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Cezar77 test scripts indentation #36

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Cezar77 test scripts indentation #36

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fe35cfb
Update test_checkm.py
cezar77 Jun 18, 2021
1aac9e0
Update test_checkm_plus.py
cezar77 Jun 18, 2021
6bfbebd
Merge pull request #3 from cezar77/cezar77-test_scripts_indentation-1
cezar77 Jun 18, 2021
a5dcd66
Update test_diamond.py
cezar77 Jun 18, 2021
0e10ece
Update test_checkm.py
cezar77 Jun 18, 2021
dd3c24c
Update test_checkm_plus.py
cezar77 Jun 18, 2021
242c685
Update test_diamond_bin_summary_plus.py
cezar77 Jun 18, 2021
c287113
Update test_diamond_report.py
cezar77 Jun 18, 2021
a78932d
Update test_pfam_scan.py
cezar77 Jun 18, 2021
7825151
Update test_phylophlan.py
cezar77 Jun 18, 2021
8888372
Update test_prodigal.py
cezar77 Jun 18, 2021
238d128
Update test_sourmash.py
cezar77 Jun 18, 2021
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46 changes: 22 additions & 24 deletions test/scripts/test_checkm.py
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -7,45 +7,43 @@
import errno

if len(sys.argv) == 1:
print "Please provide a filename"
sys.exit()
print "Please provide a filename"
sys.exit()

# output file
outfile = sys.argv[1]

if not os.path.dirname(outfile) == '':
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise

f = open(outfile, 'w+')

# try to run checkM
try:
p1 = subprocess.Popen(['checkm'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p1 = subprocess.Popen(['checkm'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

# Run the command
checkm = p1.communicate()
output = checkm[0]
error = checkm[1]
# Run the command
checkm = p1.communicate()
output = checkm[0]
error = checkm[1]
except OSError as o:
f.write('OSError: make sure checkM is installed properly' + '\n')
f.close()
sys.exit()
f.write('OSError: make sure checkM is installed properly' + '\n')
f.close()
sys.exit()
except:
f.write('Unexpected error: unable to run checkM' + '\n')
f.close()
sys.exit()
f.write('Unexpected error: unable to run checkM' + '\n')
f.close()
sys.exit()

# if we're still here, check error and print
if error == '':
f.write('CheckM ran without problems' + '\n')
else :
f.write('CheckM ran with some errors: ' + error + '\n')
f.write('CheckM ran without problems' + '\n')
else:
f.write('CheckM ran with some errors: ' + error + '\n')

f.close()


45 changes: 21 additions & 24 deletions test/scripts/test_checkm_plus.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,46 +7,43 @@
import errno

if len(sys.argv) == 1:
print("Please provide a filename")
sys.exit()
print("Please provide a filename")
sys.exit()

# output file
outfile = sys.argv[1]

if not os.path.dirname(outfile) == '':
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise

f = open(outfile, 'w+')

# try to run add_tax.py
try:
p1 = subprocess.Popen(['scripts/add_tax.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p1 = subprocess.Popen(['scripts/add_tax.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

# Run the command
addtax = p1.communicate()
output = addtax[0]
error = addtax[1]
# Run the command
addtax = p1.communicate()
output = addtax[0]
error = addtax[1]
except OSError as o:
f.write('OSError: is scripts/add_tax.py in your PATH?' + '\n')
f.close()
sys.exit()
f.write('OSError: is scripts/add_tax.py in your PATH?' + '\n')
f.close()
sys.exit()
except:
f.write('Unexpected error: unable to run scripts/add_tax.py' + '\n')
f.close()
sys.exit()
f.write('Unexpected error: unable to run scripts/add_tax.py' + '\n')
f.close()
sys.exit()

# if we're still here, check error and print
if error.decode(sys.stdout.encoding) == '':
f.write('scripts/add_tax.py ran without problems' + '\n')
f.write('scripts/add_tax.py ran without problems' + '\n')
else:
f.write('scripts/add_tax.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
f.write('scripts/add_tax.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')


f.close()


47 changes: 22 additions & 25 deletions test/scripts/test_diamond.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,46 +7,43 @@
import errno

if len(sys.argv) == 1:
print("Please provide a filename")
sys.exit()
print("Please provide a filename")
sys.exit()

# output file
outfile = sys.argv[1]

if not os.path.dirname(outfile) == '':
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise

f = open(outfile, 'w+')

# try to run checkM
try:
p1 = subprocess.Popen(['diamond','help'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p1 = subprocess.Popen(['diamond','help'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

# Run the command
allout = p1.communicate()
output = allout[0]
error = allout[1]
# Run the command
allout = p1.communicate()
output = allout[0]
error = allout[1]
except OSError as o:
f.write('OSError: make sure DIAMOND is installed properly' + '\n')
f.close()
sys.exit()
f.write('OSError: make sure DIAMOND is installed properly' + '\n')
f.close()
sys.exit()
except:
f.write('Unexpected error: unable to run DIAMOND' + '\n')
f.close()
sys.exit()
f.write('Unexpected error: unable to run DIAMOND' + '\n')
f.close()
sys.exit()

# if we're still here, check error and print
if error.decode(sys.stdout.encoding) == '':
f.write('DIAMOND ran without problems' + '\n')
else :
f.write('DIAMOND ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
f.write('DIAMOND ran without problems' + '\n')
else:
f.write('DIAMOND ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')


f.close()


46 changes: 22 additions & 24 deletions test/scripts/test_diamond_bin_summary_plus.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,45 +7,43 @@
import errno

if len(sys.argv) == 1:
print("Please provide a filename")
sys.exit()
print("Please provide a filename")
sys.exit()

# output file
outfile = sys.argv[1]

if not os.path.dirname(outfile) == '':
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise

f = open(outfile, 'w+')

# try to run checkM
try:
p1 = subprocess.Popen(['scripts/add_tax_diamond.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p1 = subprocess.Popen(['scripts/add_tax_diamond.py'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

# Run the command
allout = p1.communicate()
output = allout[0]
error = allout[1]
# Run the command
allout = p1.communicate()
output = allout[0]
error = allout[1]
except OSError as o:
f.write('OSError: is scripts/add_tax_diamond.py in your PATH?' + '\n')
f.close()
sys.exit()
f.write('OSError: is scripts/add_tax_diamond.py in your PATH?' + '\n')
f.close()
sys.exit()
except:
f.write('Unexpected error: unable to run scripts/add_tax_diamond.py' + '\n')
f.close()
sys.exit()
f.write('Unexpected error: unable to run scripts/add_tax_diamond.py' + '\n')
f.close()
sys.exit()

# if we're still here, check error and print
if error.decode(sys.stdout.encoding) == '':
f.write('scripts/add_tax_diamond.py ran without problems' + '\n')
else :
f.write('scripts/add_tax_diamond.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')
f.write('scripts/add_tax_diamond.py ran without problems' + '\n')
else:
f.write('scripts/add_tax_diamond.py ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')

f.close()


48 changes: 23 additions & 25 deletions test/scripts/test_diamond_report.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,45 +7,43 @@
import errno

if len(sys.argv) == 1:
print("Please provide a filename")
sys.exit()
print("Please provide a filename")
sys.exit()

# output file
outfile = sys.argv[1]

if not os.path.dirname(outfile) == '':
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
if not os.path.exists(os.path.dirname(outfile)):
try:
os.makedirs(os.path.dirname(outfile))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise

f = open(outfile, 'w+')

# try to run checkM
try:
p1 = subprocess.Popen(['scripts/diamond_report.pl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
p1 = subprocess.Popen(['scripts/diamond_report.pl'], stdout=subprocess.PIPE, stderr=subprocess.PIPE)

# Run the command
allout = p1.communicate()
output = allout[0]
error = allout[1]
# Run the command
allout = p1.communicate()
output = allout[0]
error = allout[1]
except OSError as o:
f.write('OSError: is scripts/diamond_report.pl in your PATH?' + '\n')
f.close()
sys.exit()
f.write('OSError: is scripts/diamond_report.pl in your PATH?' + '\n')
f.close()
sys.exit()
except:
f.write('Unexpected error: unable to run scripts/diamond_report.pl - is BioPerl installed?' + '\n')
f.close()
sys.exit()
f.write('Unexpected error: unable to run scripts/diamond_report.pl - is BioPerl installed?' + '\n')
f.close()
sys.exit()

# if we're still here, check error and print
if error.decode(sys.stdout.encoding) == '':
f.write('scripts/diamond_report.pl ran without problems' + '\n')
else :
f.write('scripts/diamond_report.pl ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')

f.close()

f.write('scripts/diamond_report.pl ran without problems' + '\n')
else:
f.write('scripts/diamond_report.pl ran with some errors: ' + error.decode(sys.stdout.encoding) + '\n')

f.close()
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