def main_page():
configure.input_seq=File_jf.check_file(target_file, hairpin_file, extra_base_file,templates_file)
feet_list=design.ptpx_foot(configure.input_seq,min_pt,max_pt,min_px,max_px,max_e,direction,pt_min_tm,pt_max_tm, px_min_tm, px_max_tm,configure.pt_foot_conc,configure.px_foot_conc)
design.write_fasta_feet(feet_list,'~feet.fasta')
(in_blast_result,ex_blast_result)=design.combine_check_exinclude('~feet.fasta',str(include_line),str(exclude_line),int(num),float(perct)/100,seq_name_list)
blast_ok_feet_list=design.blast_feet_chek(in_blast_result,ex_blast_result, feet_list,pt_min_length, px_min_length)
primer_set=design.bind_hairpin_template(blast_ok_feet_list,hairpin_file,extra_base_file)
def main_page(target_file,include_line, exclude_line, hairpin_file,extra_base_file, templates_file,\
exclude_GAGTC,two_direction,PT_foot_min,PT_foot_max,PT_Tm_above,PX_foot_min,PX_foot_max,PX_Tm_above,\
max_gap,pt_longer_num,px_longer_num,pt_foot_conc,px_foot_conc,pt_px_foot_match_max,hair_tar_max,overhang_pt_tar_max,overhang_px_tar_max, target_mismatch):
print "enter",target_file, hairpin_file, extra_base_file, templates_file
if (os.path.isfile(target_file) and os.path.isfile(hairpin_file) and os.path.isfile(extra_base_file) and os.path.isfile(templates_file)):
print os.path.isfile(target_file),os.path.isfile(hairpin_file),os.path.isfile(extra_base_file),os.path.isfile(templates_file)
print "all necessary file exist!"
File_jf.three_file_check_symbol(target_file,hairpin_file,extra_base_file)
input_content=open(target_file).read()
seq_num=[i - 1 for i in range(len(input_content)) if input_content.startswith('>', i - 1)]
if len(seq_num)!=1:
print "input should be one and only one sequence in fasta format!"
return 0
else:
for cur_record in SeqIO.parse(open(target_file), "fasta"):
input_seq=str(cur_record.seq).upper()
else:
#Form = QtGui.QWidget()
#QtGui.QMessageBox.critical(Form,"Error", "you haven't properly installed perl yet!")
print "error, necessary file is not there"
exit()
return 0
print "what's wrong with this?working on obtain pt and px foot"
configure.progress_simbol=1
check_file_size(1)
ptpx_foot_list=ptpx_foot(input_seq,PT_foot_min,PT_foot_max,PX_foot_min,PX_foot_max,e,'p')
if two_direction :
ptpx_foot_list=ptpx_foot_list|ptpx_foot(revcomp(input_seq),PT_foot_min,PT_foot_max,PX_foot_min,PX_foot_max,e,'n') ###################get the pt and px foot sequence
f_p=open(configure.temper_print,'w')
f_p2=open('del.txt','w')
print >>f_p2, ptpx_foot_list
print "done with working on obtain pt and px foot"
write_ptpx_foot_file_check_foot(ptpx_foot_list,input_seq,pt_px_foot_match_max,configure.pt_foot_file1, configure.px_foot_file1,configure.tar_file1)###################get the pt and px foot sequence stored in files
print "done with writing pt/px/target files"
configure.progress_simbol=2
#check_file_size(2)
print PT_Tm_above,PX_Tm_above
Tm_pfoot(configure.pt_foot_file1,configure.px_foot_file1,configure.tar_file1, PT_Tm_above,PX_Tm_above,configure.pt_foot_file2,configure.px_foot_file2,configure.tar_file2, configure.pt_bind_filename, configure.px_bind_filename, pt_foot_conc,px_foot_conc)
print configure.pt_foot_file2,configure.px_foot_file2,configure.tar_file2,"are generated!"
configure.progress_simbol=3
check_file_size(3)
if include_line!='': # if no include organism
combine_check_include(include_line,target_mismatch,configure.tar_file2,configure.pt_foot_file3,configure.px_foot_file3,configure.tar_file3, configure.blast_in_file)
else:
shutil.copy2(configure.pt_foot_file2,configure.pt_foot_file3)
shutil.copy2(configure.px_foot_file2,configure.px_foot_file3)
shutil.copy2(configure.tar_file2,configure.tar_file3)
print "include check over"
configure.progress_simbol=4
check_file_size(4)
bind_hairpin(hairpin_file,extra_base_file, configure.pt_foot_hair_file1, configure.px_foot_hair_file1, configure.tar_hair_file1,hair_tar_max)
print "bind_hairpin over"
configure.progress_simbol=5
check_file_size(5)
self_Tm_check_eachother(configure.pt_foot_hair_file1,configure.px_foot_hair_file1,configure.tar_hair_file1,configure.whole_PTX_tm,configure.pt_foot_hair_file2, configure.px_foot_hair_file2,configure.tar_hair_file2, configure.ptx_melt_file)
print "self Tm check over"
configure.progress_simbol=6
check_file_size(6)
combine_PT(templates_file,configure.pt_foot_hair_file2,configure.tar_hair_file1,configure.whole_PT1,configure.overhang_pt_tar_max) # bind well-performing template from templates_file and pt foot with haipin from pt_foot_hair_file3
print "combine_PT is over"
print "*******",configure.whole_PT1
configure.progress_simbol=6.5
check_file_size(6.5)
self_bind(configure.whole_PT1,configure.whole_PT_self_max,'-pt', configure.whole_PT2)
print "self_bind PT1 is over"
configure.progress_simbol=7
check_file_size(7)
self_bind(configure.px_foot_hair_file2,configure.whole_PX_self_max,'-px',configure.whole_PX1)
configure.progress_simbol=8
check_file_size(8)
if exclude_line!='':
combine_check_exclude(configure.whole_PT2, configure.whole_PX1,exclude_line,pt_longer_num,px_longer_num,configure.pt_blast,configure.px_blast,configure.finalptx)
else:
combine_pt_px_result(configure.whole_PT2, configure.whole_PX1,configure.finalptx)
#configure.progress_simbol=9
#check_file_size(9)
#print "combine_PT is over"
#print >>f_p, 'Tm_pt_foot_tar'
#print >>f_p, Tm_pt_foot_tar
#print >>f_p, 'tar_include'
#print >>f_p, tar_include
#print >>f_p, "Tm_p_foot_hair_tar"
#print >>f_p, Tm_p_foot_hair_tar
#print >>f_p, "overhang_bind_pt"
#print >>f_p, overhang_bind_pt
#print >>f_p, "whole_self_bind"
#print >>f_p, whole_self_bind
f_p.close()
configure.progress_simbol=10
check_file_size(10)
