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Added the formatter part to write html outputs
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shubhada-kulkarni committed Dec 11, 2023
1 parent 94f55cb commit b6ea2fe
Showing 1 changed file with 23 additions and 25 deletions.
48 changes: 23 additions & 25 deletions circtools/padlock/padlock.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@ def __init__(self, argparse_arguments, program_name, version):
self.output_dir = self.cli_params.output_dir
self.organism = self.cli_params.organism
self.id_list = self.cli_params.id_list
self.product_range = self.cli_params.product_size
self.product_range = self.cli_params.product_size # not required for probe designing
self.junction = self.cli_params.junction
self.no_blast = self.cli_params.blast
self.experiment_title = self.cli_params.experiment_title
Expand All @@ -64,7 +64,7 @@ def __init__(self, argparse_arguments, program_name, version):
exit(-1)

if self.id_list and self.gene_list:
print("Please specify either host genes via -G or circRNA IDs via -i.")
print("Please specify either host genes via -G/-GL or circRNA IDs via -i.")
sys.exit(-1)

self.homo_sapiens_blast_db = "GPIPE/9606/current/rna"
Expand Down Expand Up @@ -229,8 +229,8 @@ def calc_GC(seq):
blast_storage_tmp = self.temp_dir + tmp_prefix + "_circtools_blast_results.tmp"
blast_xml_tmp = self.temp_dir + tmp_prefix + "_circtools_blast_results.xml"

output_html_file = self.output_dir + self.experiment_title.replace(" ", "_") + ".html"
output_csv_file = self.output_dir + self.experiment_title.replace(" ", "_") + ".csv" # padlock probe output csv file
output_html_file = self.output_dir + "/" + self.experiment_title.replace(" ", "_") + ".html"
output_csv_file = self.output_dir + "/" + self.experiment_title.replace(" ", "_") + ".csv" # padlock probe output csv file
# erase old contents
open(exon_storage_tmp, 'w').close()

Expand Down Expand Up @@ -406,30 +406,30 @@ def calc_GC(seq):
scan_window = scan_sequence[i:i+40]
if (len(scan_window) < 40):
break
# print(i, scan_window, len(scan_window), scan_window[19:21], dict_ligation_junction[scan_window[19:21]])

junction = dict_ligation_junction[scan_window[19:21]]
# filter criteria for padlock probes - accepted ligation junction preferences
if (dict_ligation_junction[scan_window[19:21]] == "nonpreferred" ):
if (junction == "nonpreferred" ):
#print("Non-preffered Ligation junction found, skipping.")
continue
#elif (dict_ligation_junction[scan_window[19:21]] == "neutral" ): #comment later
# #print("Neutral Ligation junction found, skipping.")
# continue
elif (dict_ligation_junction[scan_window[19:21]] == "neutral" ): #comment later
#print("Neutral Ligation junction found, skipping.")
continue
else:
# send each of this to primer3
# primer3 only takes PRIMER_MAX_SIZE up to 35bp. So divide the two arms and then send to primer3
rbd5 = scan_window[:20]
rbd3 = scan_window[20:]
melt_tmp_5 = primer3.calc_tm(rbd5)
melt_tmp_3 = primer3.calc_tm(rbd3)
melt_tmp_5 = round(primer3.calc_tm(rbd5), 3)
melt_tmp_3 = round(primer3.calc_tm(rbd3), 3)
if ((melt_tmp_5 < 50) or (melt_tmp_3 < 50) or (melt_tmp_5 > 70) or (melt_tmp_3 > 70)) :
#print("Melting temperature outside range, skipping!")
continue
gc_rbd5 = calc_GC(rbd5)
gc_rbd3 = calc_GC(rbd3)
print(each_circle, rbd5, rbd3, melt_tmp_5, melt_tmp_3, dict_ligation_junction[scan_window[19:21]], gc_rbd5, gc_rbd3)
print(each_circle, rbd5, rbd3, melt_tmp_5, melt_tmp_3, gc_rbd5, gc_rbd3, junction)

designed_probes_for_blast.append([each_circle, rbd5, rbd3, melt_tmp_5, melt_tmp_3, dict_ligation_junction[scan_window[19:21]], gc_rbd5, gc_rbd3])
designed_probes_for_blast.append([each_circle, rbd5, rbd3, melt_tmp_5, melt_tmp_3, gc_rbd5, gc_rbd3, junction])
'''
# need to define path top R wrapper
print("Going to run R wrapper")
Expand All @@ -451,9 +451,8 @@ def calc_GC(seq):
blast_input_file = ""
if circ_rna_number < 50:

for entry in designed_probes_for_blast:
for entry in designed_probes_for_blast[:5]:
circular_rna_id = entry[0].split('_')
print("Entry is: ", entry, " and circular RNA id is ", circular_rna_id)

if entry[1] == "NA":
continue
Expand Down Expand Up @@ -487,8 +486,6 @@ def calc_GC(seq):
if self.no_blast:
print("User disabled BLAST search, skipping.")

print(primer_to_circ_cache)
print(blast_object_cache)
#print(blast_input_file) # this is a fasta file with primer sequences to BLAST

run_blast = 0
Expand Down Expand Up @@ -536,9 +533,10 @@ def calc_GC(seq):
#entry = line.split('\t')

# split up the identifier for final plotting
#line = line.replace("_", "\t")
entry[0] = entry[0].replace("_", "\t")
line = "\t".join(map(str, entry))

print(line)

if run_blast == 1:
left_result = "No hits"
right_result = "No hits"
Expand All @@ -555,12 +553,13 @@ def calc_GC(seq):
# update line
primex_data_with_blast_results += line + "\t" + left_result + "\t" + right_result + "\n"

print(primex_data_with_blast_results)
with open(blast_storage_tmp, 'w') as data_store:
data_store.write(primex_data_with_blast_results)
'''

# need to define path top R wrapper
primer_script = 'circtools_primex_formatter'
primer_script = 'circtools_padlockprobe_formatter.R'

# ------------------------------------ run script and check output -----------------------

Expand All @@ -573,11 +572,11 @@ def calc_GC(seq):
data_store.write(primex_data_formatted)

print("Writing results to "+output_html_file)
'''
# here we create the circular graphics for primer visualisation
for line in primex_data_with_blast_results.splitlines():
entry = line.split('\t')
print(entry)
#print(entry)
# no primers, no graphics
if entry[6] == "NA":
continue
Expand All @@ -587,7 +586,7 @@ def calc_GC(seq):
entry[2],
entry[3],
entry[4]])
print(entry)
if circular_rna_id in exon_cache:
circular_rna_id_isoform = circular_rna_id + "_" + entry[5]
Expand Down Expand Up @@ -714,9 +713,8 @@ def calc_GC(seq):
gdd.write(self.output_dir + "/" + circular_rna_id_isoform + ".svg", "svg")
print(feature)
print("Cleaning up")
'''
### cleanup / delete tmp files
#os.remove(exon_storage_tmp)
#os.remove(blast_storage_tmp)
#os.remove(blast_xml_tmp)
'''

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