def get_args():
global fi
global prop
global misc
global properties_file
global genome_name
fi = fileutils()
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='Script downloading genome files')
parser.add_argument('-p',
'--properties_file',
type=str,
help='''Please provide the properties file,
which including workdir''',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which is provided by genome_list.txt''',
required=True)
args = parser.parse_args()
# check args
fi.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
misc = misc()
misc.check_genome_avl(prop.get_attrib("available_genomes"),
args.genome_name)
# define variables
genome_name = args.genome_name
print("properties_file:", properties_file)
print("genome_name:", genome_name)
def get_args():
global prop
global properties_file
global prefix
global fi
fi = fileutils()
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='''Script creates multiQC html file using fastqc,
bcftools, snpEff, QUAST, and QualiMap
output files''')
parser.add_argument(
'-p',
'--properties_file',
type=str,
help=
'Please provide the properties file, which including the paths of workdir',
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file',
required=True)
# check args
args = parser.parse_args()
fi.check_exist(args.properties_file)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
prefix = args.prefix
print("properties_file:", str(properties_file))
print("prefix:", prefix)
def get_args():
global properties_file
global genome
global prefix
global vcf_file_pattern
global prop
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'''Script invests genes under selection pressure within species through dNdS.
Species can be chosen from genome_list.txt''')
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument(
'-g',
'--genome_name',
type=str,
help=
'''Please provide the genome name, only with those obtained from genome_list.txt''',
required=True)
parser.add_argument(
'-f',
'--vcf_file_pattern',
type=str,
help="Please provide snp vcf files' pattern with full file path",
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
fi = fileutils()
fi.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name not in (
line.rstrip()
for line in open(prop.get_attrib("available_genomes")).readlines()
) and args.genome_name != "cryptosporidium_hominis":
misc.my_exit("{} is not available, please try another genome".format(
args.genome_name))
if not re.search(".vcf", args.vcf_file_pattern):
misc.my_exit("vcf_file_pattern need to end up with .vcf")
genome = args.genome_name
vcf_file_pattern = args.vcf_file_pattern
prefix = args.prefix
print "properties_file:", properties_file
print "genome:", genome
print "vcf_file_pattern:", vcf_file_pattern
print "prefix:", prefix
def get_args():
global fi
global prop
global properties_file
global genome_name
global bam_file_pattern
global bam_files
global mapping_file
global prefix
global bam_key_pattern
# Assign description to the help doc
parser = argparse.ArgumentParser(description='Script build all individual chromosome multiple alignment for recombination')
parser.add_argument('-p', '--properties_file', type=str, help='Please provide the properties file.',
required=True)
parser.add_argument('-g', '--genome_name', type=str, help='''Please provide the genome name available
in genome_list.txt only''',
required=True)
parser.add_argument('-bp', '--bam_file_pattern', type=str, help='''Please provide the bam files' pattern
with the full path, ending with .bam, with runID
in the bam file name''',
required=True)
parser.add_argument('-m', '--mapping_file', type=str, help='''Please provide the mapping file path, containing one
column of the runID and the other column is the expression
displayed in the multiple alignment file description line''',
required=False)
parser.add_argument('-pre', '--prefix', type=str, help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
fi=fileutils()
fi.check_exist(args.properties_file)
properties_file=args.properties_file
prop=properties(properties_file)
if args.genome_name not in (line.rstrip() for line in open(prop.get_attrib("available_genomes")).readlines()):
misc.my_exit("{} is not available, please try another genome".format(args.genome_name))
if not re.search(".bam$",args.bam_file_pattern):
misc.my_exit("bam_file_pattern need to end up with .bam")
bam_file_pattern=args.bam_file_pattern
bam_files=glob.glob(bam_file_pattern)
bam_key_pattern="[A-Z]RR\d{6,}"
for bam_file in bam_files:
if not re.search(bam_key_pattern, bam_file):
misc.my_exit("There is no runID in the bam file {}".format(bam_file))
fi.check_files_exist(bam_files)
# define variables
genome_name=args.genome_name
mapping_file=args.mapping_file
prefix=args.prefix
print ("properties_file:",properties_file)
print ("genome_name:",genome_name)
print ("bam_file_pattern:",bam_file_pattern)
print ("mapping_file:",mapping_file)
print ("prefix:",prefix)
def __init__(self, properties_file, genome_name, genome_fasta, bam_file,
prefix, if_anno, subdir):
self.properties_file = properties_file
self.prop = properties(properties_file)
self.genome_name = genome_name
self.genome_fasta = genome_fasta
self.bam_file = bam_file
self.prefix = prefix
self.if_anno = if_anno
self.subdir = subdir
self.fi = fileutils()
def get_args():
global properties_file
global genome_name
global prefix
global vcf_file_pattern
global go_file
global mapping_file
global prop
# Assign description to the help doc
parser = argparse.ArgumentParser(description='''Script invests genes under selection pressure within
species through dNdS. It creates variation annotation
file for each SNP vcf file, and gene variation annotation
summary file based on all vcf files by using snpEff''')
parser.add_argument('-p', '--properties_file', type=str, help='Please provide the properties file.',
required=True)
parser.add_argument('-g', '--genome_name', type=str, help='''Please provide the genome name, only with those obtained from genome_list.txt''',
required=True)
parser.add_argument('-vp', '--vcf_file_pattern', type=str, help="Please provide snp vcf files' pattern with full file path",
required=True)
parser.add_argument('-go', '--go_file', type=str, help="Please provide the full path of the gene ontology file",
required=True)
parser.add_argument('-m', '--mapping_file', type=str, help='''Please provide the mapping file path, which contains one column of
read_ID from vcf file and one column of its corresponding sample_name''',
required=False)
parser.add_argument('-pre', '--prefix', type=str,help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
FI.check_exist(args.properties_file)
properties_file=args.properties_file
prop=properties(properties_file)
if args.genome_name not in (line.rstrip() for line in open(prop.get_attrib("available_genomes")).readlines()):
MISC.my_exit("{} is not available, please try another genome".format(args.genome_name))
if not re.search(".vcf$",args.vcf_file_pattern):
MISC.my_exit("vcf_file_pattern need to end up with .vcf")
FI.check_exist(args.go_file)
go_file=args.go_file
genome_name=args.genome_name
vcf_file_pattern=args.vcf_file_pattern
prefix=args.prefix
mapping_file=args.mapping_file
print ("properties_file:",properties_file)
print ("genome_name:",genome_name)
print ("vcf_file_pattern:",vcf_file_pattern)
print ("go_file:",go_file)
print ("mapping_file:",mapping_file)
print ("prefix:",prefix)
def get_args():
global properties_file
global g_names_str
global fi
global prop
global min_homo
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'Script invests genes under selection pressure among multiple species through dNdS'
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument(
'-g',
'--genome_names',
type=str,
help='''Please provide the genome names, seperating by ","
with the format of XXX, YYY, ZZZ''',
required=True)
parser.add_argument(
'-min',
'--min_homo',
type=int,
help=
'''Please provide the minimum poteintial homologue numbers in one group,
if not defined, 4 will be used as the default''',
required=False)
# check args
args = parser.parse_args()
fi = fileutils()
fi.check_exist(args.properties_file)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
g_names_str = args.genome_names
if args.min_homo is None:
min_homo = 4
else:
min_homo = args.min_homo
print "properties_file:", properties_file
print "gnames:", g_names_str
print "min_homo:", str(min_homo)
def get_args():
global fi
global prop
global properties_file
global genome_fasta
global bam_file_pattern
global bam_request_pattern
global bam_files
global map_fpath
global map_dict
global prefix
# Assign description to the help doc
parser = argparse.ArgumentParser(description='''Script creating relocation files for multiple bam files from
various genomes and automatically open the GUI''')
parser.add_argument('-p', '--properties_file', type=str, help='Please provide the properties file.', required=True)
parser.add_argument('-m', '--map_file', type=str, help='''Please provide the map file,
in which the first column is the full path of the genome fasta file and the second column is
the full path of the bam file and the bam files need to ended with .bam''', required=True)
parser.add_argument('-pre', '--prefix', type=str, help='Please provide the prefix for the output file.', required=True)
# check args
args = parser.parse_args()
fi=fileutils()
fi.check_files_exist([args.properties_file,args.map_file])
# define variables
properties_file=args.properties_file
prop=properties(properties_file)
map_fpath=args.map_file
fh_map=open(map_fpath, "r")
map_dict={}
for line in fh_map:
line=line.rstrip()
(fasta_fpath,bam_fpath)=getVar(line.split(),[0,1])
fi.check_files_exist([fasta_fpath,bam_fpath])
map_dict[bam_fpath]=fasta_fpath
prefix=args.prefix
print "properties_file:",properties_file
print "map_file:",map_fpath
print "prefix:",prefix
def get_args():
global fi
global prop
global properties_file
global genome_name
global vcf_file_pattern
global vcf_files
global mapping_file
global image_title
global prefix
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'Script build phylogenetic tree and dendragram for the defined group of vcf files from the same genome'
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument(
'-g',
'--genome_name',
type=str,
help=
'''Please provide the genome name, only with those obtained from genome_list.txt''',
required=True)
parser.add_argument(
'-v',
'--vcf_file_pattern',
type=str,
help='''Please provide the vcf files' pattern with the full path,
vcf files must ended with ".vcf" ''',
required=True)
parser.add_argument(
'-m',
'--mapping_file',
type=str,
help=
'''Please provide the mapping file path, which contains one column of
read_ID from vcf file and one column of its corresponding label on the tree branch,
otherwise, the read_ID will be labeled on the tree branch''',
required=False)
parser.add_argument('-t',
'--title',
type=str,
help='''Please provide the title of the image''',
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
fi = fileutils()
fi.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name not in (
line.rstrip()
for line in open(prop.get_attrib("available_genomes")).readlines()
) and args.genome_name != "cryptosporidium_hominis":
misc.my_exit("{} is not available, please try another genome".format(
args.genome_name))
if not re.search(".vcf$", args.vcf_file_pattern):
misc.my_exit("vcf_file_pattern need to end up with .vcf")
vcf_file_pattern = args.vcf_file_pattern
vcf_files = glob.glob(vcf_file_pattern)
fi.check_files_exist(vcf_files)
# define variables
genome_name = args.genome_name
mapping_file = args.mapping_file
image_title = args.title
prefix = args.prefix
print "properties_file:", properties_file
print "genome_name:", genome_name
print "vcf_file_pattern:", vcf_file_pattern
print "mapping_file:", mapping_file
print "title:", image_title
print "prefix:", prefix
def get_args():
global properties_file
global genome_name
global vcf_file_pattern
global mapping_file
global prefix
global prop
global vcf_files
global vcf_request_pattern
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='''Script creates the genome Short Tandem Repeat (STR)
variation summary file based on all vcf files and
multiple alignment files for all repeat regions'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name available in
genome_list.txt only or cryptosporidium_hominis''',
required=False)
parser.add_argument('-vp',
'--vcf_file_pattern',
type=str,
help='''Please provide the paired vcf files' pattern
with the full path, must end with .vcf''',
required=True)
parser.add_argument('-m',
'--mapping_file',
type=str,
help='''Please provide the mapping file path, which
contains one column of read_ID from vcf file
and one column of its corresponding sample_name''',
required=False)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
FI.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name not in (line.rstrip() for line in open(
prop.get_attrib("available_genomes")).readlines()):
MISC.my_exit("{} is not available, please try another genome".format(
args.genome_name))
vcf_files = glob.glob(args.vcf_file_pattern)
if len(vcf_files) == 0:
sys.exit("ERROR: no vcf files provided")
vcf_request_pattern = "^.*/?(.*?).vcf$"
for vcf_file in vcf_files:
if not re.search(vcf_request_pattern, vcf_file):
sys.exit("vcf_file not end with .vcf")
FI.check_files_exist(vcf_files)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
genome_name = args.genome_name
vcf_file_pattern = args.vcf_file_pattern
prefix = args.prefix
mapping_file = args.mapping_file
print("properties_file:", properties_file)
print("genome_name:", genome_name)
print("vcf_file_pattern:", vcf_file_pattern)
print("mapping_file:", mapping_file)
print("prefix:", prefix)
def get_args():
global properties_file
global prop
global genome_name
global fastq1
global fastq2
global prefix_ori
global runID
global mapping_file
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='''Script assembles short reads by using spades and
provides statistics summary based on the result assemblies
by using QUAST''')
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which need to be in genome_list.txt''',
required=True)
parser.add_argument('-fq1',
'--fastq1',
type=str,
help='Please provide the forward fastq file',
required=True)
parser.add_argument('-fq2',
'--fastq2',
type=str,
help='Please provide the reverse fastq file',
required=False)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file',
required=True)
parser.add_argument(
'-m',
'--mapping_file',
type=str,
help='''if map file was provided, whose first column is runID
and the second column is sample name, seperated by "\t",
sample name will be included in the output files' names''',
required=False)
# check args
args = parser.parse_args()
FI.check_files_exist([args.properties_file, args.fastq1])
properties_file = args.properties_file
prop = properties(properties_file)
MISC.check_genome_avl(prop.get_attrib("available_genomes"),
args.genome_name)
runID = MISC.get_runID(args.fastq1)
if args.fastq2 is not None:
FI.check_exist(args.fastq2)
MISC.get_runID(args.fastq2)
if args.mapping_file is not None:
FI.check_exist(args.mapping_file)
# define variables
genome_name = args.genome_name
fastq1 = args.fastq1
fastq2 = args.fastq2
prefix_ori = args.prefix
mapping_file = args.mapping_file
print("properties_file:", properties_file)
print("genome_name:", genome_name)
print("fastq1:", fastq1)
print("fastq2:", fastq2)
print("prefix:", prefix_ori)
print("mapping_file:", mapping_file)
def post_process():
print("post_processing...")
for out_file in out_pdf_files:
FI.copy_file_to_destdir(out_file, outdir)
if __name__ == '__main__':
global prop
global FI
global MISC
FI = fileutils()
MISC = misc()
get_args()
prop = properties(PROPERTIES_FILE)
getVar = lambda searchList, ind: [searchList[i] for i in ind]
print("\n", "Properties attributes:")
print(prop.__dict__)
#run the initiation code
initiate()
#execute the main part of the program
execute()
#post execution code
post_process()
print(os.path.realpath(__file__) + " DONE")
def get_args():
global properties_file
global genome
global prefix
global vcf_file_pattern
global prop
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'''Script invests genes under selection pressure within species through dNdS.
Species can be chosen from -genome_list, which including 17 genomes. They are the common genomes of protists parasite and existing in snpEff'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument('-genome_list',
'--genome_list',
help="This will display the genome name list",
action="store_true")
parser.add_argument(
'-g',
'--genome_name',
type=str,
help=
'''Please provide the genome name, only with those obtained from -genome_list''',
required='-genome_list' not in sys.argv)
parser.add_argument(
'-f',
'--vcf_file_pattern',
type=str,
help="Please provide snp vcf files' pattern with full file path",
required='-genome_list' not in sys.argv)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required='-genome_list' not in sys.argv)
# check args
args = parser.parse_args()
if args.genome_list:
print get_gene_list_str()
sys.exit(0)
fi = fileutils()
fi.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
genome = args.genome_name
if genome not in get_gene_list_str().split("\n"):
print "ERROR: genome_name {} not in the list of -genome_list".format(
genome)
sys.exit(1)
vcf_file_pattern = args.vcf_file_pattern
prefix = args.prefix
print "properties_file:", properties_file
print "genome:", genome
print "vcf_file_pattern:", vcf_file_pattern
print "prefix:", prefix
print "stage 6 has started!"
def execute_stage7():
print "stage 7 has started!"
def execute_stage8():
print "stage 8 has started!"
if __name__ == '__main__':
get_args()
global prop
prop=properties(properties_file)
print "\n","Properties attributes:"
print prop.__dict__
initiate()
execute_stage1()
execute_stage2()
execute_stage3()
execute_stage4()
execute_stage5()
execute_stage6()
execute_stage7()
execute_stage8()
print assemblers
print fastq1
def get_args():
global properties_file
global genome
global gff
global prefix
global vcf_file_pattern
global prop
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'Script invests genes under selection pressure within species through dNdS'
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name,
only "ch" for "C. hominis" or "cp" for "C. parvum" can be used''',
required=True)
parser.add_argument('-gff',
'--genome_gff_file',
type=str,
help='''Please provide the genome gff file,
only C. hominis or C. parvum gff file can be used''',
required=False)
parser.add_argument(
'-f',
'--vcf_file_pattern',
type=str,
help="Please provide vcf files' pattern with full file path",
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
fi = fileutils()
fi.check_exist(args.properties_file)
if args.genome_gff_file is not None:
fi.check_exist(args.genome_gff_file)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name != 'ch' and args.genome_name != 'cp':
print "only 'ch' or 'cp' can be used as the genome name"
sys.exit(1)
else:
genome = args.genome_name
if args.genome_gff_file is None:
gff = prop.get_attrib(genome + "_gff")
vcf_file_pattern = args.vcf_file_pattern
prefix = args.prefix
print "properties_file:", properties_file
print "genome:", genome
print "genome_gff:", gff
print "vcf_file_pattern:", vcf_file_pattern
print "prefix:", prefix
def get_args():
global prop
global properties_file
global genome_name
global gvcf_files
global gvcf_files_str
global prefix
global if_filter
filter_dict = {}
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='''Script merging gvcf files, seperating into
SNP and INDEL,and then filtering if requested'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='''Please provide the properties file,
which including the paths of workdir''',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which is provided by genome_list.txt''',
required=True)
parser.add_argument('-gv',
'--gvcf_files',
type=str,
help='Please provide gvcf files',
required=True)
parser.add_argument('-f',
'--if_filter',
default=False,
action="store_true",
help='whether to filter SNP and INDEL seperately',
required=False)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file',
required=True)
args = parser.parse_args()
# check args
FI.check_exist(args.properties_file)
FI.check_files_exist(glob.glob(args.gvcf_files))
properties_file = args.properties_file
prop = properties(properties_file)
MISC.check_genome_avl(prop.get_attrib("available_genomes"),
args.genome_name)
genome_name = args.genome_name
# define variables
properties_file = args.properties_file
gvcf_files = glob.glob(args.gvcf_files)
gvcf_files_str = ""
for gvcf_file in gvcf_files:
gvcf_files_str += gvcf_file + " "
gvcf_files_str = gvcf_files_str.rstrip(" ")
prefix = args.prefix
if_filter = args.if_filter
# print args
print("properties_file:", str(properties_file))
print("genome_name:", genome_name)
print("gvcf_files:", gvcf_files_str)
print("if_filter:", if_filter)
print("prefix:", prefix)
def get_args():
global properties_file
global cds_fna1
global cds_faa1
global cds_fna2
global cds_faa2
global genome1
global genome2
global map_file
global filter_eval
global filter_identity
global prefix
global fi
global makeblastdb_sw
global blastn_sw
global prop
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'Script invests genes under selection pressure between two species through dNdS'
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument(
'-g1',
'--genome_name1',
type=str,
help='''Please provide the first genome name, otherwise,
"ch" for "C. hominis" will be used''',
required=False)
parser.add_argument(
'-g2',
'--genome_name2',
type=str,
help='''Please provide the second genome name, otherwise,
"cp" for "C. parvum" will be used''',
required=False)
parser.add_argument(
'-fn1',
'--cds_fna1',
type=str,
help=
'Please provide the first cds fna file, otherwise, ch fna file will be used.',
required=False)
parser.add_argument(
'-fn2',
'--cds_fna2',
type=str,
help=
'Please provide the second cds fna file, otherwise, cp fna file will be used.',
required=False)
parser.add_argument(
'-fa1',
'--cds_faa1',
type=str,
help=
'Please provide the first cds faa file, otherwise, ch faa file will be used.',
required=False)
parser.add_argument(
'-fa2',
'--cds_faa2',
type=str,
help=
'Please provide the second cds faa file, otherwise, cp faa file will be used.',
required=False)
parser.add_argument(
'-m',
'--map',
type=str,
help='''Please provide the file for mapping the chromosome accessions,
one pair in each line and separated by tab,
otherwise, no chromosome information will be provided in the output file''',
required=False)
parser.add_argument(
'-fi',
'--filter_identity',
type=str,
help='the identity percentage for filtering the blast hits.',
required=False)
parser.add_argument('-fe',
'--filter_eval',
type=str,
help='the eval for filtering the blast hits.',
required=False)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
fi = fileutils()
fi.check_exist(args.properties_file)
for opt_arg_fpath in (args.cds_fna1, args.cds_fna2, args.cds_faa1,
args.cds_faa2, args.map):
if opt_arg_fpath is not None:
fi.check_exist(opt_arg_fpath)
# define variables
makeblastdb_sw = "makeblastdb"
blastn_sw = "blastn"
default_gname1 = "ch"
default_gname2 = "cp"
map_file = "None"
filter_eval = "0"
filter_identity = "0"
filter_length = "0"
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name1 is not None:
genome1 = args.genome_name1
else:
genome1 = default_gname1
if args.genome_name2 is not None:
genome2 = args.genome_name2
else:
genome2 = default_gname2
if args.cds_fna1 is not None:
cds_fna1 = args.cds_fna1
else:
cds_fna1 = prop.get_attrib(genome1 + "_cds_fna")
if args.cds_faa1 is not None:
cds_faa1 = args.cds_faa1
else:
cds_faa1 = prop.get_attrib(genome1 + "_cds_faa")
if args.cds_fna2 is not None:
cds_fna2 = args.cds_fna2
else:
cds_fna2 = prop.get_attrib(genome2 + "_cds_fna")
if args.cds_faa2 is not None:
cds_faa2 = args.cds_faa2
else:
cds_faa2 = prop.get_attrib(genome2 + "_cds_faa")
if args.map is not None:
map_file = args.map
if args.filter_eval is not None:
filter_eval = args.filter_eval
if args.filter_identity is not None:
filter_identity = args.filter_identity
prefix = args.prefix
print "properties_file:", properties_file
print "genome1:", genome1
print "genome2:", genome2
print "cds_fna1:", cds_fna1
print "cds_faa1:", cds_faa1
print "cds_fna2:", cds_fna2
print "cds_faa2:", cds_faa2
print "filter_eval:", filter_eval
print "filter_identity_perc:", filter_identity
print "prefix:", prefix
def get_args():
global fi
global prop
global properties_file
global genome_name
global genome_fasta
global bam_file_pattern
global bam_request_pattern
global bam_files
global prefix
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'''Script creating relocation files for multiple bam files from the same genome
and automatically open the GUI.''')
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument(
'-g',
'--genome_name',
type=str,
help='''if "C. hominis" or "C. parvum" will be used as the genome,
please provide "ch" for "C. hominis" or "cp" for "C. parvum"''',
required=False)
parser.add_argument(
'-f',
'--genome_fasta',
type=str,
help='''Please provide the directory for the genome fasta file,
if "ch" or "cp" is not the genome name.''',
required=False)
parser.add_argument(
'-b',
'--bam_file_pattern',
type=str,
help='''Please provide the bam files' pattern with the full path''',
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
# check args
args = parser.parse_args()
fi = fileutils()
fi.check_exist(args.properties_file)
if args.genome_name is not None and not args.genome_name == "ch" and not args.genome_name == "cp":
print "genome name need to be ch or cp"
sys.exit(1)
if args.genome_fasta is not None:
fi.check_exist(args.genome_fasta)
bam_file_pattern = args.bam_file_pattern
bam_files = glob.glob(bam_file_pattern)
bam_request_pattern = "^.*/?(.*?).bam$"
for bam_file in bam_files:
if not re.search(bam_request_pattern, bam_file):
print "bam_file not ended with .bam"
sys.exit(1)
fi.check_files_exist(bam_files)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name is not None:
genome_name = args.genome_name
if args.genome_fasta is not None:
genome_fasta = args.genome_fasta
else:
if args.genome_name is None:
print "If no genome_fasta provided, genome name must be provided as ch or cp."
sys.exit(1)
else:
genome_fasta = prop.get_attrib(genome_name + "_fasta")
prefix = args.prefix
print "properties_file:", properties_file
print "genome_name:", genome_name
print "genome_fasta:", genome_fasta
print "bam_file_pattern:", bam_file_pattern
print "prefix:", prefix
def get_args():
global prop
global properties_file
global genome_name
global bam_file
global prefix_ori
global if_filter
global mapping_file
global runID
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='''Script for getting filtered or unfiltered
SNP and INDEL vcf and gvcf files from bam
files using gatk, and then create statistics
summary by using bcf_tools'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which is provided by genome_list.txt''',
required=True)
parser.add_argument('-bam',
'--bam_file',
type=str,
help='Please provide one bam file',
required=True)
parser.add_argument('-f',
'--if_filter',
default=False,
action="store_true",
help='whether to filter SNP and INDEL',
required=False)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file',
required=True)
parser.add_argument('-m',
'--mapping_file',
type=str,
help='''if map file was provided, sample name will be
included in the output file name''',
required=False)
args = parser.parse_args()
# check args
FI.check_exist(args.properties_file)
FI.check_exist(args.bam_file)
properties_file = args.properties_file
prop = properties(properties_file)
MISC.check_genome_avl(prop.get_attrib("available_genomes"),
args.genome_name)
runID = MISC.get_runID(args.bam_file)
if args.mapping_file is not None:
FI.check_exist(args.mapping_file)
# define variable
genome_name = args.genome_name
bam_file = args.bam_file
properties_file = args.properties_file
prefix_ori = args.prefix
if_filter = args.if_filter
mapping_file = args.mapping_file
# print args
print("properties_file:", str(properties_file))
print("genome_name:", genome_name)
print("bam_file:", bam_file)
print("if_filter:", if_filter)
print("prefix:", prefix_ori)
print("mapping_file:", mapping_file)
def get_args():
global PROP
global PROPERTIES_FILE
global genome_name
global vcf_files
global vcf_files_str
global gvcf_file
global genotype_file
global prefix
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'''Script for creating images: phylogeny tree, PCA, heatmap, upset,
and SNP distribution on chromosome for vcf files'''
)
parser.add_argument(
'-p',
'--properties_file',
type=str,
help='''Please provide the properties file, which including
the paths of samtools and bcftools and workdir''',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which is provided by genome_list.txt''',
required=True)
parser.add_argument('-v',
'--vcf_files',
type=str,
help='Please provide one or multiple vcf files',
required=True)
parser.add_argument('-gv',
'--gvcf_file',
type=str,
help='Please provide one concat gvcf file',
required=True)
parser.add_argument(
'-gt',
'--genotype_file',
type=str,
help=
'''The file need to contain 3 cols: runID, isolate name, and genotype''',
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file',
required=True)
args = parser.parse_args()
# check args
FI.check_exist(args.properties_file)
PROPERTIES_FILE = args.properties_file
PROP = properties(PROPERTIES_FILE)
MISC.check_genome_avl(PROP.get_attrib("available_genomes"),
args.genome_name)
FI.check_files_exist(glob.glob(args.vcf_files))
FI.check_exist(args.gvcf_file)
FI.check_exist(args.genotype_file)
genome_name = args.genome_name
vcf_files = glob.glob(args.vcf_files)
if len(vcf_files) == 0:
sys.exit("Input vcf files not exist")
vcf_files_str = ""
for vcf_file in vcf_files:
MISC.get_runID(vcf_file)
vcf_files_str += os.path.abspath(vcf_file) + " "
gvcf_file = args.gvcf_file
genotype_file = args.genotype_file
prefix = args.prefix
# print args
print("properties_file:", PROPERTIES_FILE)
print("genome name:", genome_name)
print("vcf_files:", vcf_files_str)
print("gvcf_file:", gvcf_file)
print("genotype_file:", genotype_file)
print("prefix:", prefix)
def get_args():
global properties_file
global g_name_str
global prop
global min_homo
global in_fastq1
global in_fastq2
global fastq1_key
global fastq2_key
global fastq1_postfix
global fastq2_postfix
global qc_sw
global if_dedupQ
global if_dedupM
global prefix
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'''Script provides basic analyses for the next generation sequences, including fastq file quality control,
assembly by using spades, reference_mapping, and SNP calling using samtools
for the genome available in the genome_list'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file.',
required=True)
parser.add_argument(
'-g',
'--genome_name',
type=str,
help=
'''Please provide the genome name which is provided by genome_list.txt''',
required=True)
parser.add_argument('-qc_sw',
'--qc_software',
type=str,
help='''Please provide the quality control software,
otherwise the default trim_galore will be used''',
required=False)
parser.add_argument('-deQ',
'--dedupQ',
action='store_true',
help='if remove all the exact read duplications',
default=False)
parser.add_argument('-fq1',
'--fastq1',
type=str,
help='Please provide the forward fastq file',
required=True)
parser.add_argument('-fq2',
'--fastq2',
type=str,
help='Please provide the reverse fastq file',
required=False)
parser.add_argument(
'-deM',
'--dedupM',
action='store_true',
help='if true, remove duplications after mapping using samtools',
default=False)
# check args
args = parser.parse_args()
fi.check_exist(args.properties_file)
properties_file = args.properties_file
prop = properties(properties_file)
if args.genome_name not in (line.rstrip() for line in open(
prop.get_attrib("available_genomes")).readlines()):
misc.my_exit("{} is not available, please try another genome".format(
args.genome_name))
fi.check_exist(args.fastq1)
(fastq1_key, fastq1_postfix) = check_fastq_postfix(args.fastq1)
if args.fastq2 is not None:
fi.check_exist(args.fastq2)
(fastq2_key, fastq2_postfix) = check_fastq_postfix(args.fastq2)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
prefix = args.prefix
g_name_str = args.genome_name
in_fastq1 = args.fastq1
in_fastq2 = args.fastq2
qc_sw = args.qc_software
if qc_sw is None:
qc_sw = "trim_galore"
if_dedupQ = args.dedupQ
if_dedupM = args.dedupM
print "properties_file:", properties_file
print "prefix:", prefix
print "gname:", g_name_str
print "fastq1:", in_fastq1
print "fastq2:", in_fastq2
print "qc_software:", qc_sw
print "assembly_software:spades"
print "dedupQ:", if_dedupQ
print "dedupM:", if_dedupM
def get_args():
global properties_file
global prop
global fastq1
global fastq2
global prefix
global if_dedup
global runID
global mapping_file
# Assign description to the help doc
parser = argparse.ArgumentParser(
description=
'''Script provides quality control on fastq files using trim_galore
and remove duplicated reads using clumpify. The quality of the original
and filtered reads are monitored by fastQC and summarized by multiQC'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file.',
required=True)
parser.add_argument('-fq1',
'--fastq1',
type=str,
help='Please provide the first fastq file.',
required=True)
parser.add_argument('-fq2',
'--fastq2',
type=str,
help='Please provide the second fastq file.',
required=False)
parser.add_argument('-pre',
'--prefix',
type=str,
help='Please provide the prefix for the output file',
required=True)
parser.add_argument('-de',
'--dedup',
action='store_true',
help='if remove all the exact read duplications',
default=False)
parser.add_argument(
'-m',
'--mapping_file',
type=str,
help='''if map file was provided, whose first column is runID
and the second column is sample name, seperated by "\t",
sample name will be included in fastQC and multiQC
output file names''',
required=False)
# check args
args = parser.parse_args()
FI.check_files_exist([args.properties_file, args.fastq1])
runID = MISC.get_runID(args.fastq1)
if args.fastq2 is not None:
FI.check_exist(args.fastq2)
MISC.get_runID(args.fastq2)
# define variables
properties_file = args.properties_file
prop = properties(properties_file)
fastq1 = args.fastq1
fastq2 = args.fastq2
prefix = args.prefix
if_dedup = args.dedup
mapping_file = args.mapping_file
print("properties_file:", properties_file)
print("fastq1:", fastq1)
print("fastq2:", fastq2)
print("prefix:", prefix)
print("dedup:", if_dedup)
print("mapping_file:", mapping_file)
def get_args():
global properties_file
global prop
global mapping_tool
global genome_name
global fastq1
global fastq2
global platform
global dna_library
global if_dedup
global if_recom
global prefix_ori
global mapping_file
global runID
# Assign description to the help doc
parser = argparse.ArgumentParser(
description='''Script mapping short reads to reference genomes
using BWA or bowtie2, with the following statistics
summary files created by fastQC, qualiMap, and multipleQC'''
)
parser.add_argument('-p',
'--properties_file',
type=str,
help='Please provide the properties file',
required=True)
parser.add_argument('-t',
'--mapping_tool',
type=str,
help='Please choose mapping tool, bwa or bowtie2',
required=True)
parser.add_argument('-g',
'--genome_name',
type=str,
help='''Please provide the genome name
which need to be in genome_list.txt''',
required=True)
parser.add_argument(
'-fq1',
'--fastq1',
type=str,
help='''Please provide the paired forward fastq file or
the single fastq file, containing runID''',
required=True)
parser.add_argument('-fq2',
'--fastq2',
type=str,
help='''Please provide the paired reverse fastq file,
containing runID''',
required=False)
parser.add_argument('-f',
'--platform',
type=str,
help='Please provide the plat_form',
required=True)
parser.add_argument('-l',
'--dna_library',
type=str,
help='Please provide the DNA library',
required=True)
parser.add_argument(
'-pre',
'--prefix',
type=str,
help='Please provide the subdir for holding the output file',
required=True)
parser.add_argument(
'-de',
'--dedup',
action='store_true',
help='if true, remove duplications after mapping using samtools',
default=False)
parser.add_argument(
'-recom',
'--recombination',
action='store_true',
help='''if true, mapping with bowtie2 with be use local
alignment, which is for recombination analysis''',
default=False)
parser.add_argument('-m',
'--mapping_file',
type=str,
help='''if map file was provided, sample name will be
included in the output file name''',
required=False)
args = parser.parse_args()
# check args
FI.check_files_exist([args.properties_file, args.fastq1])
properties_file = args.properties_file
prop = properties(properties_file)
MISC.check_genome_avl(prop.get_attrib("available_genomes"),
args.genome_name)
runID = MISC.get_runID(args.fastq1)
if args.fastq2 is not None:
FI.check_exist(args.fastq2)
MISC.get_runID(args.fastq2)
if args.mapping_file is not None:
FI.check_exist(args.mapping_file)
if not args.mapping_tool == "bwa" and not args.mapping_tool == "bowtie2":
sys.exit("only bwa and bowtie2 are available for the mapping_tool")
# define variables
mapping_tool = args.mapping_tool
genome_name = args.genome_name
fastq1 = args.fastq1
fastq2 = args.fastq2
platform = args.platform
dna_library = args.dna_library
prefix_ori = args.prefix
if_dedup = args.dedup
if_recom = args.recombination
mapping_file = args.mapping_file
print("properties_file:", properties_file)
print("genome_name:", genome_name)
print("mapping_tool:", mapping_tool)
print("fastq1:", fastq1)
print("fastq2:", fastq2)
print("platform:", platform)
print("dna_library:", dna_library)
print("prefix:", prefix_ori)
print("dedup:", if_dedup)
print("recombination:", if_recom)
print("mapping_file:", mapping_file)
