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Python 3 compatibility #12

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f722e66
Converting print statements to Python 3 standard
villegar Dec 20, 2019
a517f42
Fixing error with tab
villegar Dec 20, 2019
52237e4
Fixing error with missing indentation
villegar Dec 20, 2019
353dd14
Fixing error with tab
villegar Dec 20, 2019
5a6a216
Fixing error with tab
villegar Dec 20, 2019
9f02f92
Fixing get_flash_stats function
villegar Dec 20, 2019
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53 changes: 27 additions & 26 deletions lmp_processing
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Original file line number Diff line number Diff line change
Expand Up @@ -65,8 +65,8 @@ def get_flash_stats(lib_prefix):
flash_text, err = p.communicate()
if p.returncode != 0:
raise IOError(err)

f_fields = flash_text.replace("[FLASH]", "").split("\n")
f_fields = str(flash_text).replace("[FLASH]", "").split("\\n")

with open(dedup_log, 'r') as f:
lines = f.readlines()
Expand Down Expand Up @@ -97,21 +97,21 @@ def get_nextclip_stats(lib_prefix):
if __name__ == '__main__':

if len(sys.argv) != 3 or sys.argv[1] == "--help":
print "\n#### w2rap LMP processing ####\n"
print "Usage: {0} libs_list ncpus\n".format(sys.argv[0])
print "libs_list is a text file containing a list of your FASTQ LMP read files, eg.\n" \
print("\n#### w2rap LMP processing ####\n")
print("Usage: {0} libs_list ncpus\n".format(sys.argv[0]))
print("libs_list is a text file containing a list of your FASTQ LMP read files, eg.\n" \
"/path/to/LIB1_R1.fastq\n/path/to/LIB1_R2.fastq\n/path/to/LIB2_R1.fastq\n/path/to/LIB2_R2.fastq\n\n" \
"FASTQ read files must be uncompressed and end in _R1.fastq or _R2.fastq\n"
"FASTQ read files must be uncompressed and end in _R1.fastq or _R2.fastq\n")
sys.exit()

libs_list = sys.argv[1]
ncpus = sys.argv[2]

print "\n#### w2rap LMP processing ####\n"
print("\n#### w2rap LMP processing ####\n")

# can we find the input file and does it look ok
if not os.path.exists(libs_list):
print "Cannot find libraries file {0}.\n".format(libs_list)
print("Cannot find libraries file {0}.\n".format(libs_list))
sys.exit()

# get the directory where this script is running
Expand All @@ -126,30 +126,30 @@ if __name__ == '__main__':
# read env var and add to path
bin_dir = os.environ['W2RAP_PATH']
if bin_dir == None:
print "No path to binaries, please set W2RAP_PATH environment variable"
print("No path to binaries, please set W2RAP_PATH environment variable")
sys.exit()
else:
os.environ["PATH"] += os.pathsep + bin_dir

# check the required executables exist in the path
FLASH_PATH = which("flash")
if FLASH_PATH == None:
print "ERROR: Cannot find FLASH in PATH.\n"
print("ERROR: Cannot find FLASH in PATH.\n")
sys.exit()

DEDUP_PATH = which("dedup_fastq")
if DEDUP_PATH == None:
print "ERROR: Cannot find dedup_fastq in PATH.\n"
print("ERROR: Cannot find dedup_fastq in PATH.\n")
sys.exit()

NXCLIP_PATH = which("nextclip")
if NXCLIP_PATH == None:
print "ERROR: Cannot find Nextclip in PATH.\n"
print("ERROR: Cannot find Nextclip in PATH.\n")
sys.exit()

print "FLASH found: {0}".format(FLASH_PATH)
print "dedup_fastq found: {0}".format(DEDUP_PATH)
print "Nextclip found: {0}".format(NXCLIP_PATH)
print("FLASH found: {0}".format(FLASH_PATH))
print("dedup_fastq found: {0}".format(DEDUP_PATH))
print("Nextclip found: {0}".format(NXCLIP_PATH))

cwd = os.getcwd()

Expand All @@ -162,15 +162,15 @@ if __name__ == '__main__':
r1 = os.path.abspath(r1_in)
r2 = os.path.abspath(r2_in)
if r1 == r2:
print "Read 1 and read 2 files are the same - {0}.".format(r1)
print("Read 1 and read 2 files are the same - {0}.".format(r1))
sys.exit()

if not os.path.exists(r1):
print "Read file {0} does not exist.".format(r1)
print("Read file {0} does not exist.".format(r1))
sys.exit()

if not os.path.exists(r2):
print "Read file {0} does not exist.".format(r2)
print("Read file {0} does not exist.".format(r2))
sys.exit()

# get the read length from r1 (required for flash)
Expand All @@ -183,16 +183,17 @@ if __name__ == '__main__':

# get the library prefix
base=os.path.basename(r1)
prefix = os.path.splitext(base)[0].replace("_R1", "")
prefix = os.path.splitext(base)[0].replace("_R1", "")

libraries.append({"r1": r1, "r2": r2, "read_length": read_length, "prefix": prefix})
else: break # EOF

print "Number of libraries to process: {0}".format(len(libraries))
print("Number of libraries to process: {0}".format(len(libraries)))
for lib in libraries:
print lib["r1"], lib["r2"]
print(lib["r1"])
print(lib["r2"])

print "\nRunning FLASH and de-duplicating combined reads..."
print("\nRunning FLASH and de-duplicating combined reads...")
if not os.path.exists("flash"):
os.makedirs("flash")

Expand Down Expand Up @@ -226,9 +227,9 @@ if __name__ == '__main__':

# for each library, get the stats from flash and dedup
for lib in libraries:
print get_flash_stats(lib["prefix"])
print(get_flash_stats(lib["prefix"]))

print "Running Nextclip..."
print("Running Nextclip...")
if not os.path.exists("nextclip"):
os.makedirs("nextclip")

Expand Down Expand Up @@ -273,7 +274,7 @@ if __name__ == '__main__':
os.chdir(cwd)

for lib in libraries:
print get_nextclip_stats(lib["prefix"])
print(get_nextclip_stats(lib["prefix"]))

# get rid of the temporary flash dir and extra bits in the nextclip dir
shutil.rmtree(os.path.join(cwd, "flash"))
Expand All @@ -282,4 +283,4 @@ if __name__ == '__main__':
for lib in libraries:
os.remove(os.path.join(cwd, "nextclip", "{0}.nc_counts".format(lib["prefix"])))

print "DONE."
print("DONE.")