annotate BlastParser_and_hits.py @ 7:ccffd39695ae draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 56ab3c26ee521f1396850e655ce363acf8607ae0
author drosofff
date Wed, 03 Feb 2016 04:37:00 -0500
parents 78c34df2dd8d
children 1991c830504a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
1 #!/usr/bin/python
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
2 # blastn tblastn blastx parser revised 14-1-2016.
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
3 # drosofff@gmail.com
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
4
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
5 import sys
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
6 import argparse
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
7 from collections import defaultdict
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
8
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
9 def Parser():
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
10 the_parser = argparse.ArgumentParser()
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
11 the_parser.add_argument('--blast', action="store", type=str, help="Path to the blast output (tabular format, 12 column)")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
12 the_parser.add_argument('--sequences', action="store", type=str, help="Path to the fasta file with blasted sequences")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
13 the_parser.add_argument('--fastaOutput', action="store", type=str, help="fasta output file of blast hits")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
14 the_parser.add_argument('--tabularOutput', action="store", type=str, help="tabular output file of blast analysis")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
15 the_parser.add_argument('--flanking', action="store", type=int, help="number of flanking nucleotides added to the hit sequences")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
16 the_parser.add_argument('--mode', action="store", choices=["verbose", "short"], type=str, help="reporting (verbose) or not reporting (short) oases contigs")
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
17 the_parser.add_argument('--filter_relativeCov', action="store", type=float, default=0, help="filter out relative coverages below the specified ratio (float number)")
3
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
18 the_parser.add_argument('--filter_maxScore', action="store", type=float, default=0, help="filter out best BitScores below the specified float number")
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
19 the_parser.add_argument('--filter_meanScore', action="store", type=float, default=0, help="filter out mean BitScores below the specified float number")
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
20 the_parser.add_argument('--filter_term_in', action="store", type=str, default="", help="select the specified term in the subject list")
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
21 the_parser.add_argument('--filter_term_out', action="store", type=str, default="", help="exclude the specified term from the subject list")
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
22 the_parser.add_argument('--al_sequences', action="store", type=str, help="sequences that have been blast aligned")
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
23 the_parser.add_argument('--un_sequences', action="store", type=str, help="sequences that have not been blast aligned")
6
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
24 the_parser.add_argument('--dataset_name', action="store", type=str, default="", help="the name of the dataset that has been parsed, to be reported in the output")
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
25 args = the_parser.parse_args()
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
26 if not all ( (args.sequences, args.blast, args.fastaOutput, args.tabularOutput) ):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
27 the_parser.error('argument(s) missing, call the -h option of the script')
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
28 if not args.flanking:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
29 args.flanking = 0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
30 return args
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
31
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
32 def median(lst):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
33 lst = sorted(lst)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
34 if len(lst) < 1:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
35 return None
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
36 if len(lst) %2 == 1:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
37 return lst[((len(lst)+1)/2)-1]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
38 if len(lst) %2 == 0:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
39 return float(sum(lst[(len(lst)/2)-1:(len(lst)/2)+1]))/2.0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
40
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
41 def mean(lst):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
42 if len(lst) < 1:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
43 return 0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
44 return sum(lst) / float(len(lst))
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
45
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
46 def getfasta (fastafile):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
47 fastadic = {}
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
48 for line in open (fastafile):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
49 if line[0] == ">":
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
50 header = line[1:-1]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
51 fastadic[header] = ""
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
52 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
53 fastadic[header] += line
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
54 for header in fastadic:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
55 fastadic[header] = "".join(fastadic[header].split("\n"))
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
56 return fastadic
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
57
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
58 def insert_newlines(string, every=60):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
59 lines = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
60 for i in xrange(0, len(string), every):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
61 lines.append(string[i:i+every])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
62 return '\n'.join(lines)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
63
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
64 def getblast (blastfile):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
65 '''blastinfo [0] Percentage of identical matches
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
66 blastinfo [1] Alignment length
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
67 blastinfo [2] Number of mismatches
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
68 blastinfo [3] Number of gap openings
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
69 blastinfo [4] Start of alignment in query
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
70 blastinfo [5] End of alignment in query
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
71 blastinfo [6] Start of alignment in subject (database hit)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
72 blastinfo [7] End of alignment in subject (database hit)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
73 blastinfo [8] Expectation value (E-value)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
74 blastinfo [9] Bit score
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
75 blastinfo [10] Subject length (NEED TO BE SPECIFIED WHEN RUNNING BLAST) '''
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
76 blastdic = defaultdict (dict)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
77 for line in open (blastfile):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
78 fields = line[:-1].split("\t")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
79 transcript = fields[0]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
80 subject = fields[1]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
81 blastinfo = [float(fields[2]) ] # blastinfo[0]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
82 blastinfo = blastinfo + [int(i) for i in fields[3:10] ] # blastinfo[1:8] insets 1 to 7
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
83 blastinfo.append(fields[10]) # blastinfo[8] E-value remains as a string type
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
84 blastinfo.append(float(fields[11])) # blastinfo[9] Bit score
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
85 blastinfo.append(int(fields[12])) # blastinfo[10] Subject length MUST BE RETRIEVED THROUGH A 13 COLUMN BLAST OUTPUT
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
86 try:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
87 blastdic[subject][transcript].append(blastinfo)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
88 except:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
89 blastdic[subject][transcript] = [ blastinfo ]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
90 return blastdic
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
91
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
92 def getseq (fastadict, transcript, up, down, orientation="direct"):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
93 def reverse (seq):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
94 revdict = {"A":"T","T":"A","G":"C","C":"G","N":"N"}
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
95 revseq = [revdict[i] for i in seq[::-1]]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
96 return "".join(revseq)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
97 pickseq = fastadict[transcript][up-1:down]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
98 if orientation == "direct":
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
99 return pickseq
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
100 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
101 return reverse(pickseq)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
102
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
103 def subjectCoverage (fastadict, blastdict, subject, QueriesFlankingNucleotides=0):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
104 SubjectCoverageList = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
105 HitDic = {}
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
106 bitScores = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
107 for transcript in blastdict[subject]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
108 prefix = "%s--%s_" % (subject, transcript)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
109 hitNumber = 0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
110 for hit in blastdict[subject][transcript]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
111 hitNumber += 1
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
112 suffix = "hit%s_IdMatch=%s,AligLength=%s,E-val=%s" % (hitNumber, hit[0], hit[1], hit[8])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
113 HitDic[prefix+suffix] = GetHitSequence (fastadict, transcript, hit[4], hit[5], QueriesFlankingNucleotides) #query coverage by a hit is in hit[4:6]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
114 SubjectCoverageList += range (min([hit[6], hit[7]]), max([hit[6], hit[7]]) + 1) # subject coverage by a hit is in hit[6:8]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
115 bitScores.append(hit[9])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
116 subjectLength = hit [10] # always the same value for a given subject. Stupid but simple
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
117 TotalSubjectCoverage = len ( set (SubjectCoverageList) )
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
118 RelativeSubjectCoverage = TotalSubjectCoverage/float(subjectLength)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
119 return HitDic, subjectLength, TotalSubjectCoverage, RelativeSubjectCoverage, max(bitScores), mean(bitScores)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
120
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
121 def GetHitSequence (fastadict, FastaHeader, leftCoordinate, rightCoordinate, FlankingValue):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
122 if rightCoordinate > leftCoordinate:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
123 polarity = "direct"
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
124 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
125 polarity = "reverse"
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
126 leftCoordinate, rightCoordinate = rightCoordinate, leftCoordinate
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
127 if leftCoordinate - FlankingValue > 0:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
128 leftCoordinate -= FlankingValue
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
129 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
130 leftCoordinate = 1
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
131 return getseq (fastadict, FastaHeader, leftCoordinate, rightCoordinate, polarity)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
132
6
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
133 def outputParsing (dataset_name, F, Fasta, results, Xblastdict, fastadict, filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, filter_term_in="", filter_term_out="", mode="verbose"):
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
134 def filter_results (results, filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, filter_term_in="", filter_term_out=""):
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
135 for subject in results.keys():
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
136 if results[subject]["RelativeSubjectCoverage"]<filter_relativeCov:
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
137 del results[subject]
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
138 continue
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
139 if results[subject]["maxBitScores"]<filter_maxScore:
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
140 del results[subject]
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
141 continue
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
142 if results[subject]["meanBitScores"]<filter_meanScore:
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
143 del results[subject]
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
144 continue
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
145 if filter_term_in in subject:
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
146 pass
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
147 else:
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
148 del results[subject]
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
149 continue
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
150 if filter_term_out and filter_term_out in subject:
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
151 del results[subject]
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
152 continue
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
153 return results
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
154
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
155 F= open(F, "w")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
156 Fasta=open(Fasta, "w")
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
157 blasted_transcripts = []
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
158 filter_results (results, filter_relativeCov, filter_maxScore, filter_meanScore, filter_term_in, filter_term_out)
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
159 for subject in results:
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
160 for transcript in Xblastdict[subject]:
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
161 blasted_transcripts.append(transcript)
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
162 blasted_transcripts = list( set( blasted_transcripts))
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
163 if mode == "verbose":
6
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
164 print >>F, "--- %s ---" % (dataset_name)
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
165 print >>F, "# SeqId\t%Identity\tAlignLength\tStartSubject\tEndSubject\t%QueryHitCov\tE-value\tBitScore"
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
166 for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
6
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
167 print >> F, " \n# %s" % subject
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
168 print >> F, "# Suject Length: %s" % (results[subject]["subjectLength"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
169 print >> F, "# Total Subject Coverage: %s" % (results[subject]["TotalCoverage"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
170 print >> F, "# Relative Subject Coverage: %s" % (results[subject]["RelativeSubjectCoverage"])
3
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
171 print >> F, "# Best Bit Score: %s" % (results[subject]["maxBitScores"])
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
172 print >> F, "# Mean Bit Score: %s" % (results[subject]["meanBitScores"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
173 for header in results[subject]["HitDic"]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
174 print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) )
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
175 print >> Fasta, "" # final carriage return for the sequence
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
176 for transcript in Xblastdict[subject]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
177 transcriptSize = float(len(fastadict[transcript]))
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
178 for hit in Xblastdict[subject][transcript]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
179 percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov = hit[0], hit[1], hit[6], hit[7], "%.1f" % (abs(hit[5]-hit[4])/transcriptSize*100)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
180 Eval, BitScore = hit[8], hit[9]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
181 info = [transcript] + [percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov, Eval, BitScore]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
182 info = [str(i) for i in info]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
183 info = "\t".join(info)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
184 print >> F, info
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
185 else:
6
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
186 print >>F, "--- %s ---" % (dataset_name)
3
8f5d48294f70 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3d9ddd0f6f3c3b97a3bebf52646731ad6771e178
drosofff
parents: 2
diff changeset
187 print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tBest Bit Score\tMean Bit Score"
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
188 for subject in sorted (results, key=lambda x: results[x]["meanBitScores"], reverse=True):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
189 line = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
190 line.append(subject)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
191 line.append(results[subject]["subjectLength"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
192 line.append(results[subject]["TotalCoverage"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
193 line.append(results[subject]["RelativeSubjectCoverage"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
194 line.append(results[subject]["maxBitScores"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
195 line.append(results[subject]["meanBitScores"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
196 line = [str(i) for i in line]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
197 print >> F, "\t".join(line)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
198 for header in results[subject]["HitDic"]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
199 print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]) )
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
200 print >> Fasta, "" # final carriage return for the sequence
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
201 F.close()
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
202 Fasta.close()
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
203 return blasted_transcripts
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
204
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
205 def dispatch_sequences (fastadict, blasted_transcripts, matched_sequences, unmatched_sequences):
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
206 '''to output the sequences that matched and did not matched in the blast'''
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
207 F_matched = open (matched_sequences, "w")
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
208 F_unmatched = open (unmatched_sequences, "w")
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
209 for transcript in fastadict:
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
210 if transcript in blasted_transcripts: # le list of blasted_transcripts is generated by the outputParsing function
1
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
211 print >> F_matched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]) )
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
212 else:
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
213 print >> F_unmatched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]) )
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
214 F_matched.close()
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
215 F_unmatched.close()
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8
drosofff
parents: 0
diff changeset
216 return
0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
217
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
218 def __main__ ():
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
219 args = Parser()
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
220 fastadict = getfasta (args.sequences)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
221 Xblastdict = getblast (args.blast)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
222 results = defaultdict(dict)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
223 for subject in Xblastdict:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/
drosofff
parents:
diff changeset
224 results[subject]["HitDic"], results[subject]["subjectLength"], results[subject]["TotalCoverage"], results[subject]["RelativeSubjectCoverage"], results[subject]["maxBitScores"], results[subject]["meanBitScores"] = subjectCoverage(fastadict, Xblastdict, subject, args.flanking)
6
78c34df2dd8d planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit 3048cdbea989bc7d28326bf9479fc3010ff8b33c
drosofff
parents: 5
diff changeset
225 blasted_transcripts = outputParsing (args.dataset_name, args.tabularOutput, args.fastaOutput, results, Xblastdict, fastadict,
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
226 filter_relativeCov=args.filter_relativeCov, filter_maxScore=args.filter_maxScore,
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
227 filter_meanScore=args.filter_meanScore, filter_term_in=args.filter_term_in,
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
228 filter_term_out=args.filter_term_out, mode=args.mode)
2
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
229 dispatch_sequences (fastadict, blasted_transcripts, args.al_sequences, args.un_sequences)
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82
drosofff
parents: 1
diff changeset
230
4
60b6bd959929 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit e842488e979d8a00b9646061573355cb427bc89c
drosofff
parents: 3
diff changeset
231 if __name__=="__main__": __main__()