 0)
+    >>> qver('sum(a)')
+    (2, 3)
+    >>> qver('(x*x for x in range(5))')
+    (2, 4)
+    >>> qver('class C:\\n @classmethod\\n def m(): pass')
+    (2, 4)
+    >>> qver('y if x else z')
+    (2, 5)
+    >>> qver('import hashlib')
+    (2, 5)
+    >>> qver('from hashlib import md5')
+    (2, 5)
+    >>> qver('import xml.etree.ElementTree')
+    (2, 5)
+    >>> qver('try:\\n try: pass;\\n except: pass;\\nfinally: pass')
+    (2, 0)
+    >>> qver('try: pass;\\nexcept: pass;\\nfinally: pass')
+    (2, 5)
+    >>> qver('from __future__ import with_statement\\nwith x: pass')
+    (2, 5)
+    >>> qver('collections.defaultdict(list)')
+    (2, 5)
+    >>> qver('from collections import defaultdict')
+    (2, 5)
+    >>> qver('"{0}".format(0)')
+    (2, 6)
+    >>> qver('memoryview(x)')
+    (2, 7)
+    >>> v27('{1, 2, 3}')
+    (2, 7)
+    >>> v27('{x for x in s}')
+    (2, 7)
+    >>> v27('{x: y for x in s}')
+    (2, 7)
+    >>> qver('from __future__ import with_statement\\nwith x:\\n with y: pass')
+    (2, 5)
+    >>> v27('from __future__ import with_statement\\nwith x, y: pass')
+    (2, 7)
+    >>> qver('@decorator\\ndef f(): pass')
+    (2, 4)
+    >>> qver('@decorator\\nclass test:\\n pass')
+    (2, 6)
+
+    #>>> qver('0o0')
+    #(2, 6)
+    #>>> qver('@foo\\nclass C: pass')
+    #(2, 6)
+    """
+    return max(get_versions(source).keys())
+
+Verbose = False
+MinVersion = (2, 3)
+Lint = False
+
+files = []
+i = 1
+while i < len(sys.argv):
+    a = sys.argv[i]
+    if a == "--test":
+        import doctest
+        doctest.testmod()
+        sys.exit(0)
+    if a == "-v" or a == "--verbose":
+        Verbose = True
+    elif a == "-l" or a == "--lint":
+        Lint = True
+    elif a == "-m" or a == "--min-version":
+        i += 1
+        MinVersion = tuple(map(int, sys.argv[i].split(".")))
+    else:
+        files.append(a)
+    i += 1
+
+if not files:
+    print >>sys.stderr, """Usage: %s [options] source ...
+
+    Report minimum Python version required to run given source files.
+
+    -m x.y or --min-version x.y (default 2.3)
+        report version triggers at or above version x.y in verbose mode
+    -v or --verbose
+        print more detailed report of version triggers for each version
+""" % sys.argv[0]
+    sys.exit(1)
+
+for fn in files:
+    try:
+        f = open(fn)
+        source = f.read()
+        f.close()
+        ver = get_versions(source)
+        if Verbose:
+            print fn
+            for v in sorted([k for k in ver.keys() if k >= MinVersion], reverse=True):
+                reasons = [x for x in uniq(ver[v]) if x]
+                if reasons:
+                    # each reason is (lineno, message)
+                    print "\t%s\t%s" % (".".join(map(str, v)), ", ".join([x[1] for x in reasons]))
+        elif Lint:
+            for v in sorted([k for k in ver.keys() if k >= MinVersion], reverse=True):
+                reasons = [x for x in uniq(ver[v]) if x]
+                for r in reasons:
+                    # each reason is (lineno, message)
+                    print "%s:%s: %s %s" % (fn, r[0], ".".join(map(str, v)), r[1])
+        else:
+            print "%s\t%s" % (".".join(map(str, max(ver.keys()))), fn)
+    except SyntaxError, x:
+        print "%s: syntax error compiling with Python %s: %s" % (fn, platform.python_version(), x)

--- a/vcf_to_alignment.xml	Wed Feb 01 07:07:32 2017 -0500
+++ b/vcf_to_alignment.xml	Wed Feb 01 08:45:12 2017 -0500
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="utf-8" ?>
-<tool id="vcf_to_alignment" name="Generate FASTA alignment from VCF collection" version="0.1">
+<tool id="vcf_to_alignment" name="Generate FASTA alignment from VCF collection" version="0.2">
   <description>Generate a multiple sequence alignment given a collection of variants and a reference sequence</description>
   <requirements>
       <requirement type="package" version="1.67">biopython</requirement>

--- a/vcf_to_msa.py	Wed Feb 01 07:07:32 2017 -0500
+++ b/vcf_to_msa.py	Wed Feb 01 08:45:12 2017 -0500
@@ -1,5 +1,6 @@
 #!/usr/bin/env python
 
+from __future__ import print_function
 import argparse
 import sys
 from Bio import SeqIO