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annotate rna_hmm3.py @ 0:1a12c379df0c draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rRNA commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
author bgruening
date Thu, 17 Sep 2015 16:50:41 -0400
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1a12c379df0c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rRNA commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty
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1 #! /usr/bin/env python
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2 import os
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3 import re
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4 import sys
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5 import string
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6 import optparse
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7 import fasta
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8 import math
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9 import tempfile
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11 def format(seq, N=60):
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12 nseg = int(math.ceil(len(seq)/(N+0.0)))
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13 return '\n'.join([seq[i*N:(i+1)*N] for i in range(nseg)])
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14 # write into fasta format file
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16 parser = optparse.OptionParser(version="%prog ")
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18 parser.add_option("-i", "--input", dest="input_fasta",action="store",
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19 help="name of input file in fasta format")
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20 parser.add_option("-L", "--LibHmm", dest="hmm_path",action="store",
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21 default="HMM3",help="path of hmm database")
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22 parser.add_option("--gff", dest="out_gff",action="store",
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23 help="name of output gff file")
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24 parser.add_option("--seq", dest="out_seq",action="store",
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25 help="name of output sequence file")
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26 parser.add_option("--mask", dest="out_mask",action="store",
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27 help="name of output mask file")
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28 parser.add_option("-k", "--kingdoms", dest="kingdoms",action="store",
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29 default="arc,bac,euk",help="kingdom used")
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30 parser.add_option("-m", "--moltypes", dest="moltypes",action="store",
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31 default="lsu,ssu,tsu",help="molecule type detected")
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32 parser.add_option("-e","--Evalue", dest="evalue",action="store",type="float",
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33 default=0.01,help="evalue cut-off for hmmsearch")
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34 parser.add_option("--cpu", dest="cpu",action="store",type="int",
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35 default=4,help="number of cpus hmmsearch should use")
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36
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38 try:
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39 (options, args) = parser.parse_args()
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40 except:
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41 parser.print_help()
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42 sys.exit(1)
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44 if options.input_fasta is None or options.hmm_path is None:
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45 parser.print_help()
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46 sys.exit(1)
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47
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48 #print "%s"% os.path.abspath(options.hmm_path)
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49 #os.environ["HMMERDB"] += ":"+os.path.abspath(options.hmm_path)
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50 #print os.environ["HMMERDB"]
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51 fname = os.path.abspath(options.input_fasta)
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52
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53 tr = string.maketrans("gatcryswkmbdhvnGATCRYSWKMBDHVN","ctagyrswmkvhdbnCTAGYRSWMKVHDBN")
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54
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55
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56 def rev_record(record):
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57 return ">"+record.header+"|rev\n"+format(record.sequence[::-1].translate(tr))
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58
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60 records = [rec for rec in fasta.fasta_itr(fname)]
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61 headers = [[rec.header,len(rec.sequence)] for rec in records]
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63
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64 temp_fasta = tempfile.NamedTemporaryFile(delete=False)
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65 ff = open(temp_fasta.name,'w')
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66 for (i, rec) in enumerate(records):
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67 ff.write('>s'+str(i)+'\n'+format(rec.sequence)+'\n')
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68 ff.write('>s'+str(i)+'|rev\n'+format(rec.sequence[::-1].translate(tr))+'\n')
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69 ff.close()
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70 #sys.exit(1)
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71 # a temporary fasta file, use s(int) to easy the parsing
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72
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73 def parse_hmmsearch(kingdom, moltype, src):
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74 # function to parse hmmsearch output
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75 resu = []
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76 data = open(src).readlines()
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77 inds = [-1]+[i for (i,x) in enumerate(data[2]) if x==" "]
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78 inds = [(inds[j]+1,inds[j+1]) for j in range(len(inds)-1)]
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79 data = [line for line in data if line[0] != "#"]
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80 for line in data:
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81 if not len(line.strip()):
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82 continue
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83 [read, acc, tlen, qname, qaccr, qlen, seq_evalue, seq_score, seq_bias, \
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84 seq_num, seq_of, dom_cEvalue, dom_iEvalue, dom_score, dom_bias, \
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85 hmm_start, hmm_end, dom_start, dom_end, env_start, env_end] = \
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86 line.split()[:21]
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87 # [line[x[0]:x[1]].strip() for x in inds[:21]]
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88 if string.atof(dom_iEvalue) < options.evalue:
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89 # resu.append("\t".join([read, acc, tlen, qname, qaccr, \
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90 # qlen, seq_evalue, seq_score, seq_bias, seq_num, seq_of, \
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91 # dom_cEvalue, dom_iEvalue, dom_score, dom_bias, hmm_start, \
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92 # hmm_end, dom_start, dom_end, env_start, env_end]))
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93 resu.append("\t".join([qname, dom_start, dom_end, read, dom_iEvalue]))
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94
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95 # print resu[0]
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96 # print resu[-1]
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97 return resu
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98
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99
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100
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101 hmm_resu = []
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102 for kingdom in options.kingdoms.split(','):
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103 for moltype in options.moltypes.split(','):
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104 #print kingdom, moltype
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105 #hmm_out_fname = "%s.%s_%s.out" % (out_fname, kingdom, moltype)
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106 temp_hmm_out = tempfile.NamedTemporaryFile(delete=False)
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107 #dom_out_fname = "%s.%s_%s.dom" % (out_fname, kingdom, moltype)
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108 temp_dom_out = tempfile.NamedTemporaryFile(delete=False)
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109 #cmd = '/home/thumper6/camera-annotation/sitao/hmmer3.0/hmmer-3.0-linux-intel-x86_64/binaries/hmmsearch --cpu 1 -o %s --domtblout %s -E %g %s/%s_%s.hmm %s' % \
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110 cmd = 'hmmsearch --cpu %s -o %s --domtblout %s -E %g %s/%s_%s.hmm %s' % \
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111 (options.cpu, temp_hmm_out.name, temp_dom_out.name, \
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112 options.evalue,os.path.abspath(options.hmm_path),kingdom,moltype,temp_fasta.name)
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113 # hmm_resu += parse_hmmsearch(os.popen(cmd))
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114 os.system(cmd)
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115 hmm_resu += parse_hmmsearch(kingdom, moltype, temp_dom_out.name)
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116 os.remove(temp_hmm_out.name)
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117 os.remove(temp_dom_out.name)
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118
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119 dict_read2kingdom = {}
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120 for line in hmm_resu:
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121 [feature_type, r_start, r_end, read, evalue] = line.strip().split('\t')
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122 read = read.split('|')[0]
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123 evalue = string.atof(evalue)
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124 kingdom = feature_type.split('_')[0]
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125 if read in dict_read2kingdom:
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126 if evalue < dict_read2kingdom[read][1]:
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127 dict_read2kingdom[read] = [kingdom, evalue]
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128 else:
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129 dict_read2kingdom[read] = [kingdom, evalue]
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130
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131 header = ['##seq_name','method','feature','start','end','evalue','strand','gene']
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132 ff = open(options.out_gff,"w")
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133 dict_rRNA = {'arc_lsu':'Archaeal:23S_rRNA','arc_ssu':'Archaeal:16S_rRNA','arc_tsu':'Archaeal:5S_rRNA',
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134 'bac_lsu':'Bacterial:23S_rRNA','bac_ssu':'Bacterial:16S_rRNA','bac_tsu':'Bacterial:5S_rRNA',
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135 'euk_lsu':'Eukaryotic:28S_rRNA','euk_ssu':'Eukaryotic18S_rRNA','euk_tsu':'Eukaryotic:8S_rRNA'}
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136
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137 ff.write('\t'.join(header)+'\n')
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138 for line in hmm_resu:
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139 # [kingdom, moltype, read, acc, tlen, qname, qaccr, \
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140 # qlen, seq_evalue, seq_score, seq_bias, seq_num, seq_of, \
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141 # dom_cEvalue, dom_iEvalue, dom_score, dom_bias, hmm_start, \
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142 # hmm_end, dom_start, dom_end, env_start, env_end] = line.strip().split('\t')
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143 [feature_type, r_start, r_end, read, evalue] = line.strip().split('\t')
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144 if dict_read2kingdom[read.split('|')[0]][0] != feature_type.split('_')[0]:
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145 continue
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146 feature_type = dict_rRNA[feature_type]
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147 if read.endswith('|rev'):
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148 strand = '-'
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149 tmp = map(string.atoi,[r_start,r_end])
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150 pos = string.atoi(read[1:-4])
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151 header = headers[pos][0]
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152 L = headers[pos][1]
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153 [r_end,r_start] = [str(L+1-x) for x in tmp]
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154 else:
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155 strand = '+'
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156 pos = string.atoi(read[1:])
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157 header = headers[pos][0]
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158 ff.write('\t'.join([header.split()[0], 'rna_hmm3','rRNA',r_start,r_end,evalue,strand,feature_type])+'\n')
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159 ff.close()
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160
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161
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162 os.remove(temp_fasta.name)
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163
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164 #postprocessing
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165 rRNA_dict={}
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166
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167 if options.out_gff:
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168 for line in open(options.out_gff).readlines()[1:]:
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169 line=line.strip().split()
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170 #print '%s %s'% (line[0],line[1])
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171 if rRNA_dict.get(line[0],None) is None:
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172 rRNA_dict[line[0]] = []
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173 #else:
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174 rRNA_dict[line[0]].append( (string.atoi(line[3]),string.atoi(line[4]),line[6],line[7]))
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175
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176 if options.out_mask:
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177 f_mask = open(options.out_mask,"w")
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178
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179 if options.out_seq:
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180 f_seq = open(options.out_seq,"w")
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181 for rec in fasta.fasta_itr( options.input_fasta ):
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182 header = rec.header.split()[0]
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183 seq = rec.sequence[:]
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184 tno = 1
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185 for (start,end,strand,rRNA_type) in rRNA_dict.get(header,[]):
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186 seq = seq[:(start-1)]+'N'*(end-start+1)+seq[end:]
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187
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188 #print "%s %d"% (header,tno)
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189 if options.out_seq:
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190 f_seq.write(">%s.%d /start=%d /end=%d /strand=%s %s\n" % (header,tno,start,end,strand,rRNA_type))
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191 if strand=="+": # forward strand
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192 f_seq.write(format(rec.sequence[(start-1):end])+"\n")
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193 else:
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194 f_seq.write(format(rec.sequence[(start-1):end][::-1].translate(tr))+"\n")
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195 tno = tno+1
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196
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197 #f_mask.write(">"+header+"\n")
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198 #next line by liwz
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199 if options.out_mask:
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200 f_mask.write(">"+rec.header+"\n")
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201 f_mask.write(format(seq)+"\n")
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202
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203 if options.out_mask:
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204 f_mask.close()
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205 if options.out_seq:
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206 f_seq.close()
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207
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208
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209