changeset 3:de803005027f draft

v0.0.7 internal Python style fixes

--- a/tools/align_back_trans/README.rst	Wed Aug 05 10:52:56 2015 -0400
+++ b/tools/align_back_trans/README.rst	Wed Feb 01 06:55:27 2017 -0500
@@ -69,6 +69,7 @@
 v0.0.6  - Reorder XML elements (internal change only).
         - Use ``format_source=...`` tag.
         - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+v0.0.7  - Minor Python code style improvements (internal change only).
 ======= ======================================================================
 
 
@@ -85,12 +86,12 @@
 Planemo commands (which requires you have set your Tool Shed access details in
 ``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
 
-    $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    $ planemo shed_update -t testtoolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
     ...
 
 or::
 
-    $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
+    $ planemo shed_update -t toolshed --check_diff ~/repositories/pico_galaxy/tools/align_back_trans/
     ...
 
 To just build and check the tar ball, use::

--- a/tools/align_back_trans/align_back_trans.py	Wed Aug 05 10:52:56 2015 -0400
+++ b/tools/align_back_trans/align_back_trans.py	Wed Feb 01 06:55:27 2017 -0500
@@ -8,7 +8,7 @@
 
 The development repository for this tool is here:
 
-* https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans  
+* https://github.com/peterjc/pico_galaxy/tree/master/tools/align_back_trans
 
 This tool is available with a Galaxy wrapper from the Galaxy Tool Shed at:
 
@@ -19,34 +19,30 @@
 
 import sys
 from Bio.Seq import Seq
-from Bio.Alphabet import generic_dna, generic_protein
+from Bio.Alphabet import generic_protein
 from Bio.Align import MultipleSeqAlignment
 from Bio import SeqIO
 from Bio import AlignIO
 from Bio.Data.CodonTable import ambiguous_generic_by_id
 
 if "-v" in sys.argv or "--version" in sys.argv:
-    print "v0.0.5"
+    print "v0.0.7"
     sys.exit(0)
 
-def sys_exit(msg, error_level=1):
-    """Print error message to stdout and quit with given error level."""
-    sys.stderr.write("%s\n" % msg)
-    sys.exit(error_level)
 
 def check_trans(identifier, nuc, prot, table):
     """Returns nucleotide sequence if works (can remove trailing stop)"""
     if len(nuc) % 3:
-        sys_exit("Nucleotide sequence for %s is length %i (not a multiple of three)"
+        sys.exit("Nucleotide sequence for %s is length %i (not a multiple of three)"
                  % (identifier, len(nuc)))
 
     p = str(prot).upper().replace("*", "X")
     t = str(nuc.translate(table)).upper().replace("*", "X")
     if len(t) == len(p) + 1:
         if str(nuc)[-3:].upper() in ambiguous_generic_by_id[table].stop_codons:
-            #Allow this...
+            # Allow this...
             t = t[:-1]
-            nuc  = nuc[:-3] #edit return value
+            nuc = nuc[:-3]  # edit return value
     if len(t) != len(p):
         err = ("Inconsistent lengths for %s, ungapped protein %i, "
                "tripled %i vs ungapped nucleotide %i." %
@@ -56,39 +52,39 @@
         elif t.startswith(p):
             err += "\nThere are %i extra nucleotides at the end." % (len(t) - len(p))
         elif p in t:
-            #TODO - Calculate and report the number to trim at start and end?
+            # TODO - Calculate and report the number to trim at start and end?
             err += "\nHowever, protein sequence found within translated nucleotides."
         elif p[1:] in t:
             err += "\nHowever, ignoring first amino acid, protein sequence found within translated nucleotides."
-        sys_exit(err)
-
+        sys.exit(err)
 
     if t == p:
         return nuc
     elif p.startswith("M") and "M" + t[1:] == p:
-        #Close, was there a start codon?
+        # Close, was there a start codon?
         if str(nuc[0:3]).upper() in ambiguous_generic_by_id[table].start_codons:
             return nuc
         else:
-            sys_exit("Translation check failed for %s\n"
+            sys.exit("Translation check failed for %s\n"
                      "Would match if %s was a start codon (check correct table used)\n"
                      % (identifier, nuc[0:3].upper()))
     else:
-        #Allow * vs X here? e.g. internal stop codons
-        m = "".join("." if x==y else "!" for (x,y) in zip(p,t))
+        # Allow * vs X here? e.g. internal stop codons
+        m = "".join("." if x == y else "!" for (x, y) in zip(p, t))
         if len(prot) < 70:
             sys.stderr.write("Protein:     %s\n" % p)
             sys.stderr.write("             %s\n" % m)
             sys.stderr.write("Translation: %s\n" % t)
         else:
             for offset in range(0, len(p), 60):
-                sys.stderr.write("Protein:     %s\n" % p[offset:offset+60])
-                sys.stderr.write("             %s\n" % m[offset:offset+60])
-                sys.stderr.write("Translation: %s\n\n" % t[offset:offset+60])
-        sys_exit("Translation check failed for %s\n" % identifier)
+                sys.stderr.write("Protein:     %s\n" % p[offset:offset + 60])
+                sys.stderr.write("             %s\n" % m[offset:offset + 60])
+                sys.stderr.write("Translation: %s\n\n" % t[offset:offset + 60])
+        sys.exit("Translation check failed for %s\n" % identifier)
+
 
 def sequence_back_translate(aligned_protein_record, unaligned_nucleotide_record, gap, table=0):
-    #TODO - Separate arguments for protein gap and nucleotide gap?
+    # TODO - Separate arguments for protein gap and nucleotide gap?
     if not gap or len(gap) != 1:
         raise ValueError("Please supply a single gap character")
 
@@ -99,14 +95,14 @@
     else:
         from Bio.Alphabet import Gapped
         alpha = Gapped(alpha, gap)
-        gap_codon = gap*3
+        gap_codon = gap * 3
 
     ungapped_protein = aligned_protein_record.seq.ungap(gap)
     ungapped_nucleotide = unaligned_nucleotide_record.seq
     if table:
         ungapped_nucleotide = check_trans(aligned_protein_record.id, ungapped_nucleotide, ungapped_protein, table)
     elif len(ungapped_protein) * 3 != len(ungapped_nucleotide):
-        sys_exit("Inconsistent lengths for %s, ungapped protein %i, "
+        sys.exit("Inconsistent lengths for %s, ungapped protein %i, "
                  "tripled %i vs ungapped nucleotide %i" %
                  (aligned_protein_record.id,
                   len(ungapped_protein),
@@ -124,15 +120,16 @@
     assert not nuc, "Nucleotide sequence for %r longer than protein %r" \
         % (unaligned_nucleotide_record.id, aligned_protein_record.id)
 
-    aligned_nuc = unaligned_nucleotide_record[:] #copy for most annotation
-    aligned_nuc.letter_annotation = {} #clear this
-    aligned_nuc.seq = Seq("".join(seq), alpha) #replace this
+    aligned_nuc = unaligned_nucleotide_record[:]  # copy for most annotation
+    aligned_nuc.letter_annotation = {}  # clear this
+    aligned_nuc.seq = Seq("".join(seq), alpha)  # replace this
     assert len(aligned_protein_record.seq) * 3 == len(aligned_nuc)
     return aligned_nuc
 
+
 def alignment_back_translate(protein_alignment, nucleotide_records, key_function=None, gap=None, table=0):
     """Thread nucleotide sequences onto a protein alignment."""
-    #TODO - Separate arguments for protein and nucleotide gap characters?
+    # TODO - Separate arguments for protein and nucleotide gap characters?
     if key_function is None:
         key_function = lambda x: x
     if gap is None:
@@ -143,7 +140,7 @@
         try:
             nucleotide = nucleotide_records[key_function(protein.id)]
         except KeyError:
-            raise ValueError("Could not find nucleotide sequence for protein %r" \
+            raise ValueError("Could not find nucleotide sequence for protein %r"
                              % protein.id)
         aligned.append(sequence_back_translate(protein, nucleotide, gap, table))
     return MultipleSeqAlignment(aligned)
@@ -159,7 +156,7 @@
 elif len(sys.argv) == 6:
     align_format, prot_align_file, nuc_fasta_file, nuc_align_file, table = sys.argv[1:]
 else:
-    sys_exit("""This is a Python script for 'back-translating' a protein alignment,
+    sys.exit("""This is a Python script for 'back-translating' a protein alignment,
 
 It requires three, four or five arguments:
 - alignment format (e.g. fasta, clustal),
@@ -183,8 +180,8 @@
 
 try:
     table = int(table)
-except:
-    sys_exit("Bad table argument %r" % table)
+except ValueError:
+    sys.exit("Bad table argument %r" % table)
 
 prot_align = AlignIO.read(prot_align_file, align_format, alphabet=generic_protein)
 nuc_dict = SeqIO.index(nuc_fasta_file, "fasta")

--- a/tools/align_back_trans/align_back_trans.xml	Wed Aug 05 10:52:56 2015 -0400
+++ b/tools/align_back_trans/align_back_trans.xml	Wed Feb 01 06:55:27 2017 -0500
@@ -1,4 +1,4 @@
-<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.6">
+<tool id="align_back_trans" name="Thread nucleotides onto a protein alignment (back-translation)" version="0.0.7">
     <description>Gives a codon aware alignment</description>
     <requirements>
         <requirement type="package" version="1.63">biopython</requirement>

--- a/tools/align_back_trans/tool_dependencies.xml	Wed Aug 05 10:52:56 2015 -0400
+++ b/tools/align_back_trans/tool_dependencies.xml	Wed Feb 01 06:55:27 2017 -0500
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.63">
-        <repository changeset_revision="a5c49b83e983" name="package_biopython_1_63" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ec55b787a0e1" name="package_biopython_1_63" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>