Mercurial > repos > charles_s_test > seqsero2
changeset 10:53efef402c51 draft
planemo upload commit a4fb57231f274270afbfebd47f67df05babffa4a-dirty
| author | charles_s_test |
|---|---|
| date | Wed, 29 Nov 2017 08:34:19 -0500 |
| parents | acc5cd06a36a |
| children | b4484db557ab |
| files | SeqSero.py Seqsero_result.html Seqsero_result.txt libs/BWA_analysis_H_update_new_family_dependent.py libs/BWA_analysis_O_new_dependent.py libs/H_combination_output_analysis.py libs/Otype_determine_analysis.py libs/compare_and_change_two_fastq_id.py libs/deletion_compare.py libs/run_auto_All_for_assemblies.py libs/run_auto_All_for_web_multi_revise.py libs/special_gene_test_assemblies.py run_seqsero.py seqsero.xml test.txt |
| diffstat | 15 files changed, 226 insertions(+), 190 deletions(-) [+] |
line wrap: on
line diff
--- a/SeqSero.py Tue Nov 28 21:16:36 2017 -0500 +++ b/SeqSero.py Wed Nov 29 08:34:19 2017 -0500 @@ -26,11 +26,11 @@ mapping_mode=args.b dataset=args.i if mode_choice=="1": - print(dataset[0]) + print dataset[0] os.system("cp "+dataset[0]+" "+make_dir) os.chdir(make_dir) os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 1") - print("\n\n\nResult:\n") + print "\n\n\nResult:\n" os.system("cat Seqsero_result.txt") os.system("rm "+dataset[0].split("/")[-1]) elif mode_choice=="2": @@ -39,21 +39,21 @@ fnameA=dataset[0].split("/")[-1] fnameB=dataset[1].split("/")[-1] os.chdir(make_dir) - print("check fastq id and make them in accordance with each other...please wait...") + print "check fastq id and make them in accordance with each other...please wait..." os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+fnameA+" "+mapping_mode+" "+fnameB+" 2") - print("\n\n\nResult:\n") + print "\n\n\nResult:\n" os.system("cat Seqsero_result.txt") elif mode_choice=="3": os.system("cp "+dataset[0]+" "+make_dir) os.chdir(make_dir) os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_web_multi_revise.py "+dataset[0].split("/")[-1]+" "+mapping_mode+" 3") - print("\n\n\nResult:\n") + print "\n\n\nResult:\n" os.system("cat Seqsero_result.txt") elif mode_choice=="4": os.system("cp "+dataset[0]+" "+make_dir) os.chdir(make_dir) os.system("python2.7 "+dirpath+"/libs/run_auto_All_for_assemblies.py "+dataset[0].split("/")[-1]) - print("\n\n\nResult:\n") + print "\n\n\nResult:\n" os.system("cat Seqsero_result.txt") if __name__ == '__main__':
--- a/Seqsero_result.html Tue Nov 28 21:16:36 2017 -0500 +++ b/Seqsero_result.html Wed Nov 29 08:34:19 2017 -0500 @@ -15,6 +15,21 @@ <td>Predicted antigenic profile</td> <td>Predicted serotype(s)</td> </tr> +<tr> +<td>dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq</td> +<td>O-3,10</td> +<td>e,h</td> +<td>1,6</td> +<td>3,10:e,h:1,6</td> +<td>Anatum</td> +</tr> </table> +<tr> +<p> +<td>dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq<br></td> +<td>The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes.</td> +<td>check fastq id and make them in accordance with each other...please wait...</td> +</p> +</tr> </body> </html>
--- a/Seqsero_result.txt Tue Nov 28 21:16:36 2017 -0500 +++ b/Seqsero_result.txt Wed Nov 29 08:34:19 2017 -0500 @@ -1,1 +1,6 @@ Input_Files O_antigen_prediction H1_antigen_prediction(fliC) H2_antigen_prediction(fljB) Predicted_antigenic_profile Predicted_serotype(s) +dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq O-3,10 e,h 1,6 3,10:e,h:1,6 Anatum + +dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq +The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes. +check fastq id and make them in accordance with each other...please wait...
--- a/libs/BWA_analysis_H_update_new_family_dependent.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/BWA_analysis_H_update_new_family_dependent.py Wed Nov 29 08:34:19 2017 -0500 @@ -104,23 +104,23 @@ for x in c: if x[:4]=="fljB": fljB[x]=c[x] - final_fliC=sorted(fliC.items(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list - final_fljB=sorted(fljB.items(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list - print("Final_filC_list:") - print(final_fliC) + final_fliC=sorted(fliC.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list + final_fljB=sorted(fljB.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list + print "Final_filC_list:" + print final_fliC num_1=0#new inserted num_2=0#new inserted if len(final_fliC)>0: #new inserted for x in final_fliC:#new inserted num_1=num_1+x[1]#new inserted - print("Final_fliC_number_together: ",num_1)#new inserted - print("Final_fljB_list:") - print(final_fljB) + print "Final_fliC_number_together: ",num_1#new inserted + print "Final_fljB_list:" + print final_fljB if len(final_fljB)>0: #new inserted for x in final_fljB: #new inserted num_2=num_2+x[1] #new inserted - print("Final_fljB_number_together: ",num_2)#new inserted - print("$$Genome:",sra_name) + print "Final_fljB_number_together: ",num_2#new inserted + print "$$Genome:",sra_name try: fliC_option=final_fliC[0][0].split("_")[1] except: @@ -132,16 +132,16 @@ if z==0: if len(final_fliC)==0 or num_1<=10: - print("$$$No fliC, due to no hit") + print "$$$No fliC, due to no hit" else: if final_fliC[0][1]<=1 and z==1: - print("$$$No fliC, due to the hit reads number is small.") + print "$$$No fliC, due to the hit reads number is small." else: try: family=final_fliC[0][0].split("_")[-1] Sero_list_C.append(family) description.append(final_fliC[0][0]) - print("$$Most possilble fliC family: ",Sero_list_C[0]," Number: ",final_fliC[0][1]) + print "$$Most possilble fliC family: ",Sero_list_C[0]," Number: ",final_fliC[0][1] i=0 for x in final_fliC: if x[0].split("_")[-1] not in Sero_list_C: @@ -153,7 +153,7 @@ if locals().has_key('sec_choice'): Sero_list_C.append(sec_choice) description.append(des) - print("$$Sec possilble fliC family: ",sec_choice," Number: ",number) + print "$$Sec possilble fliC family: ",sec_choice," Number: ",number j=0 for x in final_fliC: if x[0].split("_")[-1] not in Sero_list_C: @@ -165,25 +165,25 @@ if locals().has_key('third_choice'): Sero_list_C.append(third_choice) description.append(des) - print("$$Third possilble fliC family: ",third_choice," Number: ",number) + print "$$Third possilble fliC family: ",third_choice," Number: ",number except: - print("$$$No fliC, or failure of mapping") + print "$$$No fliC, or failure of mapping" try: ratio=float(num_2)/float(num_1) except: ratio=0 if len(final_fljB)==0 or num_2<=5 or ratio<0.15: - print("$$$No fljB, due to no hit") + print "$$$No fljB, due to no hit" else: if final_fljB[0][1]<=1 and z==1: - print("$$$No fljB, due to the hit reads number is small.") + print "$$$No fljB, due to the hit reads number is small." else: try: family=final_fljB[0][0].split("_")[-1] Sero_list_B.append(family) description.append(final_fljB[0][0]) - print("$$Most possilble fljB family: ",Sero_list_B[0]," Number: ",final_fljB[0][1]) + print "$$Most possilble fljB family: ",Sero_list_B[0]," Number: ",final_fljB[0][1] i=0 for x in final_fljB: if x[0].split("_")[-1] not in Sero_list_B: @@ -195,7 +195,7 @@ if locals().has_key('B_sec_choice'): Sero_list_B.append(B_sec_choice) description.append(des) - print("$$Sec possilble fljB: ",B_sec_choice," Number: ",number) + print "$$Sec possilble fljB: ",B_sec_choice," Number: ",number j=0 for x in final_fljB: if x[0].split("_")[-1] not in Sero_list_B: @@ -207,9 +207,9 @@ if locals().has_key('B_third_choice'): Sero_list_B.append(B_third_choice) description.append(des) - print("$$Third possilble fljB: ",B_third_choice," Number: ",number) + print "$$Third possilble fljB: ",B_third_choice," Number: ",number except: - print("$$$No fljB, or failure of mapping") + print "$$$No fljB, or failure of mapping" if len(description)==0: #used for the case which fljB and fliC both has no hit, it will directly cease the function return handle=SeqIO.parse("database/"+database,"fasta")########1/27/2015 @@ -250,10 +250,10 @@ Sero_list_B=[] if listtype=="fliC": if len(fliC_fljB_list)==0: - print("$$No fliC, due to no hit") #because the only possible situation for len(final_fliC)==0 is above (z=0) len(final_fliC)==0, so there is no need to use "$$$" here + print "$$No fliC, due to no hit" #because the only possible situation for len(final_fliC)==0 is above (z=0) len(final_fliC)==0, so there is no need to use "$$$" here else: if fliC_fljB_list[0][1]<=1: - print("$$No fliC, due to the hit reads number is small.") #similiar with above, no "$$$" + print "$$No fliC, due to the hit reads number is small." #similiar with above, no "$$$" else: if fliC_fljB_list[0][0].split("_")[-1]=="g,m": type="fliC" @@ -293,7 +293,7 @@ else: try: Sero_list_C.append(fliC_fljB_list[0][0].split("_")[1]) - print("$$$Most possilble fliC: ",Sero_list_C[0]," Number: ",fliC_fljB_list[0][1]) + print "$$$Most possilble fliC: ",Sero_list_C[0]," Number: ",fliC_fljB_list[0][1] i=0 for x in fliC_fljB_list: if x[0].split("_")[1] not in Sero_list_C: @@ -303,7 +303,7 @@ number=x[1] if locals().has_key('sec_choice'): Sero_list_C.append(sec_choice) - print("$$$Sec possilble fliC: ",sec_choice," Number: ",number) + print "$$$Sec possilble fliC: ",sec_choice," Number: ",number j=0 for x in fliC_fljB_list: if x[0].split("_")[1] not in Sero_list_C: @@ -313,16 +313,16 @@ number=x[1] if locals().has_key('third_choice'): Sero_list_C.append(third_choice) - print("$$$Third possilble fliC: ",third_choice," Number: ",number) + print "$$$Third possilble fliC: ",third_choice," Number: ",number except: - print("$$$No fliC, or failure of mapping (second run)") + print "$$$No fliC, or failure of mapping (second run)" if listtype=="fljB": if len(fliC_fljB_list)==0: - print("$$No fljB, due to no hit") #similiar with above, no "$$$" + print "$$No fljB, due to no hit" #similiar with above, no "$$$" else: if fliC_fljB_list[0][1]<=1: - print("$$No fljB, due to the hit reads number is small.") #similiar with above, no "$$$" + print "$$No fljB, due to the hit reads number is small." #similiar with above, no "$$$" else: if fliC_fljB_list[0][0].split("_")[-1]=="1": type="fljB" @@ -347,7 +347,7 @@ else: try: Sero_list_B.append(fliC_fljB_list[0][0].split("_")[1]) - print("$$$Most possilble fljB: ",Sero_list_B[0]," Number: ",fliC_fljB_list[0][1]) + print "$$$Most possilble fljB: ",Sero_list_B[0]," Number: ",fliC_fljB_list[0][1] i=0 for x in fliC_fljB_list: if x[0].split("_")[1] not in Sero_list_B: @@ -357,7 +357,7 @@ number=x[1] if locals().has_key('B_sec_choice'): Sero_list_B.append(B_sec_choice) - print("$$$Sec possilble fljB: ",B_sec_choice," Number: ",number) + print "$$$Sec possilble fljB: ",B_sec_choice," Number: ",number j=0 for x in fliC_fljB_list: if x[0].split("_")[1] not in Sero_list_B: @@ -367,9 +367,9 @@ number=x[1] if locals().has_key('B_third_choice'): Sero_list_B.append(B_third_choice) - print("$$$Third possilble fljB: ",B_third_choice," Number: ",number) + print "$$$Third possilble fljB: ",B_third_choice," Number: ",number except: - print("$$$No fljB, or failure of mapping (second run)") + print "$$$No fljB, or failure of mapping (second run)" def assembly(type,sra_name,for_fq,rev_fq,for_sai,rev_sai,sam,bam,database,database2,list_length,mapping_mode): @@ -421,18 +421,18 @@ score+=handle[i].alignments[j].hsps[z].bits List_score.append(score) temp=dict(zip(List,List_score)) - Final_list=sorted(temp.items(), key=lambda d:d[1], reverse = True) + Final_list=sorted(temp.iteritems(), key=lambda d:d[1], reverse = True) family=database2.split("_")[2] try: - Final_list[0][0].split("_")[1] # or it will always print("$$$Genome...."(next line) - print("$$$Genome:",sra_name) - print("$$$Most possilble "+type+": ",Final_list[0][0].split("_")[1]," Score(due_to_special_test, number changed to score): ",Final_list[0][1]) - print(Final_list) + Final_list[0][0].split("_")[1] # or it will always print "$$$Genome...."(next line) + print "$$$Genome:",sra_name + print "$$$Most possilble "+type+": ",Final_list[0][0].split("_")[1]," Score(due_to_special_test, number changed to score): ",Final_list[0][1] + print Final_list except: if type=="fliC": - print("$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fliC_option) + print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fliC_option if type=="fljB": - print("$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fljB_option) + print "$$$There may be no hit for "+type+"_"+family+" family due to the reads not covering core seqeunce, but just based on reads hit number, the most possible one is: ",fljB_option os.system("rm "+database2+"_vs_"+sam+".xml")###01/28/2015 os.system("rm "+database+sam+"_seq.txt")###01/28/2015 os.system("rm "+database+sam+"_title.txt")###01/28/2015
--- a/libs/BWA_analysis_O_new_dependent.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/BWA_analysis_O_new_dependent.py Wed Nov 29 08:34:19 2017 -0500 @@ -64,7 +64,7 @@ for_fq=for_core_id+".fastq" rev_fq=re_core_id+".fastq" dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))#######03152016 - print("check fastq id and make them in accordance with each other...please wait...") + print "check fastq id and make them in accordance with each other...please wait..." os.system("python "+dirpath+"/compare_and_change_two_fastq_id.py "+for_fq+" "+rev_fq)#######03152016 for_sai=for_core_id+".sai" rev_sai=re_core_id+".sai" @@ -117,8 +117,8 @@ c=dict(zip(a,b)) final_O=sorted(c.iteritems(), key=lambda d:d[1], reverse = True) #order from frequency high to low, but tuple while not list Sero_list_O=[] - print("Final_Otype_list:") - print(final_O) + print "Final_Otype_list:" + print final_O num_1=0#new inserted O9_wbav=0 O310_wzx=0 @@ -140,12 +140,12 @@ O_choice="" - print("$$$Genome:",sra_name) + print "$$$Genome:",sra_name if len(final_O)==0: - print("$$$No Otype, due to no hit") + print "$$$No Otype, due to no hit" else: if final_O[0][1]<8: - print("$$$No Otype, due to the hit reads number is small.") + print "$$$No Otype, due to the hit reads number is small." else: for x in final_O: if x[1]>5: @@ -154,17 +154,17 @@ for x in final_O:# if "sdf" in x[0] and x[1]>3:# qq=0# - print("$$$",x[0],"got a hit, reads:",x[1])# + print "$$$",x[0],"got a hit, reads:",x[1]# if qq!=0:# - print("$$$No sdf exists")# + print "$$$No sdf exists"# if "O-9,46_wbaV" in O_list and float(O9_wbaV)/float(num_1) > 0.1: if "O-9,46_wzy" in O_list and float(O946_wzy)/float(num_1) > 0.1: O_choice="O-9,46" - print("$$$Most possilble Otype: O-9,46") + print "$$$Most possilble Otype: O-9,46" elif "O-9,46,27_partial_wzy" in O_list and float(O94627)/float(num_1) > 0.1: O_choice="O-9,46,27" - print("$$$Most possilble Otype: O-9,46,27") + print "$$$Most possilble Otype: O-9,46,27" else: O_choice="O-9" if file_mode=="3": @@ -176,18 +176,18 @@ elif ("O-3,10_wzx" in O_list) and ("O-9,46_wzy" in O_list) and float(O310_wzx)/float(num_1) > 0.1 and float(O946_wzy)/float(num_1) > 0.1: if "O-3,10_not_in_1,3,19" in O_list and float(O310_no_1319)/float(num_1) > 0.1: O_choice="O-3,10" - print("$$$Most possilble Otype: O-3,10") + print "$$$Most possilble Otype: O-3,10" else: O_choice="O-1,3,19" - print("$$$Most possilble Otype: O-1,3,19") + print "$$$Most possilble Otype: O-1,3,19" else: try: O_choice=final_O[0][0].split("_")[0] if O_choice=="O-1,3,19": O_choice=final_O[1][0].split("_")[0] - print("$$$Most possilble Otype: ",O_choice) + print "$$$Most possilble Otype: ",O_choice except: - print("$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)") + print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)" def assembly(sra_name,potential_choice,for_fq,rev_fq,for_sai,rev_sai,sam,bam,mapping_mode): @@ -246,15 +246,15 @@ O2_bigger+=1 except: continue - print("$$$Genome:",sra_name) + print "$$$Genome:",sra_name if O9_bigger>O2_bigger: - print("$$$Most possible Otype is O-9") + print "$$$Most possible Otype is O-9" elif O9_bigger<O2_bigger: - print("$$$Most possible Otype is O-2") + print "$$$Most possible Otype is O-2" else: - print("$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility.") - print("O-9 number is:",O9_bigger) - print("O-2 number is:",O2_bigger) + print "$$$No suitable one, because can't distinct it's O-9 or O-2, but ",potential_choice," has a more possibility." + print "O-9 number is:",O9_bigger + print "O-2 number is:",O2_bigger os.system("rm "+sam+"_title.txt")###01/28/2015 os.system("rm "+sam+"_seq.txt")###01/28/2015
--- a/libs/H_combination_output_analysis.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/H_combination_output_analysis.py Wed Nov 29 08:34:19 2017 -0500 @@ -225,21 +225,21 @@ combination_score.append(score) combinationlist=dict(zip(combination,combination_score)) #we can do the filteration here final_dict=sorted(combinationlist.iteritems(), key=lambda d:d[1], reverse = True) - print("$$_H:Order:",final_dict) + print "$$_H:Order:",final_dict elif score>100 and fljB_score<100: - print("$$_H:No fljB, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice) + print "$$_H:No fljB, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice elif score<100 and fljB_score>100: - print("$$_H:No fliC, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice) + print "$$_H:No fliC, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice elif score==1 and fljB_score>100: - print("$$_H:No fliC (file) existed, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice) + print "$$_H:No fliC (file) existed, only fljB, and its order:",fljB_First_Choice,fljB_Sec_Choice,fljB_Third_Choice elif score==1 and fljB_score<100: - print("$$_H:No fliC (file) existed, and no fljB") + print "$$_H:No fliC (file) existed, and no fljB" elif score>100 and fljB_score==1: - print("$$_H:No fljB (file) existed, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice) + print "$$_H:No fljB (file) existed, only fliC, and its order:",First_Choice,Sec_Choice,Third_Choice elif score<100 and fljB_score==1: - print("$$_H:No fljB (file) existed, and no fliC") + print "$$_H:No fljB (file) existed, and no fliC" else: - print("$$_H:No fliC and fljB") + print "$$_H:No fliC and fljB" '''
--- a/libs/Otype_determine_analysis.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/Otype_determine_analysis.py Wed Nov 29 08:34:19 2017 -0500 @@ -49,17 +49,17 @@ O_2_score=O_2_score+hsp.bits if O_9_score>100: if O_9_score>O_2_score: - print('$$$ Most possible O_type: O-9','\n') - print('$$$ longest_bit_score:',O_9_score,'\n') + print '$$$ Most possible O_type: O-9','\n' + print '$$$ longest_bit_score:',O_9_score,'\n' else: - print('$$$ Most possible O_type: O-2','\n') - print('$$$ longest_bit_score:',O_2_score,'\n') + print '$$$ Most possible O_type: O-2','\n' + print '$$$ longest_bit_score:',O_2_score,'\n' else: - print("Assumpition wrong, no O2 or O9, return to re-analysis") + print "Assumpition wrong, no O2 or O9, return to re-analysis" if ('O-2_' not in Sec_Choice) and ('O-9_' not in Sec_Choice): - print('$$$ Most possible O_type Choice (no tyr difference):',Sec_Choice) + print '$$$ Most possible O_type Choice (no tyr difference):',Sec_Choice if (('O-2_' in Sec_Choice) or ('O-9_' in Sec_Choice)) and ('O-2_' not in Third_Choice) and ('O-9_' not in Third_Choice): - print('$$$ Most possible O_type Choice (no tyr difference):',Third_Choice) + print '$$$ Most possible O_type Choice (no tyr difference):',Third_Choice os.system("rm tyr_of_O2_O9.fasta_db.*")###01/28/2015 os.system("rm "+xml_file)###01/28/2015 if subdatabase=="oafA_of_O4_O5.fasta": @@ -76,17 +76,17 @@ O_2_score=O_2_score+hsp.bits if O_9_score>100: if O_9_score>O_2_score: - print('$$$O5_none_7_base_deletion','\n') - print('$$$ longest_bit_score:',O_9_score,'\n') + print '$$$O5_none_7_base_deletion','\n' + print '$$$ longest_bit_score:',O_9_score,'\n' else: - print('$$$O5-','\n' - print('$$$ longest_bit_score:',O_2_score,'\n') + print '$$$O5-','\n' + print '$$$ longest_bit_score:',O_2_score,'\n' else: - print('$$$O5_none_7_base_deletion,unsure','\n') + print '$$$O5_none_7_base_deletion,unsure','\n' os.system("rm oafA_of_O4_O5.fasta_db.*")###01/28/2015 os.system("rm "+xml_file)###01/28/2015 except: - print("No oafA genes") + print "No oafA genes" if subdatabase=="O_3,10_and_1,3,19_spe.fasta": try: for record in records: #there are many records (i.e. the '>' in query file), so change another method @@ -101,16 +101,16 @@ O_2_score=O_2_score+hsp.bits if O_9_score>200: if O_9_score>O_2_score: - print('$$$O3,10 more possible','\n' - print('$$$ longest_bit_score:',O_9_score,'\n' + print '$$$O3,10 more possible','\n' + print '$$$ longest_bit_score:',O_9_score,'\n' else: if O_2_score>100: - print('$$$O1,3,19 more possible','\n' - print('$$$ longest_bit_score:',O_2_score,'\n' + print '$$$O1,3,19 more possible','\n' + print '$$$ longest_bit_score:',O_2_score,'\n' os.system("rm O_3,10_and_1,3,19_spe.fasta_db.*")###01/28/2015 os.system("rm "+xml_file)###01/28/2015 except: - print("No O3,10_and_O1,3,19 spe sequences" + print "No O3,10_and_O1,3,19 spe sequences" def show_result(): @@ -231,25 +231,25 @@ else: names=First_Choice+Sec_Choice if score==0: - print("$$$ No O_type, due to no hit of rfb") + print "$$$ No O_type, due to no hit of rfb" names="" if 'O-2_' in names and 'O-9_' in names and ('O-2_' in First_Choice or 'O-9_' in First_Choice): - print('#Contain O2 and O9, so change to special test') + print '#Contain O2 and O9, so change to special test' test_O29("tyr_of_O2_O9.fasta") else: if score>0: - print('$$$ Most possible O_type: ',First_Choice,'\n') - print('$$$ Most bit_score:',score,'\n') + print '$$$ Most possible O_type: ',First_Choice,'\n' + print '$$$ Most bit_score:',score,'\n' if "O-4_" in First_Choice:#$$$$$$$ test_O29("oafA_of_O4_O5.fasta")#$$$$$$$ if "O-1,3,19" in First_Choice or "O-3,10" in First_Choice: test_O29("O_3,10_and_1,3,19_spe.fasta")#$$$$$$$ if secscore>0: - print('$$$ Second possible O_type: ',Sec_Choice,'\n') - print('$$$ Second bit_score:',secscore,'\n') + print '$$$ Second possible O_type: ',Sec_Choice,'\n' + print '$$$ Second bit_score:',secscore,'\n' if thirdscore>0: - print('$$$ Third possible O_type: ',Third_Choice,'\n' - print('$$$ Third bit_score:',thirdscore,'\n') + print '$$$ Third possible O_type: ',Third_Choice,'\n' + print '$$$ Third bit_score:',thirdscore,'\n' @@ -261,13 +261,13 @@ target=sys.argv[2] database=sys.argv[3] output=target.split('.')[0]+'_out.fa' -print("$$:",target +print "$$:",target os.system(Makebltdb+' -in '+target+' -out '+target+'_db '+'-dbtype nucl')###01/28/2015 os.system(Blastnpth+' -query '+queries+' -db '+target+'_db '+'-out '+queries+'_vs_'+target+'.xml '+'-outfmt 5')###01/28/2015, since it's abs address for "run_auto*.py", so no need to change "query" address this time xml_file=queries+'_vs_'+target+'.xml' -print('\n' +print '\n' result_handle=open(xml_file) blast_record=NCBIXML.parse(result_handle) blast_record=list(blast_record) @@ -277,13 +277,13 @@ #os.system("rm "+target+'_db.*')###01/28/2015 if len(blast_record)==2: - print('Hits have been got'+'\n') + print 'Hits have been got'+'\n' if len(blast_record[0].alignments)==1 and len(blast_record[1].alignments)==1: - print('Checking the number of alignments: 2 alignments obtained'+'\n') + print 'Checking the number of alignments: 2 alignments obtained'+'\n' if len(blast_record[0].alignments[0].hsps)==1 and len(blast_record[1].alignments[0].hsps)==1: - print('Checking the number of hsps: each alignment has 1 hsp'+'\n') + print 'Checking the number of hsps: each alignment has 1 hsp'+'\n' if blast_record[0].alignments[0].hit_def==blast_record[1].alignments[0].hit_def: - print('Checking locations of hits: Both hits are located in '+'"'+str(blast_record[0].alignments[0].hit_def)+'"'+'...'+'\n') + print 'Checking locations of hits: Both hits are located in '+'"'+str(blast_record[0].alignments[0].hit_def)+'"'+'...'+'\n' hit_1_start=blast_record[0].alignments[0].hsps[0].sbjct_start hit_1_end=blast_record[0].alignments[0].hsps[0].sbjct_end @@ -301,11 +301,11 @@ hit_2_start=hit_2_end hit_2_end=buffer - print('hit_1_start: '+str(hit_1_start) - print('hit_1_end: '+str(hit_1_end) + print 'hit_1_start: '+str(hit_1_start) + print 'hit_1_end: '+str(hit_1_end) - print('hit_2_start: '+str(hit_2_start) - print('hit_2_end: '+str(hit_2_end) + print 'hit_2_start: '+str(hit_2_start) + print 'hit_2_end: '+str(hit_2_end) if hit_1_end<hit_2_start: @@ -315,15 +315,15 @@ extract_start=hit_2_end+1 extract_end=hit_1_start-1 - print('start: '+str(extract_start), 'end: '+str(extract_end)+'\n') + print 'start: '+str(extract_start), 'end: '+str(extract_end)+'\n' for contig in target_seq: if (contig.description==blast_record[0].alignments[0]) or (contig.description.replace(" ","")==blast_record[0].alignments[0].hit_def.replace(" ","")): target_contig=contig rfb_region=target_contig[extract_start:extract_end] - print('Extracted rfb region length: '+str(len(rfb_region.seq.tostring()))+'\n') - print('Extracted rfb region saved in: '+output+'\n') + print 'Extracted rfb region length: '+str(len(rfb_region.seq.tostring()))+'\n' + print 'Extracted rfb region saved in: '+output+'\n' outfile=open(output,'w') title='>'+target.split('.')[0]+' rfb region:'+blast_record[0].alignments[0].hit_def+':'+str(extract_start)+' to '+str(extract_end)+'_'+str(len(rfb_region.seq.tostring()))+'bp'+')' @@ -336,7 +336,7 @@ os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl') os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5') xml_file='Blast_Otype_'+target+'.xml' - print('\n' + print '\n' filehandle=open(xml_file) @@ -349,7 +349,7 @@ show_result() else: - print('Checking locations of hits: the two hits are not located in same contig......'+'\n') + print 'Checking locations of hits: the two hits are not located in same contig......'+'\n' hit_1_start=blast_record[0].alignments[0].hsps[0].sbjct_start hit_1_end=blast_record[0].alignments[0].hsps[0].sbjct_end hit_2_start=blast_record[1].alignments[0].hsps[0].sbjct_start @@ -400,7 +400,7 @@ os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl') os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5') xml_file='Blast_Otype_'+target+'.xml' - print('\n') + print '\n' filehandle=open(xml_file) @@ -431,7 +431,7 @@ os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5') xml_file='Combined_seq_blast_'+target+'.xml' - print('\n' + print '\n' filehandle=open(xml_file) records=NCBIXML.parse(filehandle) @@ -443,18 +443,18 @@ else: - print('$$$ No O_type result, please check the number of hsps: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for for our short sequence gnd and galF, please check your submited sequence'+'\n' + print '$$$ No O_type result, please check the number of hsps: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for for our short sequence gnd and galF, please check your submited sequence'+'\n' elif len(blast_record[0].alignments)>1 and len(blast_record[1].alignments)==1: - print('The gnd gene is splited on different contigs of your submitted sequence' +'\n' + print 'The gnd gene is splited on different contigs of your submitted sequence' +'\n' for record in blast_record: for alignment in record.alignments: if len(alignment.hsps)!=1: - print('$$$ No O_type result, please check the number of hsp: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n' + print '$$$ No O_type result, please check the number of hsp: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n' break - print('Each alignment has one hsps'+'\n' + print 'Each alignment has one hsps'+'\n' @@ -515,12 +515,12 @@ os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl') os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5') - print('\n') + print '\n' xml_file2='Blast_Otype_'+target+'.xml' filehandle=open(xml_file2) records=NCBIXML.parse(filehandle) records=list(records) - print(len(records)) + print len(records) realrecord1=records[0] if len(records[1].alignments)>len(records[0].alignments): realrecord1=records[1] @@ -548,7 +548,7 @@ os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5') xml_file='Combined_seq_blast_'+target+'.xml' - print('\n') + print '\n' filehandle=open(xml_file) @@ -560,14 +560,14 @@ elif len(blast_record[0].alignments)==1 and len(blast_record[1].alignments)>1: - print('The galF gene is splited on different contigs of your submitted sequence' +'\n') + print 'The galF gene is splited on different contigs of your submitted sequence' +'\n' for record in blast_record: for alignment in record.alignments: if len(alignment.hsps)!=1: - print('$$$ No O_type result, please check the number of hsps: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n') + print '$$$ No O_type result, please check the number of hsps: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n' break - print('Each alignment has one hsp'+'\n') + print 'Each alignment has one hsp'+'\n' outfile=open(output,'w') for alignment in blast_record[0].alignments: @@ -622,7 +622,7 @@ os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl') os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5') - print('\n') + print '\n' xml_file='Blast_Otype_'+target+'.xml' filehandle=open(xml_file) records=NCBIXML.parse(filehandle) @@ -654,7 +654,7 @@ os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5') xml_file='Combined_seq_blast_'+target+'.xml' - print('\n') + print '\n' filehandle=open(xml_file) @@ -665,14 +665,14 @@ elif len(blast_record[0].alignments)>1 and len(blast_record[1].alignments)>1: - print('The gnd and galF gene are both splited on different contigs of your submitted sequence' +'\n') + print 'The gnd and galF gene are both splited on different contigs of your submitted sequence' +'\n' for record in blast_record: for alignment in record.alignments: if len(alignment.hsps)!=1: - print('$$$ No O_type result, please check the number of hsp: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n') + print '$$$ No O_type result, please check the number of hsp: some alignment have more than 1 hsp (galF or gnd sequences has one more hits in tested genome), that\'s unusual for our short sequence gnd and galF, please check your submited sequence'+'\n' break - print('Each alignment has one hsps'+'\n') + print 'Each alignment has one hsps'+'\n' outfile=open(output,'w') for alignment in blast_record[0].alignments: @@ -728,7 +728,7 @@ os.system(Makebltdb+' -in '+database+' -out '+database+'_db '+'-dbtype nucl') os.system(Blastnpth+' -query '+output+' -db '+database+'_db '+'-out '+'Blast_Otype_'+target+'.xml '+'-outfmt 5') xml_file='Blast_Otype_'+target+'.xml' - print('\n') + print '\n' filehandle=open(xml_file) records=NCBIXML.parse(filehandle) records=list(records) @@ -759,7 +759,7 @@ os.system(Blastnpth+' -query combined_sequence.fasta'+' -db '+database+'_db '+'-out '+'Combined_seq_blast_'+target+'.xml '+'-outfmt 5') xml_file='Combined_seq_blast_'+target+'.xml' - print('\n') + print '\n' filehandle=open(xml_file) @@ -771,7 +771,7 @@ else: - print('$$$ $$$ No O_type result, Attention: unusual number of hits, no hits for galF or gnd! Check blast output...'+'\n') + print '$$$ $$$ No O_type result, Attention: unusual number of hits, no hits for galF or gnd! Check blast output...'+'\n' os.system('rm '+target+'_db.'+'*')
--- a/libs/compare_and_change_two_fastq_id.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/compare_and_change_two_fastq_id.py Wed Nov 29 08:34:19 2017 -0500 @@ -17,11 +17,11 @@ if a_title==b_title: pass else: - print("changing the title of two seperated fastq files...") - print(a_title,b_title) + print "changing the title of two seperated fastq files..." + print a_title,b_title os.system("sed "+"-i 's/.1 / /g' "+file1) - print("finished file1") + print "finished file1" os.system("sed "+"-i 's/.2 / /g' "+file2) - print("finished file2") + print "finished file2" compare_and_change_two_fastq_id(file1,file2) \ No newline at end of file
--- a/libs/deletion_compare.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/deletion_compare.py Wed Nov 29 08:34:19 2017 -0500 @@ -120,15 +120,15 @@ O2_bigger+=1 except: continue - print("$$$Genome:",sra_name) + print "$$$Genome:",sra_name if O9_bigger>O2_bigger: - print("$$$Typhimurium") + print "$$$Typhimurium" elif O9_bigger<O2_bigger: - print("$$$Typhimurium_O5-") + print "$$$Typhimurium_O5-" else: - print("$$$Typhimurium, even no 7 bases difference") - print("O-4 number is:",O9_bigger) - print("O-4_5- number is:",O2_bigger) + print "$$$Typhimurium, even no 7 bases difference" + print "O-4 number is:",O9_bigger + print "O-4_5- number is:",O2_bigger os.system("rm "+sam+"_title.txt")###01/28/2015 os.system("rm "+sam+"_seq.txt")###01/28/2015 os.system("rm "+sam+".fasta")###01/28/2015
--- a/libs/run_auto_All_for_assemblies.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/run_auto_All_for_assemblies.py Wed Nov 29 08:34:19 2017 -0500 @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python2.7 @@ -51,11 +51,11 @@ real_file=file2 except: real_file=file1 - #print("###The genome name:",file1 + #print "###The genome name:",file1 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015 os.system('touch result.txt') database_path="database"###01/27/2015 - os.system('python '+dirpath+'/Otype_determine_analysis.py '+database_path+'/Typhimurium_LT2_gnd_galF.fasta '+real_file+' '+database_path+'/new_Oserotype.fasta >temp_result_'+str(q)+'O.txt') + os.system('python2.7 '+dirpath+'/Otype_determine_analysis.py '+database_path+'/Typhimurium_LT2_gnd_galF.fasta '+real_file+' '+database_path+'/new_Oserotype.fasta >temp_result_'+str(q)+'O.txt') os.system('cat temp_result_'+str(q)+'O.txt>>data_log.txt') handle=open('temp_result_'+str(q)+'O.txt',"r") handle=handle.readlines() @@ -81,8 +81,8 @@ elif O1_3_19=="+": Otype="1,3,19" else: - print("No_O3,10_O1,3,19_spe_sequences") - os.system('python '+dirpath+'/H_combination_output_analysis.py '+real_file+' '+database_path+'/H_new_fliC_protein_database.fasta '+database_path+'/H_new_fljB_protein_database.fasta >temp_result_'+str(q)+'H.txt') + print "No_O3,10_O1,3,19_spe_sequences" + os.system('python2.7 '+dirpath+'/H_combination_output_analysis.py '+real_file+' '+database_path+'/H_new_fliC_protein_database.fasta '+database_path+'/H_new_fljB_protein_database.fasta >temp_result_'+str(q)+'H.txt') os.system('cat temp_result_'+str(q)+'H.txt>>data_log.txt') handle2=open('temp_result_'+str(q)+'H.txt',"r") handle2=handle2.readlines() @@ -103,7 +103,7 @@ fljB="-" #print line, if Otype=="9" and fliC=="g,m" and fljB=="-": - os.system('python '+dirpath+'/special_gene_test_assemblies.py '+database_path+'/specific_genes.fasta '+real_file+' sdf >temp_result_'+str(q)+'sdf.txt') + os.system('python2.7 '+dirpath+'/special_gene_test_assemblies.py '+database_path+'/specific_genes.fasta '+real_file+' sdf >temp_result_'+str(q)+'sdf.txt') os.system('cat temp_result_'+str(q)+'sdf.txt>>data_log.txt') handle3=open('temp_result_'+str(q)+'sdf.txt',"r") sdf="" @@ -166,18 +166,18 @@ if len(seronames)>1: star="*" star_line="The predicted serotypes share the same general formula:\t"+Otype+":"+fliC+":"+fljB+"\n"## - #print("$$$The most possible formula is: (by the order O:H1:H2) ",Otype,":",fliC,":",fljB - #print("$$$The possible serotyes are:",seronames + #print "$$$The most possible formula is: (by the order O:H1:H2) ",Otype,":",fliC,":",fljB + #print "$$$The possible serotyes are:",seronames m=0 for y in seronames: if y in file1: - #print("$$$ Is the judgement true? Answer:Yes!" #here we use file1, because we want ":", while file2 turned it to "__" + #print "$$$ Is the judgement true? Answer:Yes!" #here we use file1, because we want ":", while file2 turned it to "__" answer="Yes" m=1 if m==0: - #print("$$$ Is the judgement true? Answer: Need to check the records and file names" + #print "$$$ Is the judgement true? Answer: Need to check the records and file names" answer="Not sure" - print("\n","\n") + print "\n","\n" predict_form=Otype+":"+fliC+":"+fljB predict_sero=(" or ").join(seronames) if predict_form=="9:g,m:-":# @@ -250,12 +250,12 @@ txt_names.append(file_names[j+i].replace(' ','_').replace(":","__").replace("[","").replace("]","")+".txt") print txt_names for j in xrange(len(txt_names)): - print(i,"and",j) - print(i+j+1) + print i,"and",j + print i+j+1 file=open(txt_names[j],"r") handle=list(file) b=handle[0].split("\t") - print(b) + print b sheet.write(i+j+1,0,b[0]) sheet.write(i+j+1,1,b[1]) sheet.write(i+j+1,2,b[2]) @@ -265,7 +265,7 @@ sheet.write(i+j+1,6,b[6]) sheet.write(i+j+1,7,b[7]) - print("End time,",time.time()) + print "End time,",time.time() file3.save("Seqsero_result2.xls") '''
--- a/libs/run_auto_All_for_web_multi_revise.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/run_auto_All_for_web_multi_revise.py Wed Nov 29 08:34:19 2017 -0500 @@ -1,4 +1,4 @@ -#!/usr/bin/env python +#!/usr/bin/env python2.7 @@ -63,16 +63,16 @@ additional_file=file2 except: pass - #print("###The genome name:",file1 + #print "###The genome name:",file1 dirpath = os.path.abspath(os.path.dirname(os.path.realpath(__file__)))###01/27/2015 os.system('touch result.txt') database_path="database"###01/27/2015, because we add one directory to the result directory if file_mode=="1": - os.system('python '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'O.txt')###01/27/2015 + os.system('python2.7 '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'O.txt')###01/27/2015 elif file_mode=="2": - os.system('python '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'O.txt')###01/27/2015 + os.system('python2.7 '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'O.txt')###01/27/2015 elif file_mode=="3": - os.system('python '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'O.txt')###01/27/2015 + os.system('python2.7 '+dirpath+'/BWA_analysis_O_new_dependent.py '+real_file+' '+database_path+'/special_new_O_genes.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'O.txt')###01/27/2015 os.system('cat temp_result_'+str(q)+'O.txt>>data_log.txt')###01/28/2015 handle=open('temp_result_'+str(q)+'O.txt',"r") handle=handle.readlines() @@ -92,11 +92,11 @@ if sdf!="+":# sdf="-"# if file_mode=="1": - os.system('python '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'H.txt')###01/27/2015 + os.system('python2.7 '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 1 >temp_result_'+str(q)+'H.txt')###01/27/2015 if file_mode=="2": - os.system('python '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+" "+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' '+additional_file+' 2 >temp_result_'+str(q)+'H.txt')###01/27/2015 + os.system('python2.7 '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+" "+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' '+additional_file+' 2 >temp_result_'+str(q)+'H.txt')###01/27/2015 if file_mode=="3": - os.system('python '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'H.txt')###01/27/2015 + os.system('python2.7 '+dirpath+'/BWA_analysis_H_update_new_family_dependent.py '+real_file+' '+database_path+'/H_combine_update_9_03_2014_new.fasta '+mapping_mode+' 3 >temp_result_'+str(q)+'H.txt')###01/27/2015 os.system('cat temp_result_'+str(q)+'H.txt>>data_log.txt') handle2=open('temp_result_'+str(q)+'H.txt',"r") handle2=handle2.readlines() @@ -176,18 +176,18 @@ if len(seronames)>1: star="*" star_line="The predicted serotypes share the same general formula:\t"+Otype+":"+fliC+":"+fljB+"\n"## - #print("$$$The most possible formula is: (by the order O:H1:H2) ",Otype,":",fliC,":",fljB - #print("$$$The possible serotyes are:",seronames + #print "$$$The most possible formula is: (by the order O:H1:H2) ",Otype,":",fliC,":",fljB + #print "$$$The possible serotyes are:",seronames m=0 for y in seronames: if y in file1: - #print("$$$ Is the judgement true? Answer:Yes!" #here we use file1, because we want ":", while file2 turned it to "__" + #print "$$$ Is the judgement true? Answer:Yes!" #here we use file1, because we want ":", while file2 turned it to "__" answer="Yes" m=1 if m==0: - #print("$$$ Is the judgement true? Answer: Need to check the records and file names" + #print "$$$ Is the judgement true? Answer: Need to check the records and file names" answer="Not sure" - print("\n","\n") + print "\n","\n" predict_form=Otype+":"+fliC+":"+fljB# predict_sero=(" or ").join(seronames)# if predict_form=="9:g,m:-":# @@ -216,11 +216,11 @@ ''' if "Typhimurium" in predict_sero or predict_form=="4:i:-":#03252016# if file_mode=="1": - os.system('python '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 1 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015 + os.system('python2.7 '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 1 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015 if file_mode=="2": - os.system('python '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015 + os.system('python2.7 '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+" "+additional_file+' 2 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015 if file_mode=="3": - os.system('python '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 3 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015 + os.system('python2.7 '+dirpath+'/deletion_compare.py '+real_file+' oafA '+mapping_mode+' 3 >temp_result_'+str(q)+'Typhim.txt')###02/06/2015 os.system('cat temp_result_'+str(q)+'Typhim.txt>>data_log.txt')###01/28/2015 handle=open('temp_result_'+str(q)+'Typhim.txt',"r") handle=handle.readlines() @@ -299,16 +299,16 @@ for j in xrange(len(jobs)): jobs[j].join() txt_names.append(file_names[j+i].replace(' ','_').replace(":","__").replace("[","").replace("]","")+".txt") - print(txt_names) + print txt_names for j in xrange(len(txt_names)): - print(i,"and",j) - print(i+j+1) + print i,"and",j + print i+j+1 file=open(txt_names[j],"r") handle=list(file) b=handle[0].split("\t") - print(b) + print b - print("End time,",time.time()) + print "End time,",time.time() ''' if __name__ == '__main__':
--- a/libs/special_gene_test_assemblies.py Tue Nov 28 21:16:36 2017 -0500 +++ b/libs/special_gene_test_assemblies.py Wed Nov 29 08:34:19 2017 -0500 @@ -31,7 +31,7 @@ for record in records: for alignment in record.alignments: if x in alignment.hit_def: #multi gene database, so... - print(x,"got a hit, evaluating the hit quality...") + print x,"got a hit, evaluating the hit quality..." score=0 for hsp in alignment.hsps: if hsp.expect<E_thresh: @@ -46,9 +46,9 @@ First_Choice=Htype score=scorelist[Htype] if float(score)>=0.1*aver_len: - print("$$$",First_Choice,"got a hit, score:",score) + print "$$$",First_Choice,"got a hit, score:",score else: - print("$$$No ",x,"exists") + print "$$$No ",x,"exists" os.system("rm "+database+"_db.*")##########1/28/2015 os.system("rm "+xml_file)##########1/28/2015
--- a/run_seqsero.py Tue Nov 28 21:16:36 2017 -0500 +++ b/run_seqsero.py Wed Nov 29 08:34:19 2017 -0500 @@ -96,9 +96,9 @@ for run in run2fastqs: seqsero_cmd = [] if len(run2fastqs[run]) == 2: - seqsero_cmd = ['python', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]] + seqsero_cmd = ['python2.7', seqsero, '-m', '2', '-i', run2fastqs[run][0], run2fastqs[run][1]] elif len(run2fastqs[run]) == 1: - seqsero_cmd = ['python', seqsero, '-m', '1', '-i', run2fastqs[run][0]] + seqsero_cmd = ['python2,7', seqsero, '-m', '1', '-i', run2fastqs[run][0]] p = Popen(seqsero_cmd, stdout=PIPE) output = p.communicate() outputs.append(output)
--- a/seqsero.xml Tue Nov 28 21:16:36 2017 -0500 +++ b/seqsero.xml Wed Nov 29 08:34:19 2017 -0500 @@ -12,9 +12,9 @@ <exit_code range="0:" level="warning"/> <regex match="Error:"/> </stdio> - <command> + <command interpreter="python2.7"> - python $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/ + $__tool_directory__/run_seqsero.py $input1 $__tool_directory__/ </command> <inputs>
--- a/test.txt Tue Nov 28 21:16:36 2017 -0500 +++ b/test.txt Wed Nov 29 08:34:19 2017 -0500 @@ -3,6 +3,22 @@ /galaxydir/galaxy/tools/GalaxySeqsero/run_seqsero.py /galaxydir/galaxy/database/files/000/dataset_170.dat,/galaxydir/galaxy/database/files/000/dataset_171.dat /galaxydir/galaxy/tools/GalaxySeqsero/ 3 2 -b"('\\n', '\\n')\nInput files:\tdataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq\nO antigen prediction:\tO-?\nH1 antigen prediction(fliC):\t-\nH2 antigen prediction(fljB):\t1,6\nPredicted antigenic profile:\t?:-:1,6\nPredicted serotype(s):\tN/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)\n\ncheck fastq id and make them in accordance with each other...please wait...\n\n\n\nResult:\n\n" + + + +Input files: dataset_170_SRR6325381.fastq dataset_171_SRR6325381.fastq +O antigen prediction: O-3,10 +H1 antigen prediction(fliC): e,h +H2 antigen prediction(fljB): 1,6 +Predicted antigenic profile: 3,10:e,h:1,6 +Predicted serotype(s): Anatum +The serotype(s) is/are the only serotype(s) with the indicated antigenic profile currently recognized in the Kauffmann White Scheme. New serotypes can emerge and the possibility exists that this antigenic profile may emerge in a different subspecies. Identification of strains to the subspecies level should accompany serotype determination; the same antigenic profile in different subspecies is considered different serotypes. +check fastq id and make them in accordance with each other...please wait... + + + +Result: + + None -Tue Nov 28 19:30:26 2017 \ No newline at end of file +Wed Nov 29 07:50:31 2017 \ No newline at end of file