Update master branch to V 1.2b7

README.md

@@ -51,8 +51,7 @@ Each tool in the BuddySuite has been extensively documented in the [wiki](https:
 All of the individual Buddy toolkits are located in the 'buddysuite' directory and the 
  ['develop' branch](https://github.com/biologyguy/BuddySuite/tree/develop) is where all new features have been
  implemented. If you're interested in contributing, please refer to the
- [developer page](https://github.com/biologyguy/BuddySuite/wiki/Developers) for further information on dependencies
- and instructions.
+ [developer page](https://github.com/biologyguy/BuddySuite/wiki/Developers) for further information.
 
 ## Citation
 We are currently working on a [peer reviewed manuscript](https://github.com/biologyguy/BuddySuite/tree/develop/manuscript), but until then

README.rst

@@ -60,7 +60,7 @@ branch <https://github.com/biologyguy/BuddySuite/tree/develop>`__ is
 where all new features have been implemented. If you're interested in
 contributing, please refer to the `developer
 page <https://github.com/biologyguy/BuddySuite/wiki/Developers>`__ for
-further information on dependencies and instructions.
+further information.
 
 Citation
 --------

buddysuite/AlignBuddy.py

@@ -28,11 +28,15 @@
 
 # BuddySuite specific
 try:
- from . import buddy_resources as br
- from . import SeqBuddy as Sb
-except SystemError:
  import buddy_resources as br
  import SeqBuddy as Sb
+except ImportError:
+ try:
+ import buddysuite.buddy_resources as br
+ import buddysuite.SeqBuddy as Sb
+ except AttributeError:
+ from . import buddy_resources as br
+ from . import SeqBuddy as Sb
 
 # Standard library
 import sys
@@ -65,7 +69,7 @@
 
 # ################################################ GLOBALS ###################################################### #
 GAP_CHARS = ["-", ".", " "]
-VERSION = br.Version("AlignBuddy", 1, "2b6", br.contributors, {"year": 2016, "month": 10, "day": 3})
+VERSION = br.Version("AlignBuddy", 1, "2b7", br.contributors, {"year": 2016, "month": 10, "day": 19})
 
 
 # #################################################### ALIGNBUDDY #################################################### #

buddysuite/BuddySuite.py

@@ -24,12 +24,21 @@
 from configparser import ConfigParser, NoOptionError
 import os
 import re
-import buddysuite
-import buddysuite.buddy_resources as br
 import shutil
 import random
 import string
 
+try:
+ import buddysuite
+ import buddy_resources as br
+except ImportError:
+ try:
+ import buddysuite
+ import buddysuite.buddy_resources as br
+ except AttributeError:
+ from . import buddysuite
+ from . import buddy_resources as br
+
 
 def setup(): # ToDo: Check permissions?
  print("\033[1mWelcome to BuddySuite!\033[m\nLet's configure your installation:\n")

buddysuite/DatabaseBuddy.py

@@ -30,9 +30,12 @@
 
 # BuddySuite specific
 try:
- from . import buddy_resources as br
-except SystemError:
  import buddy_resources as br
+except ImportError:
+ try:
+ import buddysuite.buddy_resources as br
+ except AttributeError:
+ from . import buddy_resources as br
 
 # Standard library
 import sys
@@ -77,7 +80,7 @@
  "fastq-solexa", "fastq-illumina", "genbank", "gb", "imgt", "nexus", "phd", "phylip", "seqxml",
  "stockholm", "tab", "qual"]
 CONFIG = br.config_values()
-VERSION = br.Version("DatabaseBuddy", 1, "2b6", br.contributors, {"year": 2016, "month": 10, "day": 3})
+VERSION = br.Version("DatabaseBuddy", 1, "2b7", br.contributors, {"year": 2016, "month": 10, "day": 19})
 
 GREY = "\033[90m"
 RED = "\033[91m"

buddysuite/PhyloBuddy.py

@@ -27,11 +27,15 @@
 
 # BuddySuite specific
 try:
- from . import buddy_resources as br
- from . import AlignBuddy as Alb
-except SystemError:
  import buddy_resources as br
  import AlignBuddy as Alb
+except ImportError:
+ try:
+ import buddysuite.buddy_resources as br
+ import buddysuite.AlignBuddy as Alb
+ except AttributeError:
+ from . import buddy_resources as br
+ from . import AlignBuddy as Alb
 
 # Standard library
 import sys
@@ -143,7 +147,7 @@ def ascending_order(phylobuddy):
 
 # ##################################################### GLOBALS ###################################################### #
 CONFIG = br.config_values()
-VERSION = br.Version("PhyloBuddy", 1, "2b6", br.contributors, {"year": 2016, "month": 10, "day": 3})
+VERSION = br.Version("PhyloBuddy", 1, "2b7", br.contributors, {"year": 2016, "month": 10, "day": 19})
 OUTPUT_FORMATS = ["newick", "nexus", "nexml"]
 PHYLO_INFERENCE_TOOLS = ["raxml", "phyml", "fasttree"]
 

buddysuite/SeqBuddy.py

@@ -31,11 +31,15 @@
 
 # BuddySuite specific
 try:
- from . import buddy_resources as br
- from . import AlignBuddy as Alb
-except SystemError:
  import buddy_resources as br
  import AlignBuddy as Alb
+except ImportError:
+ try:
+ import buddysuite.buddy_resources as br
+ import buddysuite.AlignBuddy as Alb
+ except AttributeError:
+ from . import buddy_resources as br
+ from . import AlignBuddy as Alb
 
 # Standard library
 import sys
@@ -153,7 +157,7 @@ def incremental_rename(query, replace):
 # - Try to speed things up by reading in all sequence data only when necessary
 
 # ###################################################### GLOBALS ##################################################### #
-VERSION = br.Version("SeqBuddy", 1, "2b6", br.contributors, {"year": 2016, "month": 10, "day": 3})
+VERSION = br.Version("SeqBuddy", 1, "2b7", br.contributors, {"year": 2016, "month": 10, "day": 19})
 OUTPUT_FORMATS = ["ids", "accessions", "summary", "full-summary", "clustal", "embl", "fasta", "fastq", "fastq-sanger",
  "fastq-solexa", "fastq-illumina", "genbank", "gb", "imgt", "nexus", "phd", "phylip", "phylip-relaxed",
  "phylipss", "phylipsr", "raw", "seqxml", "sff", "stockholm", "tab", "qual"]
@@ -1355,11 +1359,11 @@ def count_residues(seqbuddy):
  neut = len(re.findall("[GAVLIPFYWSTNQM]", seq))
  resid_count['% Uncharged'] = round(100 * neut / seq_len, 2)
 
- hyrdophobic = len(re.findall("[AVLIPYFWMC]", seq))
- resid_count['% Hyrdophobic'] = round(100 * hyrdophobic / seq_len, 2)
+ hydrophobic = len(re.findall("[AVLIPYFWMC]", seq))
+ resid_count['% Hydrophobic'] = round(100 * hydrophobic / seq_len, 2)
 
- hyrdophilic = len(re.findall("[NQSTKRHDE]", seq))
- resid_count['% Hyrdophilic'] = round(100 * hyrdophilic / seq_len, 2)
+ hydrophilic = len(re.findall("[NQSTKRHDE]", seq))
+ resid_count['% Hydrophilic'] = round(100 * hydrophilic / seq_len, 2)
 
  for residue in ["A", "C", "D", "E", "F", "G", "H", "I", "K", "L", "M",
  "N", "P", "Q", "R", "S", "T", "V", "W", "Y"]:

buddysuite/buddy_resources.py

@@ -23,9 +23,8 @@
 """
 from __future__ import print_function
 import sys
-if float("%s.%s" % (sys.version_info[0], sys.version_info[1])) < 3.5:
- print("Error: Attempting to run BuddySuite with Python %s.%s. Python 3.5+ required." %
- (sys.version_info[0], sys.version_info[1]))
+if int(sys.version_info[0]) < 3:
+ print("Error: Attempting to run BuddySuite with Python %s. Python 3+ required." % sys.version_info[0])
  sys.exit()
 import argparse
 import datetime

buddysuite/tests/__init__.py

@@ -1,13 +1,17 @@
 # coding=utf-8
 import os
+import sys
 from copy import deepcopy
 from hashlib import md5
 from collections import OrderedDict
 
-from .. import AlignBuddy as Alb
-from .. import SeqBuddy as Sb
-from .. import PhyloBuddy as Pb
-from .. import DatabaseBuddy as Db
+DIRECTORY_SCRIPT = os.path.dirname(os.path.realpath(__file__))
+sys.path.insert(0, "%s%s.." % (DIRECTORY_SCRIPT, os.sep))
+
+import AlignBuddy as Alb
+import SeqBuddy as Sb
+import PhyloBuddy as Pb
+import DatabaseBuddy as Db
 
 # This file (conftest.py) must be in the same directory as unit_test_resources
 RESOURCE_PATH = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'unit_test_resources') + os.path.sep
@@ -21,7 +25,7 @@ def __init__(self):
  @staticmethod
  def buddy2hash(buddy):
  if type(buddy) not in [Sb.SeqBuddy, Alb.AlignBuddy, Pb.PhyloBuddy, Db.DbBuddy]:
- raise AttributeError("Buddy object required")
+ raise AttributeError("Buddy object required, not %s" % type(buddy))
  _hash = md5("{0}".format(str(buddy)).encode("utf-8")).hexdigest()
  return _hash
 
@@ -320,7 +324,7 @@ def get_one(self, code, mode="objs"):
  if len(code.split()) != 3:
  raise AttributeError("Only explicit three-component codes are accepted")
  output = self.get_list(code, mode)
- return None if not output or len(output) > 1else output[0]
+ return None if not output or len(output) > 1 else output[0]
 
 
 # ################################ - PhyloBuddy - ################################# #

buddysuite/tests/conftest.py

@@ -33,19 +33,19 @@ def sb_resources():
 def sb_odd_resources():
  # A dict of invalid file resources
  resource_list = {file_format: name.format(path=RESOURCE_PATH) for file_format, name in [
- ('blank', '{path}/blank.fa'),
- ('figtree', '{path}/figtree.nexus'),
- ('unrecognizable', '{path}/unrecognizable.phy'),
- ('gibberish', '{path}/gibberish.fa'),
- ('phylipss_cols', '{path}/malformed_phylip_columns.physs'),
- ('duplicate', '{path}/Duplicate_seqs.fa'),
- ('ambiguous_dna', '{path}/ambiguous_dna.fa'),
- ('ambiguous_rna', '{path}/ambiguous_rna.fa'),
- ('blastn', '{path}/blast/Mnemiopsis_cds.n'),
- ('blastp', '{path}/blast/Mnemiopsis_pep.p'),
- ('dummy_feats', '{path}/Mnemiopsis_cds_dummy_features.gb'),
- ('cnidaria_pep', '{path}/Cnidaria_pep.nexus'),
- ('mixed', '{path}/mixed_alpha.fa')
+ ('blank', '{path}blank.fa'),
+ ('figtree', '{path}figtree.nexus'),
+ ('unrecognizable', '{path}unrecognizable.phy'),
+ ('gibberish', '{path}gibberish.fa'),
+ ('phylipss_cols', '{path}malformed_phylip_columns.physs'),
+ ('duplicate', '{path}Duplicate_seqs.fa'),
+ ('ambiguous_dna', '{path}ambiguous_dna.fa'),
+ ('ambiguous_rna', '{path}ambiguous_rna.fa'),
+ ('blastn', '{path}blast/Mnemiopsis_cds.n'),
+ ('blastp', '{path}blast/Mnemiopsis_pep.p'),
+ ('dummy_feats', '{path}Mnemiopsis_cds_dummy_features.gb'),
+ ('cnidaria_pep', '{path}Cnidaria_pep.nexus'),
+ ('mixed', '{path}mixed_alpha.fa')
  ]}
  return resource_list
 
@@ -66,16 +66,16 @@ def alb_odd_resources():
  resource_list = {
  'dna': {
  'single': {file_format: name.format(path=RESOURCE_PATH) for file_format, name in [
- ('fasta', '{path}/gibberish.fa'),
- ('phylipss_recs', '{path}/malformed_phylip_records.physs'),
- ('phylipss_cols', '{path}/malformed_phylip_columns.physs'),
- ('ambiguous', '{path}/ambiguous_dna_alignment.fa')]}
+ ('fasta', '{path}gibberish.fa'),
+ ('phylipss_recs', '{path}malformed_phylip_records.physs'),
+ ('phylipss_cols', '{path}malformed_phylip_columns.physs'),
+ ('ambiguous', '{path}ambiguous_dna_alignment.fa')]}
  },
  'protein': {
  'single': {file_format: name.format(path=RESOURCE_PATH) for file_format, name in [
- ('phylip', '{path}/unrecognizable.phy')]}
+ ('phylip', '{path}unrecognizable.phy')]}
  },
- 'blank': "%s/blank.fa" % RESOURCE_PATH
+ 'blank': "%sblank.fa" % RESOURCE_PATH
  }
  return resource_list
 
@@ -94,13 +94,13 @@ def pb_resources():
 def pb_odd_resources():
  # A dict of invalid file resources
  resource_list = {file_format: name.format(path=RESOURCE_PATH) for file_format, name in [
- ('blank', '{path}/blank.fa'),
- ('unrecognizable', '{path}/unrecognizable.phy'),
- ('figtree', '{path}/figtree.nexus'),
- ('compare', '{path}/compare_trees.newick'),
- ('node_lables', '{path}/tree_with_node_lables.nwk'),
- ('lengths', '{path}/Mnemiopsis_pep.newick'),
- ('bootstraps', '{path}/Mnemiopsis_pep_bootstraps.newick'),
- ('support', '{path}/Mnemiopsis_pep_support.newick')
+ ('blank', '{path}blank.fa'),
+ ('unrecognizable', '{path}unrecognizable.phy'),
+ ('figtree', '{path}figtree.nexus'),
+ ('compare', '{path}compare_trees.newick'),
+ ('node_lables', '{path}tree_with_node_lables.nwk'),
+ ('lengths', '{path}Mnemiopsis_pep.newick'),
+ ('bootstraps', '{path}Mnemiopsis_pep_bootstraps.newick'),
+ ('support', '{path}Mnemiopsis_pep_support.newick')
  ]}
  return resource_list

buddysuite/tests/test_alignbuddy/test_alb_3rd_party.py

@@ -12,9 +12,9 @@
 from unittest import mock
 from shutil import which
 from subprocess import Popen, PIPE
-from ... import AlignBuddy as Alb
-from ... import SeqBuddy as Sb
-from ... import buddy_resources as br
+import AlignBuddy as Alb
+import SeqBuddy as Sb
+import buddy_resources as br
 
 
 # ########################################### 'ga', '--generate_alignment' ########################################## #
@@ -237,17 +237,11 @@ def ask_true(*ask_args):
  pass
  return True
 
- try:
- monkeypatch.setattr("buddysuite.buddy_resources.ask", ask_false)
- except ImportError:
- monkeypatch.setattr("buddy_resources.ask", ask_false)
+ monkeypatch.setattr(br, "ask", ask_false)
  with pytest.raises(SystemExit):
  Alb.generate_msa(tester, clustalo_bin, keep_temp="%s%sga_temp_files" % (temp_dir.path, os.sep))
 
- try:
- monkeypatch.setattr("buddysuite.buddy_resources.ask", ask_true)
- except ImportError:
- monkeypatch.setattr("buddy_resources.ask", ask_true)
+ monkeypatch.setattr(br, "ask", ask_true)
  Alb.generate_msa(tester, clustalo_bin, keep_temp="%s%sga_temp_files" % (temp_dir.path, os.sep))
  assert os.path.isfile("{0}{1}ga_temp_files{1}result".format(temp_dir.path, os.sep))
  assert os.path.isfile("{0}{1}ga_temp_files{1}tmp.fa".format(temp_dir.path, os.sep))

buddysuite/tests/test_alignbuddy/test_alb_api.py

@@ -9,9 +9,9 @@
 from Bio.SeqRecord import SeqRecord
 from Bio.AlignIO import MultipleSeqAlignment
 from Bio.Alphabet import IUPAC
-from ... import AlignBuddy as Alb
-from ... import SeqBuddy as Sb
-from ... import buddy_resources as br
+import AlignBuddy as Alb
+import SeqBuddy as Sb
+import buddy_resources as br
 from .. import __init__
 from collections import OrderedDict
 

buddysuite/tests/test_alignbuddy/test_alb_class_and_helpers.py

@@ -9,9 +9,9 @@
 from Bio.Alphabet import IUPAC
 from Bio import AlignIO
 
-from ... import buddy_resources as br
-from ...AlignBuddy import AlignBuddy, guess_alphabet, guess_format, make_copy
-from ...buddy_resources import GuessError, parse_format
+import buddy_resources as br
+from AlignBuddy import AlignBuddy, guess_alphabet, guess_format, make_copy
+from buddy_resources import GuessError, parse_format
 
 
 def mock_valueerror(*args, **kwargs):

buddysuite/tests/test_alignbuddy/test_alb_ui.py

@@ -29,9 +29,9 @@
 import argparse
 from copy import deepcopy
 
-from ... import AlignBuddy as Alb
-from ... import SeqBuddy as Sb
-from ... import buddy_resources as br
+import AlignBuddy as Alb
+import SeqBuddy as Sb
+import buddy_resources as br
 
 TEMP_DIR = br.TempDir()
 VERSION = Sb.VERSION