Cleanup code after flake8.

workflow/scripts/check_design.py

@@ -11,7 +11,7 @@ For more details:
         %(prog)s --help
 '''
 
-## SETTINGS
+# SETTINGS
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
@@ -57,7 +57,7 @@ def check_design_headers(design, paired):
 
     design_headers = list(design.columns.values)
 
-    if paired: # paired-end data
+    if paired:  # paired-end data
         design_template.extend(['fastq_read2'])
 
     # Check if headers
@@ -79,7 +79,8 @@ def check_controls(design):
 
     if len(missing_controls) > 0:
         logger.error('Missing control experiments: %s', list(missing_controls))
-        raise Exception("Missing control experiments: %s" % list(missing_controls))
+        raise Exception("Missing control experiments: %s" %
+                        list(missing_controls))
 
 
 def check_files(design, fastq, paired):
@@ -87,9 +88,9 @@ def check_files(design, fastq, paired):
 
     logger.info("Running file check.")
 
-    if paired: # paired-end data
+    if paired:  # paired-end data
         files = list(design['fastq_read1']) + list(design['fastq_read2'])
-    else: # single-end data
+    else:  # single-end data
         files = design['fastq_read1']
 
     files_found = fastq['name']
@@ -98,13 +99,14 @@ def check_files(design, fastq, paired):
 
     if len(missing_files) > 0:
         logger.error('Missing files from design file: %s', list(missing_files))
-        raise Exception("Missing files from design file: %s" % list(missing_files))
+        raise Exception("Missing files from design file: %s" %
+                        list(missing_files))
     else:
         file_dict = fastq.set_index('name').T.to_dict()
 
         design['fastq_read1'] = design['fastq_read1'] \
                                 .apply(lambda x: file_dict[x]['path'])
-        if paired: # paired-end data
+        if paired:  # paired-end data
             design['fastq_read2'] = design['fastq_read2'] \
                                     .apply(lambda x: file_dict[x]['path'])
     return design

workflow/scripts/map_reads.py

@@ -8,7 +8,6 @@ import argparse
 import shutil
 import shlex
 import logging
-import sys
 from multiprocessing import cpu_count
 import json
 import utils
@@ -18,7 +17,7 @@ For more details:
         %(prog)s --help
 '''
 
-## SETTINGS
+# SETTINGS
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
@@ -56,8 +55,7 @@ def get_args():
     return args
 
 
-
-## Functions
+# Functions
 
 
 def check_tools():
@@ -102,7 +100,6 @@ def generate_sa(fastq, reference):
 def align_se(fastq, sai, reference, fastq_basename):
     '''Use BWA to align SE data.'''
 
-    sam_filename = "%s.sam" % (fastq_basename)
     bam_filename = '%s.srt.bam' % (fastq_basename)
 
     steps = [
@@ -118,6 +115,7 @@ def align_se(fastq, sai, reference, fastq_basename):
 
     return bam_filename
 
+
 def align_pe(fastq, sai, reference, fastq_basename):
     '''Use BWA to align PE data.'''
 
@@ -173,7 +171,7 @@ def main():
         sai.append(sai_filename)
 
     # Run alignment for either PE or SE
-    if paired: # paired-end data
+    if paired:  # paired-end data
         fastq_r1_basename = os.path.basename(
             utils.strip_extensions(fastq[0], STRIP_EXTENSIONS))
         fastq_r2_basename = os.path.basename(

workflow/scripts/trim_reads.py

@@ -2,19 +2,17 @@
 
 '''Trim low quality reads and remove sequences less than 35 base pairs.'''
 
-import os
 import subprocess
 import argparse
 import shutil
 import logging
-import sys
 
 EPILOG = '''
 For more details:
         %(prog)s --help
 '''
 
-## SETTINGS
+# SETTINGS
 
 logger = logging.getLogger(__name__)
 logger.addHandler(logging.NullHandler())
@@ -65,7 +63,7 @@ def check_tools():
 def trim_reads(fastq, paired):
     '''Run trim_galore on 1 or 2 files.'''
 
-    if paired: # paired-end data
+    if paired:  # paired-end data
         trim_params = '--paired -q 25 --illumina --gzip --length 35'
         trim_command = "trim_galore %s %s %s " \
                     % (trim_params, fastq[0], fastq[1])

workflow/scripts/utils.py

@@ -3,9 +3,6 @@
 '''General utilities.'''
 
 
-import sys
-import os
-import subprocess
 import shlex
 import logging
 

workflow/tests/test_check_design.py

 #!/usr/bin/env python3
 
-import os
 import pytest
 import pandas as pd
 from io import StringIO
 import check_design
-import sys
 
 
 DESIGN_STRING = """sample_id\tbiosample\tfactor\ttreatment\treplicate\tcontrol_id\tfastq_read1
@@ -49,11 +47,12 @@ def design_2(design):
     design_df = design.drop(design.index[2])
     return design_df
 
+
 @pytest.fixture
 def design_3(design):
     # Drop A_2 and B_2 and append as fastq_read2
-    design_df = design.drop(design.index[[1,3]])
-    design_df['fastq_read2'] = design.loc[[1,3],'fastq_read1'].values
+    design_df = design.drop(design.index[[1, 3]])
+    design_df['fastq_read2'] = design.loc[[1, 3], 'fastq_read1'].values
     return design_df
 
 
@@ -94,10 +93,10 @@ def test_check_files_missing_files(design, fastq_files_1):
 def test_check_files_output_singleend(design, fastq_files):
     paired = False
     new_design = check_design.check_files(design, fastq_files, paired)
-    assert new_design.loc[0,'fastq_read1'] == "/path/to/file/A_1.fastq.gz"
+    assert new_design.loc[0, 'fastq_read1'] == "/path/to/file/A_1.fastq.gz"
 
 
 def test_check_files_output_pairedend(design_3, fastq_files):
     paired = True
     new_design = check_design.check_files(design_3, fastq_files, paired)
-    assert new_design.loc[0,'fastq_read2'] == "/path/to/file/A_2.fastq.gz"
+    assert new_design.loc[0, 'fastq_read2'] == "/path/to/file/A_2.fastq.gz"

workflow/tests/test_utils.py

 #!/usr/bin/env python3
 
 import pytest
-import shutil
-import shlex
 import utils
 
 
 STRIP_EXTENSIONS = ['.gz', '.fq', '.fastq', '.fa', '.fasta']
 
+
 @pytest.fixture
 def steps():
     steps = []
@@ -56,15 +55,15 @@ def test_run_last_step_file(steps_2, capsys, tmpdir):
 
 
 def test_strip_extensions():
-    filename = utils.strip_extensions('ENCFF833BLU.fastq.gz',STRIP_EXTENSIONS)
+    filename = utils.strip_extensions('ENCFF833BLU.fastq.gz', STRIP_EXTENSIONS)
     assert filename == 'ENCFF833BLU'
 
 
 def test_strip_extensions_not_valid():
-    filename = utils.strip_extensions('ENCFF833BLU.not.valid',STRIP_EXTENSIONS)
+    filename = utils.strip_extensions('ENCFF833BLU.not.valid', STRIP_EXTENSIONS)
     assert filename == 'ENCFF833BLU.not.valid'
 
 
 def test_strip_extensions_missing_basename():
-    filename = utils.strip_extensions('.fastq.gz',STRIP_EXTENSIONS)
+    filename = utils.strip_extensions('.fastq.gz', STRIP_EXTENSIONS)
     assert filename == '.fastq'