msp_blastparser_and_hits: BlastParser_and

annotate BlastParser_and_hits.py @ 16:0e51eef139ab draft default tip

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit c81a2a37d69ad570068741411bae12dd8289d60c-dirty

author	drosofff
date	Wed, 11 Oct 2017 12:43:04 -0400
parents	1991c830504a
children

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 argparse
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	6 from collections import defaultdict
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	7
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	8
0 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")
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	15 the_parser.add_argument('--flanking', action="store", type=int, help="number of flanking nucleotides added to the hit sequences")
0 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()
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	26 if not all((args.sequences, args.blast, args.fastaOutput, args.tabularOutput)):
0 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
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	32
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	33 def median(lst):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	34 lst = sorted(lst)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	35 if len(lst) < 1:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	36 return None
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	37 if len(lst) % 2 == 1:
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	38 return lst[((len(lst)+1)/2)-1]
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	39 if len(lst) % 2 == 0:
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	40 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	41
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	42
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	43 def mean(lst):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	44 if len(lst) < 1:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	45 return 0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	46 return sum(lst) / float(len(lst))
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	47
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	48
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	49 def getfasta(fastafile):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	50 fastadic = {}
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	51 for line in open(fastafile):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	52 if line[0] == ">":
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	53 header = line[1:-1]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	54 fastadic[header] = ""
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	55 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	56 fastadic[header] += line
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	57 for header in fastadic:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	58 fastadic[header] = "".join(fastadic[header].split("\n"))
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	59 return fastadic
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	60
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	61
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	62 def insert_newlines(string, every=60):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	63 lines = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	64 for i in xrange(0, len(string), every):
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	65 lines.append(string[i:i+every])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	66 return '\n'.join(lines)
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	67
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	68
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	69 def getblast(blastfile):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	70 '''blastinfo [0] Percentage of identical matches
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	71 blastinfo [1] Alignment length
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	72 blastinfo [2] Number of mismatches
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	73 blastinfo [3] Number of gap openings
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	74 blastinfo [4] Start of alignment in query
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	75 blastinfo [5] End of alignment in query
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	76 blastinfo [6] Start of alignment in subject (database hit)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	77 blastinfo [7] End of alignment in subject (database hit)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	78 blastinfo [8] Expectation value (E-value)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	79 blastinfo [9] Bit score
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	80 blastinfo [10] Subject length (NEED TO BE SPECIFIED WHEN RUNNING BLAST) '''
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	81 blastdic = defaultdict(dict)
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	82 for line in open(blastfile):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	83 fields = line[:-1].split("\t")
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	84 transcript = fields[0]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	85 subject = fields[1]
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	86 blastinfo = [float(fields[2])] # blastinfo[0]
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	87 blastinfo = blastinfo + [int(i) for i in fields[3:10]] # blastinfo[1:8] insets 1 to 7
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	88 blastinfo.append(fields[10]) # blastinfo[8] E-value remains as a string type
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	89 blastinfo.append(float(fields[11])) # blastinfo[9] Bit score
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	90 blastinfo.append(int(fields[12])) # blastinfo[10] Subject length MUST BE RETRIEVED THROUGH A 13 COLUMN BLAST OUTPUT
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	91 try:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	92 blastdic[subject][transcript].append(blastinfo)
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	93 except Exception:
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	94 blastdic[subject][transcript] = [blastinfo]
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	95 return blastdic
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	96
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	97
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	98 def getseq(fastadict, transcript, up, down, orientation="direct"):
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	99 def reverse(seq):
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	100 revdict = {"A": "T", "T": "A", "G": "C", "C": "G", "N": "N"}
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	101 revseq = [revdict[i] for i in seq[::-1]]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	102 return "".join(revseq)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	103 pickseq = fastadict[transcript][up-1:down]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	104 if orientation == "direct":
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	105 return pickseq
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	106 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	107 return reverse(pickseq)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	108
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	109
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	110 def subjectCoverage(fastadict, blastdict, subject, QueriesFlankingNucleotides=0):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	111 SubjectCoverageList = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	112 HitDic = {}
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	113 bitScores = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	114 for transcript in blastdict[subject]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	115 prefix = "%s--%s_" % (subject, transcript)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	116 hitNumber = 0
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	117 for hit in blastdict[subject][transcript]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	118 hitNumber += 1
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	119 suffix = "hit%s_IdMatch=%s,AligLength=%s,E-val=%s" % (hitNumber, hit[0], hit[1], hit[8])
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	120 HitDic[prefix+suffix] = GetHitSequence(fastadict, transcript, hit[4], hit[5], QueriesFlankingNucleotides) # query coverage by a hit is in hit[4:6]
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	121 SubjectCoverageList += range(min([hit[6], hit[7]]), max([hit[6], hit[7]]) + 1) # subject coverage by a hit is in hit[6:8]
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	122 bitScores.append(hit[9])
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	123 subjectLength = hit[10] # always the same value for a given subject. Stupid but simple
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	124 TotalSubjectCoverage = len(set(SubjectCoverageList))
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	125 RelativeSubjectCoverage = TotalSubjectCoverage/float(subjectLength)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	126 return HitDic, subjectLength, TotalSubjectCoverage, RelativeSubjectCoverage, max(bitScores), mean(bitScores)
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	127
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	128
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	129 def GetHitSequence(fastadict, FastaHeader, leftCoordinate, rightCoordinate, FlankingValue):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	130 if rightCoordinate > leftCoordinate:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	131 polarity = "direct"
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	132 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	133 polarity = "reverse"
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	134 leftCoordinate, rightCoordinate = rightCoordinate, leftCoordinate
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	135 if leftCoordinate - FlankingValue > 0:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	136 leftCoordinate -= FlankingValue
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	137 else:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	138 leftCoordinate = 1
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	139 return getseq(fastadict, FastaHeader, leftCoordinate, rightCoordinate, polarity)
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	140
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	141
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	142 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"):
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	143 def filter_results(results, filter_relativeCov=0, filter_maxScore=0, filter_meanScore=0, filter_term_in="", filter_term_out=""):
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	144 for subject in results.keys():
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	145 if results[subject]["RelativeSubjectCoverage"] < filter_relativeCov:
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	146 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	147 continue
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	148 if results[subject]["maxBitScores"] < 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	149 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	150 continue
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	151 if results[subject]["meanBitScores"] < filter_meanScore:
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	152 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	153 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	154 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	155 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	156 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	157 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	158 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	159 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	160 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	161 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	162 return results
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	163
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	164 F = open(F, "w")
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	165 Fasta = open(Fasta, "w")
2 bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82 drosofff parents: 1 diff changeset	166 blasted_transcripts = []
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	167 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	168 for subject in results:
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82 drosofff parents: 1 diff changeset	169 for transcript in Xblastdict[subject]:
bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82 drosofff parents: 1 diff changeset	170 blasted_transcripts.append(transcript)
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	171 blasted_transcripts = list(set(blasted_transcripts))
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	172 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	173 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	174 print >>F, "# SeqId\t%Identity\tAlignLength\tStartSubject\tEndSubject\t%QueryHitCov\tE-value\tBitScore"
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	175 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	176 print >> F, " \n# %s" % subject
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	177 print >> F, "# Suject Length: %s" % (results[subject]["subjectLength"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	178 print >> F, "# Total Subject Coverage: %s" % (results[subject]["TotalCoverage"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	179 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	180 print >> F, "# Best Bit Score: %s" % (results[subject]["maxBitScores"])
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	181 print >> F, "# Mean Bit Score: %s" % (results[subject]["meanBitScores"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	182 for header in results[subject]["HitDic"]:
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	183 print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]))
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	184 print >> Fasta, "" # final carriage return for the sequence
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	185 for transcript in Xblastdict[subject]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	186 transcriptSize = float(len(fastadict[transcript]))
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	187 for hit in Xblastdict[subject][transcript]:
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	188 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	189 Eval, BitScore = hit[8], hit[9]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	190 info = [transcript] + [percentIdentity, alignLenght, subjectStart, subjectEnd, queryCov, Eval, BitScore]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	191 info = [str(i) for i in info]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	192 info = "\t".join(info)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	193 print >> F, info
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	194 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	195 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	196 print >>F, "# subject\tsubject length\tTotal Subject Coverage\tRelative Subject Coverage\tBest Bit Score\tMean Bit Score"
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	197 for subject in sorted(results, key=lambda x: results[x]["meanBitScores"], reverse=True):
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	198 line = []
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	199 line.append(subject)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	200 line.append(results[subject]["subjectLength"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	201 line.append(results[subject]["TotalCoverage"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	202 line.append(results[subject]["RelativeSubjectCoverage"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	203 line.append(results[subject]["maxBitScores"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	204 line.append(results[subject]["meanBitScores"])
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	205 line = [str(i) for i in line]
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	206 print >> F, "\t".join(line)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	207 for header in results[subject]["HitDic"]:
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	208 print >> Fasta, ">%s\n%s" % (header, insert_newlines(results[subject]["HitDic"][header]))
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	209 print >> Fasta, "" # final carriage return for the sequence
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	210 F.close()
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	211 Fasta.close()
2 bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82 drosofff parents: 1 diff changeset	212 return blasted_transcripts
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	213
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	214
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	215 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	216 '''to output the sequences that matched and did not matched in the blast'''
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	217 F_matched = open(matched_sequences, "w")
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	218 F_unmatched = open(unmatched_sequences, "w")
1 1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8 drosofff parents: 0 diff changeset	219 for transcript in fastadict:
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	220 if transcript in blasted_transcripts: # list of blasted_transcripts is generated by the outputParsing function
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	221 print >> F_matched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]))
1 1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8 drosofff parents: 0 diff changeset	222 else:
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	223 print >> F_unmatched, ">%s\n%s" % (transcript, insert_newlines(fastadict[transcript]))
1 1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8 drosofff parents: 0 diff changeset	224 F_matched.close()
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8 drosofff parents: 0 diff changeset	225 F_unmatched.close()
1964514aabde planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 1cc2b50091f512593c502176619998f5908fc8e8 drosofff parents: 0 diff changeset	226 return
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	227
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	228
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	229 def __main__():
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	230 args = Parser()
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	231 fastadict = getfasta(args.sequences)
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	232 Xblastdict = getblast(args.blast)
0 69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	233 results = defaultdict(dict)
69ea2a13947f planemo upload for repository https://bitbucket.org/drosofff/gedtools/ drosofff parents: diff changeset	234 for subject in Xblastdict:
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	235 results[subject]["HitDic"], results[subject]["subjectLength"], results[subject]["TotalCoverage"], results[subject]["RelativeSubjectCoverage"], results[subject]["maxBitScores"], results[subject]["meanBitScores"] = subjectCoverage(fastadict, Xblastdict, subject, args.flanking)
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	236 blasted_transcripts = outputParsing(args.dataset_name, args.tabularOutput,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	237 args.fastaOutput, results, Xblastdict, fastadict,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	238 filter_relativeCov=args.filter_relativeCov,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	239 filter_maxScore=args.filter_maxScore,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	240 filter_meanScore=args.filter_meanScore,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	241 filter_term_in=args.filter_term_in,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	242 filter_term_out=args.filter_term_out,
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	243 mode=args.mode)
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	244 dispatch_sequences(fastadict, blasted_transcripts, args.al_sequences, args.un_sequences)
2 bb0d4cd765c5 planemo upload for repository https://bitbucket.org/drosofff/gedtools/ commit 6dee2ab33610e7724e9423cc09818bcbbf11ea82 drosofff parents: 1 diff changeset	245
15 1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	246 if __name__ == "__main__":
1991c830504a planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/msp_blastparser_and_hits commit b6de14061c479f0418cd89e26d6f5ac26e565a07 drosofff parents: 6 diff changeset	247 __main__()

Mercurial > repos > drosofff > msp_blastparser_and_hits

annotate BlastParser_and_hits.py @ 16:0e51eef139ab draft default tip