Add info to log files

juliema · Jan 19, 2018 · b9ee180 · b9ee180
1 parent 2d2b33c
commit b9ee180
Show file tree

Hide file tree

Showing 6 changed files with 19 additions and 15 deletions.
diff --git a/atram.py b/atram.py
@@ -41,7 +41,7 @@ def assemble(args):
                     assembler.write_final_output(blast_db, query)
                 except (TimeoutError, RuntimeError):
                     pass
-                except Exception as err:
+                except Exception as err:  # pylint: disable=broad-except
                     log.error('Exception: ' + err)
 
                 db.aux_detach(db_conn)

diff --git a/atram_preprocessor.py b/atram_preprocessor.py
@@ -184,12 +184,8 @@ def parse_command_line(temp_dir_default):
         formatter_class=argparse.RawDescriptionHelpFormatter,
         description=textwrap.dedent(description))
 
-    parser.add_argument('--mixed-ends', '-m', metavar='FASTA_or_FASTQ', nargs='+',
-                        help='''Sequence read archive files that have a mix of
-                             both end 1 and end 2 sequences (or single ends).
-                             The files are in fasta or fastq format. You may
-                             enter more than one file or you may use wildcards.
-                             ''')
+    parser.add_argument('--version', action='version',
+                        version='%(prog)s {}'.format(db.ATRAM_VERSION))
 
     parser.add_argument('--end-1', '-1', metavar='FASTA_or_FASTQ', nargs='+',
                         help='''Sequence read archive files that have only
@@ -207,16 +203,22 @@ def parse_command_line(temp_dir_default):
                              enter more than one file or you may use wildcards.
                              ''')
 
-    parser.add_argument('--single-ends', '-0', metavar='FASTA_or_FASTQ', nargs='+',
+    parser.add_argument('--mixed-ends', '-m', metavar='FASTA_or_FASTQ',
+                        nargs='+',
+                        help='''Sequence read archive files that have a mix of
+                             both end 1 and end 2 sequences (or single ends).
+                             The files are in fasta or fastq format. You may
+                             enter more than one file or you may use wildcards.
+                             ''')
+
+    parser.add_argument('--single-ends', '-0', metavar='FASTA_or_FASTQ',
+                        nargs='+',
                         help='''Sequence read archive files that have only
                              unpaired sequences. Any sequence suffix will be
                              ignored. The files are in fasta or fastq format.
                              You may enter more than one file or you may use
                              wildcards.''')
 
-    parser.add_argument('--version', action='version',
-                        version='%(prog)s {}'.format(db.ATRAM_VERSION))
-
     group = parser.add_argument_group('preprocessor arguments')
 
     blast_db = os.path.join('.', 'atram_' + date.today().isoformat())

diff --git a/lib/assemblers/base.py b/lib/assemblers/base.py
@@ -118,7 +118,7 @@ def assembled_contigs_count(self, high_score):
 
         if not count:
             log.info('No contigs had a bit score greater than {} and are at '
-                     'least {} long in iteration {}. The highest score for '
+                     'least {} bp long in iteration {}. The highest score for '
                      'this iteration is {}'.format(
                          self.args['bit_score'],
                          self.args['contig_length'],

diff --git a/lib/db.py b/lib/db.py
@@ -6,7 +6,7 @@
 from os.path import basename, join, exists
 
 
-ATRAM_VERSION = '2.0'
+ATRAM_VERSION = '2.0.alpha.5'
 DB_VERSION = '2.0'
 
 BATCH_SIZE = 1e6  # How many sequence records to insert at a time

diff --git a/lib/log.py b/lib/log.py
@@ -5,6 +5,7 @@
 import logging
 import tempfile
 import subprocess
+import lib.db as db
 
 LOGGER = None  # Global logger so we can switch between queries & blast DBs
 FORMATTER = logging.Formatter('%(asctime)s %(levelname)s: %(message)s',
@@ -32,7 +33,8 @@ def setup(log_file, blast_db, query_file=''):
         LOGGER.addHandler(handler)
         LOGGER.addHandler(stream)
 
-        info(" ".join(sys.argv[:]))
+        info('aTRAM version: {}'.format(db.ATRAM_VERSION))
+        info(' '.join(sys.argv[:]))
 
 
 def file_name(log_file, blast_db, query_file=''):

diff --git a/tests/lib/assemblers/test_base.py b/tests/lib/assemblers/test_base.py
@@ -275,7 +275,7 @@ def test_assembled_contigs_count_0(self, assembled_contigs_count, info):
             assembler.args['contig_length'])
 
         expect = ('No contigs had a bit score greater than {} and are at '
-                  'least {} long in iteration {}. The highest score for '
+                  'least {} bp long in iteration {}. The highest score for '
                   'this iteration is {}').format(
                       assembler.args['bit_score'],
                       assembler.args['contig_length'],