def unknown_primer(primers=None, input_file=None,output_file=None,
hg_version="hg19"):
''' From a given primer pair, generate amplicon sequence information by
parsing to the UCSC isPCR tool
\b\n
'''
header = "\t".join(("Primer", "F_Primer","R_Primer", "Gene", "Product_Size",
"Primer_Range","GC%","Number_Amplicons", "\n"))
print(header[:-1])
# determine whether the input is a file or string and process accordingly
if input_file:
all_matched_primers = []
for line in [line.rstrip("\n").split("\t") for line in open(input_file)]:
primer_name = line[0]
f_primer = line[1].upper()
r_primer = line[2].upper()
full_amplicon_info = get_all_primer_info(primer_name, hg_version,
f_primer, r_primer)
if not full_amplicon_info:
full_amplicon_info = "\t".join((primer_name, "-", "-", "-",
"-", "-", "-", "-"))
all_matched_primers.append(full_amplicon_info)
print(full_amplicon_info)
else:
primer_name = "query"
f_primer = primers[0]
r_primer = primers[1]
full_amplicon_info = get_all_primer_info(primer_name, hg_version,
f_primer, r_primer)
print(full_amplicon_info)
if output_file:
write_to_output(all_matched_primers, output_file, header)
def main(input_file, output_file=None, upstream=20, downstream=20,
hg_version=default_hg_version, download='n', configure='n',seq_dir=file_path[:-8]+"test/test_files/", genome=genome_path, vcf=None):
'''
From a genomic postion, genomic range or tab-deliminated file produce a
reference sequence that can be compared with a sanger trace along with
said position/ranges gene/transcript/exon information.
'''
# whether to download ttuner and or human genomes
if download:
subprocess.call([file_path+"download.sh"])
config.config()
sys.exit()
# write a config file
if configure:
config.config()
sys.exit()
# convert vcf to input file
if vcf:
vcf2input.vcf2input(vcf, "temp.tsv")
sys.exit(0)
# ensures the wrong human genome isnt used
if hg_version not in genome:
genome = None
# intiate the classes in UCSC
reference = ScrapeSeq(input_file, upstream, downstream, hg_version)
# if the arg given is a file, parse it in line by line otherwise assume its a string
all_scrapped_info = parse_file(input_file, output_file, upstream, downstream,
hg_version, seq_dir, reference, genome)
# write the header and each element per line to the file
if output_file:
header = "\t".join(("Name", "Position", "Seq_Range", "AB1", "NGS", "Ref", "Seq",
"Result", "\n"))
write_to_output(all_scrapped_info, output_file, header)
def main(input_file, distance, size, gc, output_file=None,
primer_database=file_path[:-8]+"test/primer_database.txt"):
''' Takes variant postion(s) as input and matches it with an appropriate primer
pair in a given primer database.
'''
# allows one to pipe in an argument at the cmd, requires required=False in
# @click.argument()
if not input_file:
input_file = input()
# get all genomic locations within primer pairs, from all primers in the database
all_primer_pos = get_all_primer_pos(primer_database)
header = "\t".join(("Variant","Primer", "Position", "Gene_Name",
"Amplicon_Size", "GC%", "Amplicon_Number",
"Dist_from_F","Dist_from_R","\n"))
print(header[:-1])
# determine input type and process accordingly
if os.path.isfile(input_file) is True:
all_matched_primers = []
for line in [line.rstrip("\n").split("\t") for line in open(input_file)]:
var_name = line[0]
var_pos = line[1].replace("chr","")
filtered_primer_pos = filter_positions(distance, size, gc,
all_primer_pos)
matched_primers = match(var_pos,filtered_primer_pos,var_name)
all_matched_primers.append(matched_primers)
print(matched_primers)
else:
output_file = None
position = input_file.replace("chr","")
filtered_primer_pos = filter_positions(distance, size, gc, all_primer_pos)
matched_primers = match(position, filtered_primer_pos,"query")
print(matched_primers)
if output_file:
write_to_output(all_matched_primers, output_file, header)
