seqsero_v2: libs/mapping_and_assembly

annotate libs/mapping_and_assembly_hybrid.py @ 3:62f8b9e226c2 draft default tip

planemo upload commit 9b152b4a900a8cd70df992da881c7e3fa00d4e4c-dirty

author	charles_s_test
date	Thu, 21 Dec 2017 11:06:32 -0500
parents	343e38c6798f
children

rev	line source
0 343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	1 import os,sys,glob,time,itertools,subprocess
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	2 from Initial_Conditions import phase1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	3 from Initial_Conditions import phase2
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	4 from Initial_Conditions import phaseO
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	5 from Initial_Conditions import sero
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	6 from distutils.version import LooseVersion
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	7
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	8
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	9
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	10
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	11 def xml_parse_score_comparision_seqsero(xmlfile):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	12 #used to do seqsero xml analysis
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	13 from Bio.Blast import NCBIXML
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	14 handle=open(xmlfile)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	15 handle=NCBIXML.parse(handle)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	16 handle=list(handle)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	17 List=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	18 List_score=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	19 List_ids=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	20 for i in range(len(handle)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	21 if len(handle[i].alignments)>0:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	22 for j in range(len(handle[i].alignments)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	23 score=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	24 ids=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	25 List.append(handle[i].query.strip()+"___"+handle[i].alignments[j].hit_def)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	26 for z in range(len(handle[i].alignments[j].hsps)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	27 if "last" in handle[i].query or "first" in handle[i].query:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	28 score+=handle[i].alignments[j].hsps[z].bits
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	29 ids+=float(handle[i].alignments[j].hsps[z].identities)/handle[i].query_length
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	30 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	31 if handle[i].alignments[j].hsps[z].align_length>=30:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	32 #for the long alleles, filter noise parts
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	33 score+=handle[i].alignments[j].hsps[z].bits
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	34 ids+=float(handle[i].alignments[j].hsps[z].identities)/handle[i].query_length
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	35 List_score.append(score)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	36 List_ids.append(ids)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	37 temp=zip(List,List_score,List_ids)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	38 Final_list=sorted(temp, key=lambda d:d[1], reverse = True)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	39 return Final_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	40
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	41
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	42 def Uniq(L,sort_on_fre="none"): #return the uniq list and the count number
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	43 Old=L
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	44 L.sort()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	45 L = [L[i] for i in range(len(L)) if L[i] not in L[:i]]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	46 count=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	47 for j in range(len(L)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	48 y=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	49 for x in Old:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	50 if L[j]==x:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	51 y+=1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	52 count.append(y)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	53 if sort_on_fre!="none":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	54 d=zip(*sorted(zip(count, L)))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	55 L=d[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	56 count=d[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	57 return (L,count)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	58
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	59
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	60 def judge_fliC_or_fljB_from_head_tail_for_one_contig(nodes_vs_score_list):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	61 #used to predict it's fliC or fljB for one contig, based on tail and head score, but output the score difference,if it is very small, then not reliable, use blast score for whole contig to test
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	62 #this is mainly used for
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	63 a=nodes_vs_score_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	64 fliC_score=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	65 fljB_score=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	66 for z in a:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	67 if "fliC" in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	68 fliC_score+=z[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	69 elif "fljB" in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	70 fljB_score+=z[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	71 if fliC_score>=fljB_score:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	72 role="fliC"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	73 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	74 role="fljB"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	75 return (role,abs(fliC_score-fljB_score))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	76
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	77 def judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(node_name,Final_list_passed):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	78 #used to predict contig is fliC or fljB, if the differnce score value on above head_and_tail is less than 10 (quite small)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	79 #also used when no head or tail got blasted score for the contig
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	80 role=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	81 for z in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	82 if node_name in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	83 role=z[0].split("_")[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	84 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	85 return role
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	86
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	87
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	88 def fliC_or_fljB_judge_from_head_tail_sequence(nodes_list,tail_head_list,Final_list_passed):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	89 #nodes_list is the c created by c,d=Uniq(nodes) in below function
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	90 first_target=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	91 role_list=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	92 for x in nodes_list:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	93 a=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	94 role=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	95 for y in tail_head_list:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	96 if x in y[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	97 a.append(y)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	98 if len(a)==4:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	99 #compare two heads (37 > 30)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	100 #four contigs, most perfect assembly, high quality
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	101 """
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	102 for z in a:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	103 if "fliC_first_37" in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	104 t1=z[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	105 elif "fljB_first_37" in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	106 t2=z[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	107 if t1>=t2:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	108 role="fliC"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	109 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	110 role="fljB"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	111 """
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	112 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	113 if diff<20:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	114 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	115 elif len(a)==3:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	116 """
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	117 #compare the number, because hybrid problem
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	118 temp=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	119 for z in a:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	120 temp.append(z[0].split("_")[0])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	121 m,n=Uniq(temp)#only two choices in m or n
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	122 if n[0]>n[1]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	123 role=m[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	124 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	125 role=m[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	126 """
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	127 ###however, if the one with highest score is the fewer one, compare their accumulation score
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	128 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	129 if diff<20:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	130 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	131 ###end of above score comparison
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	132 elif len(a)==2:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	133 #must on same node, if not, then decide with unit blast score, blast-score/length_of_special_sequence(30 or 37)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	134 temp=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	135 for z in a:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	136 temp.append(z[0].split("_")[0])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	137 m,n=Uniq(temp)#should only have one choice, but weird situation might occur too
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	138 if len(m)==1:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	139 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	140 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	141 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	142 #print "head and tail not belong to same role, now let's guess based on maximum likelihood"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	143 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	144 if diff<20:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	145 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	146 """
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	147 max_unit_score=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	148 for z in a:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	149 unit_score=z[-1]/int(z[0].split("__")[1])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	150 if unit_score>=max_unit_score:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	151 role=z[0].split("_")[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	152 max_unit_score=unit_score
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	153 """
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	154 ###need to desgin a algorithm to guess most possible situation for nodes_list, See the situations of test evaluation
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	155 elif len(a)==1:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	156 #that one
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	157 role,diff=judge_fliC_or_fljB_from_head_tail_for_one_contig(a)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	158 if diff<20:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	159 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	160 #role=a[0][0].split("_")[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	161 #need to evaluate, in future, may set up a cut-off, if not met, then just find Final_list_passed best match,like when "a==0"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	162 else:#a==0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	163 #use Final_list_passed best match
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	164 for z in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	165 if x in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	166 role=z[0].split("_")[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	167 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	168 #print x,role,len(a)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	169 role_list.append((role,x))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	170 if len(role_list)==2:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	171 if role_list[0][0]==role_list[1][0]:#this is the most cocmmon error, two antigen were assigned to same phase
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	172 #just use score to do a final test
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	173 role_list=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	174 for x in nodes_list:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	175 role=judge_fliC_or_fljB_from_whole_contig_blast_score_ranking(x,Final_list_passed)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	176 role_list.append((role,x))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	177 return role_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	178
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	179 def decide_contig_roles_for_H_antigen(Final_list):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	180 #used to decide which contig is FliC and which one is fljB
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	181 contigs=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	182 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1])>=3.5 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]))]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	183 nodes=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	184 for x in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	185 if x[0].startswith("fl") and "last" not in x[0] and "first" not in x[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	186 nodes.append(x[0].split("___")[1].strip())
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	187 c,d=Uniq(nodes)#c is node_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	188 #print c
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	189 tail_head_list=[x for x in Final_list if ("last" in x[0] or "first" in x[0])]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	190 roles=fliC_or_fljB_judge_from_head_tail_sequence(c,tail_head_list,Final_list_passed)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	191 return roles
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	192
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	193 def Combine(b,c):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	194 fliC_combinations=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	195 fliC_combinations.append(",".join(c))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	196 temp_combinations=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	197 for i in range(len(b)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	198 for x in itertools.combinations(b,i+1):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	199 temp_combinations.append(",".join(x))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	200 for x in temp_combinations:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	201 temp=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	202 for y in c:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	203 temp.append(y)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	204 temp.append(x)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	205 temp=",".join(temp)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	206 temp=temp.split(",")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	207 temp.sort()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	208 temp=",".join(temp)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	209 fliC_combinations.append(temp)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	210 return fliC_combinations
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	211
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	212 def decide_O_type_and_get_special_genes(Final_list):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	213 #decide O based on Final_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	214 O_choice="?"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	215 O_list=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	216 special_genes=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	217 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1])>=3.5 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]))]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	218 nodes=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	219 for x in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	220 if x[0].startswith("O-"):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	221 nodes.append(x[0].split("___")[1].strip())
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	222 elif not x[0].startswith("fl"):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	223 special_genes.append(x)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	224 #print "special_genes:",special_genes
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	225 c,d=Uniq(nodes)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	226 #print "potential O antigen contig",c
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	227 final_O=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	228 O_nodes_list=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	229 for x in c:#c is the list for contigs
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	230 temp=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	231 for y in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	232 if x in y[0] and y[0].startswith("O-"):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	233 final_O.append(y)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	234 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	235 ### O contig has the problem of two genes on same contig, so do additional test
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	236 potenial_new_gene=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	237 for x in final_O:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	238 pointer=0 #for genes merged or not
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	239 #not consider O-1,3,19_not_in_3,10, too short compared with others
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	240 if "O-1,3,19_not_in_3,10" not in x[0] and int(x[0].split("__")[1].split("___")[0])+800 <= int(x[0].split("length_")[1].split("_")[0]):#gene length << contig length; for now give 3002 (for secureity can use 4002) as flank region
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	241 pointer=x[0].split("___")[1].strip()#store the contig name
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	242 print pointer
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	243 if pointer!=0:#it has potential merge event
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	244 for y in Final_list:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	245 if pointer in y[0] and y not in final_O and (y[1]>=int(y[0].split("__")[1].split("___")[0])1.5 or (y[1]>=int(y[0].split("__")[1].split("___")[0])y[2] and y[1]>=400)):#that's a realtively strict filter now; if passed, it has merge event and add one more to final_O
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	246 potenial_new_gene=y
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	247 print potenial_new_gene
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	248 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	249 if potenial_new_gene!="":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	250 print "two differnt genes in same contig, fix it for O antigen"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	251 final_O.append(potenial_new_gene)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	252 ### end of the two genes on same contig test
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	253 if len(final_O)==0:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	254 #print "$$$No Otype, due to no hit"#may need to be changed
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	255 O_choice="-"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	256 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	257 O_list=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	258 for x in final_O:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	259 O_list.append(x[0].split("__")[0])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	260 if not "O-1,3,19_not_in_3,10__130" in x[0]:#O-1,3,19_not_in_3,10 is too small, which may affect further analysis
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	261 O_nodes_list.append(x[0].split("___")[1])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	262 ### special test for O9,46 and O3,10 family
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	263 if "O-9,46_wbaV" in O_list:#not sure should use and float(O9_wbaV)/float(num_1) > 0.1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	264 if "O-9,46_wzy" in O_list:#and float(O946_wzy)/float(num_1) > 0.1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	265 O_choice="O-9,46"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	266 #print "$$$Most possilble Otype: O-9,46"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	267 elif "O-9,46,27_partial_wzy" in O_list:#and float(O94627)/float(num_1) > 0.1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	268 O_choice="O-9,46,27"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	269 #print "$$$Most possilble Otype: O-9,46,27"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	270 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	271 O_choice="O-9"#next, detect O9 vs O2?
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	272 O2=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	273 O9=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	274 for z in special_genes:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	275 if "tyr-O-9" in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	276 O9=z[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	277 elif "tyr-O-2" in z[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	278 O2=z[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	279 if O2>O9:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	280 O_choice="O-2"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	281 elif O2<O9:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	282 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	283 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	284 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	285 #print "$$$No suitable one, because can't distinct it's O-9 or O-2, but O-9 has a more possibility."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	286 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
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	287 if "O-3,10_not_in_1,3,19" in O_list:#and float(O310_no_1319)/float(num_1) > 0.1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	288 O_choice="O-3,10"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	289 #print "$$$Most possilble Otype: O-3,10 (contain O-3,10_not_in_1,3,19)"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	290 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	291 O_choice="O-1,3,19"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	292 #print "$$$Most possilble Otype: O-1,3,19 (not contain O-3,10_not_in_1,3,19)"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	293 ### end of special test for O9,46 and O3,10 family
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	294 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	295 try:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	296 max_score=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	297 for x in final_O:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	298 if x[1]>=max_score:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	299 max_score=x[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	300 O_choice=x[0].split("_")[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	301 if O_choice=="O-1,3,19":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	302 O_choice=final_O[1][0].split("_")[0]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	303 #print "$$$Most possilble Otype: ",O_choice
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	304 except:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	305 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	306 #print "$$$No suitable Otype, or failure of mapping (please check the quality of raw reads)"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	307 #print "O:",O_choice,O_nodes_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	308 return O_choice,O_nodes_list,special_genes,final_O
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	309
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	310 def seqsero_from_formula_to_serotypes(Otype,fliC,fljB,special_gene_list):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	311 #like test_output_06012017.txt
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	312 #can add more varialbles like sdf-type, sub-species-type in future (we can conclude it into a special-gene-list)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	313 from Initial_Conditions import phase1
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	314 from Initial_Conditions import phase2
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	315 from Initial_Conditions import phaseO
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	316 from Initial_Conditions import sero
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	317 seronames=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	318 for i in range(len(phase1)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	319 fliC_combine=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	320 fljB_combine=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	321 if phaseO[i]==Otype:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	322 ### for fliC, detect every possible combinations to avoid the effect of "["
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	323 if phase1[i].count("[")==0:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	324 fliC_combine.append(phase1[i])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	325 elif phase1[i].count("[")>=1:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	326 c=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	327 b=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	328 if phase1[i][0]=="[" and phase1[i][-1]=="]" and phase1[i].count("[")==1:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	329 content=phase1[i].replace("[","").replace("]","")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	330 fliC_combine.append(content)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	331 fliC_combine.append("-")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	332 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	333 for x in phase1[i].split(","):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	334 if "[" in x:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	335 b.append(x.replace("[","").replace("]",""))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	336 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	337 c.append(x)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	338 fliC_combine=Combine(b,c) #Combine will offer every possible combinations of the formula, like f,[g],t: f,t f,g,t
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	339 ### end of fliC "[" detect
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	340 ### for fljB, detect every possible combinations to avoid the effect of "["
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	341 if phase2[i].count("[")==0:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	342 fljB_combine.append(phase2[i])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	343 elif phase2[i].count("[")>=1:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	344 d=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	345 e=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	346 if phase2[i][0]=="[" and phase2[i][-1]=="]" and phase2[i].count("[")==1:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	347 content=phase2[i].replace("[","").replace("]","")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	348 fljB_combine.append(content)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	349 fljB_combine.append("-")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	350 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	351 for x in phase2[i].split(","):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	352 if "[" in x:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	353 d.append(x.replace("[","").replace("]",""))
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	354 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	355 e.append(x)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	356 fljB_combine=Combine(d,e)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	357 ### end of fljB "[" detect
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	358 new_fliC=fliC.split(",") #because some antigen like r,[i] not follow alphabetical order, so use this one to judge and can avoid missings
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	359 new_fliC.sort()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	360 new_fliC=",".join(new_fliC)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	361 new_fljB=fljB.split(",")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	362 new_fljB.sort()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	363 new_fljB=",".join(new_fljB)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	364 if (new_fliC in fliC_combine or fliC in fliC_combine) and (new_fljB in fljB_combine or fljB in fljB_combine):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	365 seronames.append(sero[i])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	366 #analyze seronames
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	367 if len(seronames)==0:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	368 seronames=["N/A (The predicted antigenic profile does not exist in the White-Kauffmann-Le Minor scheme)"]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	369 star=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	370 star_line=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	371 if len(seronames)>1:#there are two possible predictions for serotypes
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	372 star="*"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	373 star_line="The predicted serotypes share the same general formula:\t"+Otype+":"+fliC+":"+fljB+"\n"##
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	374 print "\n"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	375 predict_form=Otype+":"+fliC+":"+fljB#
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	376 predict_sero=(" or ").join(seronames)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	377 ###special test for Enteritidis
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	378 if predict_form=="9:g,m:-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	379 sdf="-"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	380 for x in special_gene_list:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	381 if x[0].startswith("sdf"):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	382 sdf="+"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	383 predict_form=predict_form+"\nSdf prediction:"+sdf
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	384 if sdf=="-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	385 star="*"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	386 star_line="Additional characterization is necessary to assign a serotype to this strain. Commonly circulating strains of serotype Enteritidis are sdf+, although sdf- strains of serotype Enteritidis are known to exist. Serotype Gallinarum is typically sdf- but should be quite rare. Sdf- strains of serotype Enteritidis and serotype Gallinarum can be differentiated by phenotypic profile or genetic criteria.\n"#+##
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	387 predict_sero="See comments below"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	388 ###end of special test for Enteritidis
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	389 elif predict_form=="4:i:-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	390 predict_sero="potential monophasic variant of Typhimurium"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	391 elif predict_form=="4:r:-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	392 predict_sero="potential monophasic variant of Heidelberg"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	393 elif predict_form=="4:b:-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	394 predict_sero="potential monophasic variant of Paratyphi B"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	395 elif predict_form=="8:e,h:1,2":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	396 predict_sero="Newport"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	397 star="*"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	398 star_line="Serotype Bardo shares the same antigenic profile with Newport, but Bardo is exceedingly rare."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	399 claim="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."##
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	400 if "N/A" in predict_sero:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	401 claim=""
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	402 if "Typhimurium" in predict_sero or predict_form=="4:i:-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	403 normal=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	404 mutation=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	405 for x in special_gene_list:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	406 if "oafA-O-4_full" in x[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	407 normal=x[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	408 elif "oafA-O-4_5-" in x[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	409 mutation=x[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	410 if normal>mutation:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	411 #print "$$$Typhimurium"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	412 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	413 elif normal<mutation:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	414 predict_sero=predict_sero.strip()+"(O5-)"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	415 star="*"#
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	416 star_line="Detected the deletion of O5-."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	417 #print "$$$Typhimurium_O5-"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	418 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	419 #print "$$$Typhimurium, even no 7 bases difference"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	420 pass
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	421 return predict_form,predict_sero,star,star_line,claim
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	422
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	423 def main():
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	424 database=sys.argv[1]#used to extract reads
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	425 mapping_mode=sys.argv[2]#mem or sampe
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	426 threads=sys.argv[3]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	427 for_fq=sys.argv[4]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	428 rev_fq=sys.argv[5]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	429 current_time=time.strftime("%Y_%m_%d_%H_%M_%S", time.localtime())
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	430 sam=for_fq+".sam"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	431 bam=for_fq+".bam"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	432 sorted_bam=for_fq+"_sorted.bam"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	433 mapped_fq1=for_fq+"_mapped.fq"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	434 mapped_fq2=rev_fq+"_mapped.fq"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	435 combined_fq=for_fq+"_combined.fq"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	436 for_sai=for_fq+".sai"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	437 rev_sai=rev_fq+".sai"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	438 print "building database..."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	439 #os.system("bwa index "+database+ " 2> /dev/null")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	440 os.system("bwa index "+database+ " 2>> data_log.txt ")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	441 print "mapping..."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	442 if mapping_mode=="mem":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	443 os.system("bwa mem -t "+threads+" "+database+" "+for_fq+" "+rev_fq+" > "+sam+ " 2>> data_log.txt")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	444 elif mapping_mode=="sam":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	445 os.system("bwa aln -t "+threads+" "+database+" "+for_fq+" > "+for_sai+ " 2>> data_log.txt")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	446 os.system("bwa aln -t "+threads+" "+database+" "+rev_fq+" > "+rev_sai+ " 2>> data_log.txt")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	447 os.system("bwa sampe "+database+" "+for_sai+" "+ rev_sai+" "+for_fq+" "+rev_fq+" > "+sam+ " 2>> data_log.txt")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	448 os.system("samtools view -@ "+threads+" -F 4 -Sbh "+sam+" > "+bam)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	449 os.system("samtools view -@ "+threads+" -h -o "+sam+" "+bam)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	450 ### check the version of samtools then use differnt commands
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	451 samtools_version=subprocess.Popen(["samtools"],stdout=subprocess.PIPE,stderr=subprocess.PIPE)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	452 out, err = samtools_version.communicate()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	453 version = err.split("ersion:")[1].strip().split(" ")[0].strip()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	454 print "check samtools version:",version
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	455 if LooseVersion(version)<=LooseVersion("1.2"):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	456 os.system("samtools sort -@ "+threads+" -n "+bam+" "+for_fq+"_sorted")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	457 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	458 os.system("samtools sort -@ "+threads+" -n "+bam+" >"+sorted_bam)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	459 ### end of samtools version check and its analysis
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	460 os.system("bamToFastq -i "+sorted_bam+" -fq "+combined_fq)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	461 os.system("bamToFastq -i "+sorted_bam+" -fq "+mapped_fq1+" -fq2 "+mapped_fq2 + " 2>> data_log.txt")#2> /dev/null if want no output
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	462 outdir=current_time+"_temp"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	463 print "assembling..."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	464 if int(threads)>4:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	465 t="4"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	466 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	467 t=threads
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	468 os.system("spades.py --careful --pe1-s "+combined_fq+" --pe1-1 "+mapped_fq1+" --pe1-2 "+mapped_fq2+" -t "+t+" -o "+outdir+ " >> data_log.txt 2>&1")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	469 new_fasta=for_fq+"_"+database+"_"+mapping_mode+".fasta"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	470 os.system("mv "+outdir+"/contigs.fasta "+new_fasta+ " 2> /dev/null")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	471 #os.system("mv "+outdir+"/scaffolds.fasta "+new_fasta+ " 2> /dev/null") contigs.fasta
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	472 os.system("rm -rf "+outdir+ " 2> /dev/null")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	473 ### begin blast
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	474 print "blasting..."
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	475 print "\n"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	476 xmlfile=for_fq+"-extracted_vs_"+database+"_"+mapping_mode+".xml"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	477 os.system('makeblastdb -in '+new_fasta+' -out '+new_fasta+'_db '+'-dbtype nucl >> data_log.txt 2>&1') #temp.txt is to forbid the blast result interrupt the output of our program###1/27/2015
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	478 os.system("blastn -word_size 10 -query "+database+" -db "+new_fasta+"_db -out "+xmlfile+" -outfmt 5 >> data_log.txt 2>&1")###1/27/2015
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	479 Final_list=xml_parse_score_comparision_seqsero(xmlfile)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	480 Final_list_passed=[x for x in Final_list if float(x[0].split("_cov_")[1])>=3.5 and (x[1]>=int(x[0].split("__")[1]) or x[1]>=int(x[0].split("___")[1].split("_")[3]))]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	481 fliC_choice="-"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	482 fljB_choice="-"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	483 fliC_contig="NA"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	484 fljB_contig="NA"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	485 fliC_length=0 #can be changed to coverage in future
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	486 fljB_length=0 #can be changed to coverage in future
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	487 O_choice=""#no need to decide O contig for now, should be only one
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	488 O_choice,O_nodes,special_gene_list,O_nodes_roles=decide_O_type_and_get_special_genes(Final_list)#decide the O antigen type and also return special-gene-list for further identification
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	489 O_choice=O_choice.split("-")[-1].strip()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	490 H_contig_roles=decide_contig_roles_for_H_antigen(Final_list)#decide the H antigen contig is fliC or fljB
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	491 log_file=open("SeqSero_hybrid_assembly_log.txt","a")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	492 print "O_contigs:"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	493 log_file.write("O_contigs:\n")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	494 for x in O_nodes_roles:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	495 if "O-1,3,19_not_in_3,10" not in x[0]:#O-1,3,19_not_in_3,10 is just a small size marker
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	496 print x[0].split("___")[-1],x[0].split("__")[0],"blast score:",x[1],"identity%:",str(round(x[2]*100,2))+"%"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	497 log_file.write(x[0].split("___")[-1]+" "+x[0].split("__")[0]+" "+"blast score: "+str(x[1])+"identity%:"+str(round(x[2]*100,2))+"%"+"\n")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	498 print "H_contigs:"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	499 log_file.write("H_contigs:\n")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	500 H_contig_stat=[]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	501 for i in range(len(H_contig_roles)):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	502 x=H_contig_roles[i]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	503 a=0
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	504 for y in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	505 if x[1] in y[0] and y[0].startswith(x[0]):
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	506 if "first" in y[0] or "last" in y[0]: #this is the final filter to decide it's fliC or fljB, if can't pass, then can't decide
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	507 for y in Final_list_passed: #it's impossible to has the "first" and "last" allele as prediction, so re-do it
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	508 if x[1] in y[0]:#it's very possible to be third phase allele, so no need to make it must be fliC or fljB
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	509 print x[1],"can't_decide_fliC_or_fljB",y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	510 log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+" "+"blast_score: "+str(y[1])+" identity%:"+str(round(y[2]*100,2))+"%"+"\n")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	511 H_contig_roles[i]="can't decide fliC or fljB, may be third phase"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	512 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	513 else:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	514 print x[1],x[0],y[0].split("_")[1],"blast_score:",y[1],"identity%:",str(round(y[2]*100,2))+"%"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	515 log_file.write(x[1]+" "+x[0]+" "+y[0].split("_")[1]+" "+"blast_score: "+str(y[1])+" identity%:"+str(round(y[2]*100,2))+"%"+"\n")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	516 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	517 for x in H_contig_roles:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	518 #if multiple choices, temporately select the one with longest length for now, will revise in further change
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	519 if "fliC" == x[0] and int(x[1].split("_")[3])>=fliC_length and x[1] not in O_nodes:#remember to avoid the effect of O-type contig, so should not in O_node list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	520 fliC_contig=x[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	521 fliC_length=int(x[1].split("_")[3])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	522 elif "fljB" == x[0] and int(x[1].split("_")[3])>=fljB_length and x[1] not in O_nodes:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	523 fljB_contig=x[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	524 fljB_length=int(x[1].split("_")[3])
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	525 for x in Final_list_passed:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	526 if fliC_choice=="-" and "fliC_" in x[0] and fliC_contig in x[0] :
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	527 fliC_choice=x[0].split("_")[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	528 elif fljB_choice=="-" and "fljB_" in x[0] and fljB_contig in x[0]:
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	529 fljB_choice=x[0].split("_")[1]
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	530 elif fliC_choice!="-" and fljB_choice!="-":
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	531 break
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	532 print "\n"
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	533 print "SeqSero Input files:",for_fq,rev_fq
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	534 print "Most possible O antigen:",O_choice
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	535 print "Most possible H1 antigen:",fliC_choice
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	536 print "Most possible H2 antigen:",fljB_choice
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	537 #print Final_list
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	538 ###output
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	539 predict_form,predict_sero,star,star_line,claim=seqsero_from_formula_to_serotypes(O_choice,fliC_choice,fljB_choice,special_gene_list)
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	540 new_file=open("Seqsero_result.txt","w")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	541 new_file.write("Input files:\t"+for_fq+" "+rev_fq+"\n"+"O antigen prediction:\t"+"O-"+O_choice+"\n"+"H1 antigen prediction(fliC):\t"+fliC_choice+"\n"+"H2 antigen prediction(fljB):\t"+fljB_choice+"\n"+"Predicted antigenic profile:\t"+predict_form+"\n"+"Predicted serotype(s):\t"+predict_sero+star+"\n"+star+star_line+claim+"\n")#+##
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	542 new_file.close()
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	543 os.system("cat Seqsero_result.txt")
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	544
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	545 if __name__ == '__main__':
343e38c6798f planemo upload commit 3f94d8852b51fc041ae5ad5a1929cdce302145a0-dirty charles_s_test parents: diff changeset	546 main()

Mercurial > repos > charles_s_test > seqsero_v2

annotate libs/mapping_and_assembly_hybrid.py @ 3:62f8b9e226c2 draft default tip