Merge pull request #79 from andrewjpage/prog_versions

Prog versions

AUTHORS

@@ -1 +1,3 @@
 Martin Hunt (path-help@sanger.ac.uk)
+Andrew J. Page (path-help@sanger.ac.uk)
+Sascha Steinbiss (path-help@sanger.ac.uk)

iva/external_progs.py

@@ -37,7 +37,7 @@ def is_in_path(prog):
  'nucmer': ('nucmer --version', re.compile('^NUCmer \(NUCleotide MUMmer\) version (.*)$')),
  'R': ('R --version', re.compile('^R version (.*) \(.*\) --')),
  'smalt': ('smalt version', re.compile('^Version: (.*)$')),
- 'samtools': ('samtools', re.compile('^Version: ([^ ]+)')),
+ 'samtools': ('samtools', re.compile('(\d+\.\d+[\.\d]*)')),
 }
 
 

iva/tests/external_progs_test.py

@@ -19,28 +19,158 @@ class TestExternalProgs(unittest.TestCase):
  def test_kmc_in_path(self):
  '''Test kmc in path'''
  self.assertTrue(external_progs.is_in_path('kmc'), 'Error! Did not find kmc in your path! Please install kmc')
-
+ 
  def test_kmc_dump_in_path(self):
  '''Test kmc_dump in path'''
  self.assertTrue(external_progs.is_in_path('kmc_dump'), 'Error! Did not find kmc_dump in your path! Please install kmc')
-
+ 
  def test_nucmer_in_path(self):
  '''Test nucmer in path'''
  self.assertTrue(external_progs.is_in_path('nucmer'), 'Error! Did not find nucmer in your path! Please install MUMmer')
-
+ 
  def test_delta_filter_in_path(self):
  '''Test delta-filter in path'''
  self.assertTrue(external_progs.is_in_path('delta-filter'), 'Error! Did not find delta-filter in your path! Please install MUMmer')
-
+ 
  def test_show_coords_in_path(self):
  '''Test show-coords in path'''
  self.assertTrue(external_progs.is_in_path('show-coords'), 'Error! Did not find show-coords in your path! Please install MUMmer')
-
+ 
  def test_samtools_in_path(self):
  '''Test samtools in path'''
  self.assertTrue(external_progs.is_in_path('samtools'), 'Error! Did not find samtools in your path! Please install samtools')
-
+ 
  def test_smalt_in_path(self):
  '''Test smalt in path'''
  self.assertTrue(external_progs.is_in_path('smalt'), 'Error! Did not find smalt in your path! Please install smalt')
+
+ def test_r_version(self):
+ '''Test R versions'''
+ self.assertEqual('3.4.0', self.check_regex_version_extraction('R', """
+R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
+Copyright (C) 2017 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('3.3.2', self.check_regex_version_extraction('R', """
+R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"
+Copyright (C) 2016 The R Foundation for Statistical Computing
+Platform: x86_64-apple-darwin13.4.0 (64-bit)
+ """ ))
+
+ self.assertEqual('3.2.2', self.check_regex_version_extraction('R', """
+R version 3.2.2 (2015-08-14) -- "Fire Safety"
+Copyright (C) 2015 The R Foundation for Statistical Computing
+Platform: x86_64-pc-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('3.1.2', self.check_regex_version_extraction('R', """
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
+Copyright (C) 2014 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('3.0.0', self.check_regex_version_extraction('R', """
+R version 3.0.0 (2013-04-03) -- "Masked Marvel"
+Copyright (C) 2013 The R Foundation for Statistical Computing
+Platform: x86_64-unknown-linux-gnu (64-bit)
+ """ ))
+
+ self.assertEqual('2.15.2', self.check_regex_version_extraction('R', """
+R version 2.15.2 (2012-10-26) -- "Trick or Treat"
+Copyright (C) 2012 The R Foundation for Statistical Computing
+ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
+ """ ))
+
+
+ def test_blastn_version(self):
+ '''Test blastn version'''
+ self.assertEqual('2.7.0+', self.check_regex_version_extraction('blastn', """
+blastn: 2.7.0+
+ Package: blast 2.7.0, build Sep 12 2017 15:51:33
+ """ ))
+ self.assertEqual('2.6.0+', self.check_regex_version_extraction('blastn', """
+blastn: 2.6.0+
+ Package: blast 2.6.0, build Aug 23 2017 22:18:50
+ """ ))
+ self.assertEqual('2.2.31+', self.check_regex_version_extraction('blastn', """
+blastn: 2.2.31+
+Package: blast 2.2.31, build Jul 6 2015 15:14:27
+ """ ))
+
+ def test_makeblastdb_version(self):
+ '''Test makeblastdb version'''
+ self.assertEqual('2.7.0+', self.check_regex_version_extraction('makeblastdb', """
+makeblastdb: 2.7.0+
+ Package: blast 2.7.0, build Sep 12 2017 15:51:33
+ """ ))
+ self.assertEqual('2.6.0+', self.check_regex_version_extraction('makeblastdb', """
+makeblastdb: 2.6.0+
+ Package: blast 2.6.0, build Aug 23 2017 22:18:50
+ """ ))
+ self.assertEqual('2.2.31+', self.check_regex_version_extraction('makeblastdb', """
+makeblastdb: 2.2.31+
+Package: blast 2.2.31, build Jul 6 2015 15:14:27
+ """ ))
+
+ def test_kmc_version(self):
+ '''Test kmc version'''
+ self.assertTrue(external_progs.get_version('kmc',must_be_in_path=True))
+ self.assertEqual('2.3.0', self.check_regex_version_extraction('kmc', """
+K-Mer Counter (KMC) ver. 2.3.0 (2015-08-21)
+ """ ))
+ self.assertEqual('3.0.0', self.check_regex_version_extraction('kmc', """
+K-Mer Counter (KMC) ver. 3.0.0 (2017-01-28)
+ """ ))
+
+ def test_kmc_dump_version(self):
+ '''Test kmc_dump version'''
+ self.assertTrue(external_progs.get_version('kmc_dump',must_be_in_path=True))
+ self.assertEqual('3.0.0', self.check_regex_version_extraction('kmc_dump', """
+KMC dump ver. 3.0.0 (2017-01-28)
+ """ ))
+ self.assertEqual('2.3.0', self.check_regex_version_extraction('kmc_dump', """
+KMC dump ver. 2.3.0 (2015-08-21)
+ """ ))
+
+ def test_nucmer_version(self):
+ '''Test nucmer version'''
+ self.assertTrue(external_progs.get_version('nucmer',must_be_in_path=True))
+ self.assertEqual('3.1', self.check_regex_version_extraction('nucmer', """
+nucmer
+NUCmer (NUCleotide MUMmer) version 3.1
+ """ ))
+
+ def test_samtools_version(self):
+ '''Test samtools version'''
+ self.assertTrue(external_progs.get_version('samtools', must_be_in_path=True))
+ self.assertEqual('1.6', self.check_regex_version_extraction('samtools', """
+samtools 1.6
+Using htslib 1.6
+Copyright (C) 2017 Genome Research Ltd.""" ))
+
+ def test_samtools_original_version(self):
+ '''Test samtools original version'''
+ self.assertEqual('0.1.19', self.check_regex_version_extraction('samtools', """
+Program: samtools (Tools for alignments in the SAM format)
+Version: 0.1.19-44428cd
 
+Usage: samtools <command> [options]""" ))
+
+ def test_smalt_version(self):
+ '''Test smalt version'''
+ self.assertTrue(external_progs.get_version('smalt',must_be_in_path=True))
+ self.assertEqual('0.7.6', self.check_regex_version_extraction('smalt', """
+ SMALT - Sequence Mapping and Alignment Tool
+Version: 0.7.6
+Date: 21-03-2014""" ))
+
+ def check_regex_version_extraction(self, prog, raw_version_output ):
+ cmd, regex = external_progs.prog_to_version_cmd[prog]
+ raw_output_lines = raw_version_output.splitlines()
+ for line in raw_output_lines:
+ hits = regex.search(line)
+ if hits:
+ return str(hits.group(1))
+ return None

setup.py

@@ -47,7 +47,7 @@
 
 setup(
  name='iva',
- version='1.0.8',
+ version='1.0.9',
  description='Iterative Virus Assembler',
  packages = find_packages(),
  package_data={'iva': ['gage/*', 'ratt/*', 'read_trim/*', 'test_run_data/*']},