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author boris
date Mon, 03 Feb 2014 13:01:44 -0500
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1 #!/usr/bin/env python
2 #
3 #Boris Rebolledo-Jaramillo (boris-at-bx.psu.edu)
4 #usage: phylorelatives.py [-h] [-i FASTA] [-b INT] [-p] [-r FASTA] [-j]
5 #
6 #Constructs relatedness of a set of sequences based on the pairwise proportion
7 #of different sites. It reports the test sequences relatives, NJ tree plot and
8 #Newick string. One or more test sequences are accepted as long as their name
9 #includes the strict suffix "_minor" or "_test" (i.e. >seq1_minor). IMPORTANT:
10 #Sequences must have the same length!
11 #
12 #optional arguments:
13 # -h, --help show this help message and exit
14 # -i FASTA, --input FASTA
15 # This option can be specified multiple times. Sequences
16 # will be added to "multi-fasta.fa". (e.g. -i major1.fa
17 # -i major2.fa -i minor1.fa)
18 # -b INT, --bootstrap INT
19 # Change number of replicas. 0 to deactivate. (Default:
20 # 1000)
21 # -p, --pairwise Use pairwise deletion of gaps/missing data. (Default:
22 # Complete deletion)
23 # -r FASTA, --root FASTA
24 # Root trees using FASTA sequence as outgroup. (Default:
25 # Display unrooted trees)
26 # -j, --major-only In major-only mode no minor allele sequence is
27 # required and each sequence is treated as a major
28 # allele sequence (Default: Require minor allele
29 # sequences)
30
31 import sys
32 import argparse
33 import array
34 import dendropy
35 import rpy2.rinterface
36 rpy2.rinterface.set_initoptions(('rpy2','--vanilla','--quiet'))
37 import rpy2.robjects as robjects
38 from rpy2.robjects.packages import importr
39
40
41 def ape_read_dna(infasta):
42 """Read multi-fasta into phylo object"""
43 ape = importr('ape')
44 data = ape.read_dna(file=infasta,format="fasta")
45 return data
46
47 def ape_nj(data,missing_info_option=0):
48 """Return ape nj tree"""
49 ape = importr('ape')
50 dist = ape.dist_dna(data,model="raw",pairwise=missing_info_option)
51 nj_tree = ape.nj(dist)
52 return nj_tree
53
54 def ape_bootstrap(tree,tree_function,data,iters=1000):
55 """Return bootstrap tree with bootstrap values on nodes"""
56 ape = importr('ape')
57 tree_func = robjects.r(tree_function)
58 bootstrap = ape.boot_phylo(tree, data, tree_func,
59 B=iters, quiet=1, trees=1)
60 robjects.r('''
61 add_bs_value = function(tree, boot, iters) {
62 tree$node.label = ((boot$BP)/iters)*100
63 return(tree)
64 }''')
65 add_bs_value = robjects.r['add_bs_value']
66 bs_tree = add_bs_value(tree, bootstrap, iters)
67 #bs_trees = bootstrap.rx('trees')[0]
68 #bs_tree = ape.consensus(bs_trees,p=0.5)
69 return bs_tree
70
71
72 def dendro_relatives(tree,minor):
73 """Return minor allele sequence relatives in tree"""
74 ape = importr('ape')
75 newick = list(ape.write_tree(tree))[0]
76 t = dendropy.Tree.get_from_string(newick,"newick")
77 minor_leaf = [node for node in t.leaf_nodes()
78 if node.get_node_str() == minor][0]
79 parent = minor_leaf.parent_node
80 relatives = []
81 while len(relatives) == 0:
82 output = [relative.get_node_str() for relative in parent.leaf_nodes()]
83 relatives = [relative for relative in output if not (relative.endswith('minor') or relative.endswith('test'))]
84 parent = parent.parent_node
85 return output
86
87
88 def dendro_plot(tree, root=False ):
89 """Plot tree to file in ascii format"""
90 ape = importr('ape')
91 if root:
92 newick = list(ape.write_tree(ape.root(tree,root)))[0]
93 else:
94 newick = list(ape.write_tree(tree))[0]
95 t = dendropy.Tree.get_from_string(newick,"newick")
96 ascii_tree = t.as_ascii_plot()
97 return ascii_tree
98
99
100 def ape_plot_tree(outfile, tree1, root=False):
101 """Plot tree to png file"""
102 ape = importr('ape')
103 graphics = importr('graphics')
104 grdevices = importr('grDevices')
105 grdevices.png(file=outfile, width=1024, height=768,type="cairo")
106 if root:
107 tree = ape.root(tree1,root)
108 labels = list(tree.rx("tip.label")[0])
109 colors = robjects.StrVector(["red" if tip.endswith("_minor") else "black" for tip in labels])
110 ape.plot_phylo(tree,tip_color=colors,use_edge_length=0,
111 show_node_label=1,edge_width=2, font=2,
112 cex=1,underscore=0, no_margin=1)
113 else:
114 tree = tree1
115 labels = list(tree.rx("tip.label")[0])
116 colors = robjects.StrVector(["red" if tip.endswith("_minor") else "black" for tip in labels])
117 ape.plot_phylo(tree,tip_color=colors,use_edge_length=0,
118 show_node_label=1,edge_width=2, font=2,
119 cex=1,underscore=0, no_margin=1)
120 #graphics.title(main='Neighbor Joining')
121 return
122
123
124 def write_nwk(tree):
125 "Write proper Newick string"
126 ape = importr('ape')
127 nwk = list(ape.write_tree(tree))[0]
128 return nwk
129
130 def main():
131 # Parse command line options
132 parser = argparse.ArgumentParser(description='Constructs relatedness of a set of sequences based on the pairwise proportion of different sites. It reports the test sequences relatives, NJ tree plot and Newick string. One or more test sequences are accepted as long as their name includes the strict suffix "_minor" or "_test" (i.e. >seq1_minor). IMPORTANT: Sequences must have the same length!', epilog='Boris Rebolledo-Jaramillo (boris-at-bx.psu.edu)')
133 parser.add_argument('-i', '--input', metavar='FASTA', action='append', type=str, help='This option can be specified multiple times. Sequences will be added to "multi-fasta.fa". (e.g. -i major1.fa -i major2.fa -i minor1.fa)')
134 parser.add_argument('-b', '--bootstrap', type=int, metavar='INT',default=1000, help='Change number of replicas. 0 to deactivate. (Default: 1000)')
135 parser.add_argument('-p', '--pairwise', action='store_true', help='Use pairwise deletion of gaps/missing data. (Default: Complete deletion)')
136 parser.add_argument('-r', '--root', type=str, metavar='FASTA', default=False, help='Root trees using FASTA sequence as outgroup. (Default: Display unrooted trees)')
137 parser.add_argument('-j', '--major-only', action='store_true', help='In major-only mode no minor allele sequence is required and each sequence is treated as a major allele sequence (Default: Require minor allele sequences)')
138 parser.add_argument('--relatives-out', type=str, metavar='FILE', default=None, help=argparse.SUPPRESS)
139 parser.add_argument('--newick-out', type=str, metavar='FILE', default=None, help=argparse.SUPPRESS)
140 parser.add_argument('--trees-out', type=str, metavar='FILE', default=None, help=argparse.SUPPRESS)
141 parser.add_argument('-m', '--multi-fasta', type=str, default='multi-fasta.fa', help=argparse.SUPPRESS)
142 args = parser.parse_args()
143 #parser.print_help()
144
145 if args.input:
146 for fasta in args.input:
147 try:
148 open(fasta)
149 except:
150 sys.exit("\nERROR: Could not open %s\n" % fasta)
151 try:
152 multi = open(args.multi_fasta, 'w+')
153 except:
154 sys.exit("\nERROR: Could not create %s\n" % args.multi_fasta)
155
156 for fasta in args.input:
157 for line in list(open(fasta)):
158 multi.write(line.replace('-', '_'))
159
160
161 if args.root:
162 try:
163 root = list(open(args.root))
164 root_id = [line.strip()[1:].replace('-', '_') for line in root if line.strip().startswith(">")][0]
165 for line in root:
166 multi.write(line.replace('-', '_'))
167 except:
168 sys.exit("\nERROR: Could not open %s\n" % args.root)
169 else:
170 root_id = args.root
171 multi.close()
172
173 try:
174 data = ape_read_dna(args.multi_fasta)
175 except:
176 sys.exit("\nERROR: Check existence or proper format of %s\n" % args.multi_fasta)
177
178 # Get sequence ids in alignment and identify test sequences
179 fasta_ids = [seqname.strip()[1:] for seqname in list(open(args.multi_fasta)) if seqname.startswith('>')]
180 minor_ids = [seqname for seqname in fasta_ids if seqname.endswith('minor') or seqname.endswith('test')]
181
182 if len(minor_ids) == 0 and not args.major_only:
183 sys.exit("\nERROR: No test sequences found. _minor or _test suffixes are required in the sequence name!\n")
184 else:
185 pass
186
187 if args.pairwise:
188 nj_tree = ape_nj(data,1)
189 nj_func = 'function (xx) nj(dist.dna(xx, model="raw", pair=1))'
190 else:
191 nj_tree = ape_nj(data)
192 nj_func = 'function (xx) nj(dist.dna(xx, model="raw"))'
193
194 if args.bootstrap == 0:
195 bs_tree = nj_tree
196 elif args.bootstrap !=1000:
197 bs_tree = ape_bootstrap(nj_tree,nj_func,data,iters=args.bootstrap)
198 else:
199 bs_tree = ape_bootstrap(nj_tree,nj_func,data)
200
201 # Generate report, trees, and Newick strings
202 if args.relatives_out is not None:
203 relatives = open(args.relatives_out,'w+')
204 else:
205 relatives = open(args.multi_fasta+'-relatives.tab','w+')
206 if args.newick_out is not None:
207 newick = open(args.newick_out,'w+')
208 else:
209 newick = open(args.multi_fasta+'-newick.nwk','w+')
210 if args.trees_out is not None:
211 tree_plot_file = args.trees_out
212 else:
213 #tree_plot_file = open(args.multi_fasta+'-tree-ascii.txt', 'w+')
214 tree_plot_file = args.multi_fasta+'-tree.png'
215
216 newick.write('%s\n' % (write_nwk(bs_tree)))
217 #tree_plot_file.write(dendro_plot(bs_tree,root=root_id))
218 ape_plot_tree(tree_plot_file,bs_tree,root=root_id)
219
220 if args.major_only:
221 relatives.write('Major allele only mode cannot generate a report')
222 else:
223 relatives.write('#source\tsample\trelatives\n')
224 for node in minor_ids:
225 nj_relatives = [relative for relative in dendro_relatives(bs_tree,node) if relative != node]
226 relatives.write( 'Neighbor_Joining_tree\t%s\t%s\n' % (node,','.join(sorted(nj_relatives))) )
227
228 newick.close()
229 relatives.close()
230
231 if __name__ == "__main__": main()