def write_align_makeflow(samples,genome_dir,makeflow,input_d,output_d):
if not os.path.exists(genome_dir):
print "%s dir not exists, please check!" %genome_dir
sys.exit(0)
gtf = glob.glob(os.path.join(genome_dir,"*.gtf"))[0]
fa = glob.glob(os.path.join(genome_dir,"*.fa"))[0]
if not fa or not gtf:
print "please check the fa and gtf file in %s" %genome_dir
sys.exists(0)
genome_prefix = os.path.splitext(fa)[0]
fo =open(makeflow,"a+")
fo.write("CATEGORY=Bowtie2-build\n")
fo.write("%s : %s\n"%(genome_dir+"/build-genome.log",fa))
fo.write("\t/lustre/work/yongdeng/software/protokaryon/soft/Align/bowtie2-2.3.3.1/bowtie2-build --threads 8 %s %s &> %s\n\n" %(fa,genome_prefix,genome_dir+"/build-genome.log"))
fo.write("CATEGORY=create_refFlat\n")
fo.write(gtf + ".refFlat : " + gtf + "\n")
fo.write("\tperl /lustre/work/yongdeng/software/protokaryon/soft/Align/create_refFlat.pl %s %s &> %s\n\n"%(gtf,gtf + ".refFlat",genome_dir+"/refflat.err"))
for sn in samples:
r1 = os.path.join(input_d,sn,"R1.clean.fq.gz")
r2 = os.path.join(input_d,sn,"R2.clean.fq.gz")
od = os.path.join(output_d,sn)
fo.write("CATEGORY=Bowtie2-align_%s\n"%sn)
fo.write(os.path.join(od,"bowtie.err ") + os.path.join(od,"accepted_hits.sam : ") + r1 + " " + r2 + " " + genome_dir + "/build-genome.log\n")
fo.write("@BATCH_OPTIONS = -l h_vmem=50G\n")
fo.write("\t/lustre/work/yongdeng/software/protokaryon/soft/Align/bowtie2-2.3.3.1/bowtie2 -p 8 -x %s -1 %s -2 %s -S %s "%(genome_prefix,r1,r2,os.path.join(od,"accepted_hits.sam")))
fo.write("> %s 2> %s\n\n" %(os.path.join(od,"bowtie.out"),os.path.join(od,"bowtie.err")))
fo.close()
def main():
if len(sys.argv) != 2:
print "We need ONE keyword to search!"
sys.exists(1)
#create a new folder and cd to it
path = r'/Users/yzhang250/Desktop/计算机学习/Staff/' + sys.argv[1]
if not os.path.exists(path):
os.makedirs(path)
os.chdir(path)
#scrolling the pages in search results
for page in range(1, 200):
#start to parse the search result of the key word----sys.argv[1]
url_kw = 'http://www.everyonepiano.cn/Music-search/?word=' + sys.argv[
1] + '&come=web&p=' + str(page)
r_kw = requests.get(url_kw)
soup_kw = BeautifulSoup(r_kw.content, 'lxml')
if soup_kw.find('span', {"class": "current"}).text != str(page):
break
else:
#list out all the musics from the key word and put into a list of links
tags = soup_kw.find_all("a",
{"class": "Title"}) # this find all the
links = []
for i in range(0, len(tags)):
links.append(tags[i].get('href'))
#get and print out the stave from EACH link in links list
for i in range(0, len(links)):
#get the soup_music, which is the page for each music
url_music = url_basic + links[i]
r_music = requests.get(url_music)
soup_music = BeautifulSoup(r_music.content, 'lxml')
num_match = re.search(
"\d+", str(soup_music.find("div",
{"class": "EOPRTRight"})))
if num_match != None:
music_num = num_match.group()
url_img = "http://www.everyonepiano.cn/Stave-" + music_num + ".html"
r_img = requests.get(url_img)
soup_img = BeautifulSoup(r_img.content, 'lxml')
# this is to determine the name of the music
name = soup_music.h1.text
if not os.path.exists(path + '/' + name.encode("utf8")):
os.makedirs(path + "/" + name.encode("utf8"))
os.chdir(path + "/" + name.encode("utf8"))
print_staff_from_soup_img(soup_img, name)
os.chdir(path)
else:
continue
def judgeImageExists(image):
i = 0
ok = "再找一次"
cancel = "中断程序"
while ai.locateOnScreen(image) == None:
i += 1
if i >= 10:
res = ai.confirm(text="找了%s次找到%s" % (i, image),
buttons=("%s" % ok, "%s" % cancel))
if res == ok:
continue
else:
sys.exists()
def run_remote_backup(config, connection):
day_cron = date.today().isoweekday()
for command in config['backup_command']:
cron = command[0].split(',')
if command:
logging.info('***Run remote commands')
try:
if str(day_cron) in cron:
logging.info('***Run cron %s command: %s' % (day_cron, command[1]))
stdin, stdout, stderr = connection.exec_command(command[1], bufsize=1024)
if stderr.read():
logging.error('***Error to run remote command: %s' % stderr.read())
if stdout.read():
logging.info("***Stdout: %s" % stdout.read())
except IOError:
logging.error('***Error to run remote command, system exist.')
try:
connection.close()
logging.info('***Disconnected.')
except:
pass
sys.exists()
def write_align_makeflow(samples, genome_dir, makeflow, input_d, output_d,
thread, strand):
gff2gtf = RNA.get_bin_abspath("gff2gtf.for.NCBIgff.pl")
build_index = RNA.get_soft_abspath("bowtie2-build")
bowtie = RNA.get_soft_abspath("bowtie2")
reflat = RNA.get_bin_abspath("create_refFlat.pl")
if not os.path.exists(genome_dir):
print "%s dir not exists, please check!" % genome_dir
sys.exit(0)
gtf = glob.glob(os.path.join(genome_dir, "*.gtf"))
gff = glob.glob(os.path.join(genome_dir, "*.gff"))
fa = glob.glob(os.path.join(genome_dir, "*.fa"))
if gtf and fa:
fa = fa[0]
gtf = gtf[0]
elif not gtf and gff and fa:
fa = fa[0]
gff = gff[0]
gtf = os.path.splitext(gff) + ".gtf"
fo.write('CATEGORY=gff2gtf\n')
fo.write(os.path.splitext(gff) + ".gtf : " + gff + "\n")
fo.write("\tperl %s %s %s &> %s\n\n" %
(gff2gtf, gff, gtf,
os.path.join(os.path.dirname(gff) + "gff2gtf.log")))
else:
print "Error: No gtf or gff file in %s dir" % genome_dir
sys.exit(1)
if not fa:
print "please check the fa and gtf file in %s" % genome_dir
sys.exists(1)
genome_prefix = os.path.splitext(fa)[0] + '.bowtie'
fo = open(makeflow, "a+")
if not os.path.exists(genome_dir + "/bowtie_build-genome.log"):
fo.write("CATEGORY=Bowtie2-build\n")
fo.write("%s : %s\n" % (genome_dir + "/bowtie_build-genome.log", fa))
fo.write("\t%s --threads %d %s %s &> %s\n\n" %
(build_index, thread, fa, genome_prefix,
genome_dir + "/bowtie_build-genome.log"))
if not os.path.exists(gtf + ".refFlat"):
fo.write("CATEGORY=create_refFlat\n")
fo.write(gtf + ".refFlat : " + gtf + "\n")
fo.write("\tperl %s %s %s &> %s\n\n" %
(reflat, gtf, gtf + ".refFlat", genome_dir + "/refflat.err"))
for sn in samples:
r1 = os.path.join(input_d, sn, "R1.clean.fq.gz")
r2 = os.path.join(input_d, sn, "R2.clean.fq.gz")
od = os.path.join(output_d, sn)
fo.write("CATEGORY=Bowtie2-align_%s\n" % sn)
fo.write(
os.path.join(od, "bowtie.err ") +
os.path.join(od, "accepted_hits.sam : ") + r1 + " " + r2 + " " +
genome_dir + "/bowtie_build-genome.log\n")
fo.write("@BATCH_OPTIONS = -l h_vmem=50G\n")
if strand:
fo.write("\t%s --ff -p %d -x %s -1 %s -2 %s -S %s " %
(bowtie, thread, genome_prefix, r1, r2,
os.path.join(od, "accepted_hits.sam")))
else:
fo.write("\t%s --fr -p %d -x %s -1 %s -2 %s -S %s " %
(bowtie, thread, genome_prefix, r1, r2,
os.path.join(od, "accepted_hits.sam")))
fo.write(
"> %s 2> %s\n\n" %
(os.path.join(od, "bowtie.out"), os.path.join(od, "bowtie.err")))
fo.close()
# write .ra2, .uv and .n file for each material
for m in mats:
if m.users == 0: continue
mfilename = m.name.replace("/", "_")
curr_mat = 0
for i in range(0, len(materials)):
if m.name == materials[i]:
curr_mat = mat_num[i]
# basefilename = filename[:-5] + "/" + sys.basename(filename)[:-5] + mfilename
basefilename = sys.dirname(filename) + "/" + mfilename
if not sys.exists(basefilename + ".ra2"):
# matfile.write(str(curr_mat) + ' ' + filename[:-5] + mfilename + '.ra2\n')
file_str.write(str(curr_mat) + ' ' + mfilename + '.ra2\n')
numObjects = numObjects + 1
# append the data to files
meshfile = open(basefilename + ".ra2", "ab")
normfile = open(basefilename + ".n", "ab")
uvfile = open(basefilename + ".uv", "ab")
for face in tmpMesh.faces:
if mats[face.mat] != m: continue
for lfn in range(2, len(face.v)):
for i in [0, lfn - 1, lfn]:
meshfile.write(
blank_rect = plt.bar(index + bar_width, blank_line, bar_width,
alpha=opacity,
color='r',
error_kw=error_config,
label='Blanklines')
plt.xlabel('Language')
plt.ylabel('Line')
plt.title('COUNTING_CODE')
plt.xticks(
index + bar_width, tuple(map(lambda s: s[1:], CODE_FILE_SUFFIXES)))
plt.legend()
plt.tight_layout()
plt.show()
os.chdir(args.directory)
counting_code()
if args.graphic:
try:
import numpy as np
import matplotlib.pyplot as plt
except ImportError:
print "numpy or matplotlib may not be installed! cannot use -g argument"
sys.exists()
paint_chart()
else:
print detail