1+ #!/usr/bin/env python
2+
3+ from numpy import random as npr
4+ from .lib import adrsmlib as ad
5+ from . import __version__
6+ import click
7+
8+ @click .command ()
9+ @click .version_option (__version__ )
10+ @click .argument ('confFile' , type = click .Path (exists = True ,
11+ readable = True ,
12+ resolve_path = True ))
13+ @click .option ('-r' ,
14+ '--readLength' ,
15+ default = '76' ,
16+ type = int ,
17+ show_default = True ,
18+ help = 'Average read length' )
19+ @click .option ('-n' ,
20+ '--nbinom' ,
21+ default = 8 ,
22+ type = int ,
23+ show_default = True ,
24+ help = 'n parameter for Negative Binomial insert length distribution' )
25+ @click .option ('-fwd' ,
26+ '--fwdAdapt' ,
27+ default = 'AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG' ,
28+ type = str ,
29+ show_default = True ,
30+ help = 'Forward adaptor sequence' )
31+ @click .option ('-rev' ,
32+ '--revAdapt' ,
33+ default = 'AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT' ,
34+ type = str ,
35+ show_default = True ,
36+ help = 'Reverse adaptor sequence' )
37+ @click .option ('-p' ,
38+ '--geom_p' ,
39+ default = 0.5 ,
40+ type = click .FloatRange (min = 0.0 , max = 1.0 ),
41+ show_default = True ,
42+ help = 'Geometric distribution parameter for deamination' )
43+ @click .option ('-m' ,
44+ '--minD' ,
45+ default = 0.01 ,
46+ type = click .FloatRange (min = 0.0 , max = 1.0 ),
47+ show_default = True ,
48+ help = 'Deamination substitution base frequency' )
49+ @click .option ('-M' ,
50+ '--maxD' ,
51+ default = 0.3 ,
52+ type = click .FloatRange (min = 0.0 , max = 1.0 ),
53+ show_default = True ,
54+ help = 'Deamination substitution max frequency' )
55+ @click .option ('-s' ,
56+ '--seed' ,
57+ default = 42 ,
58+ type = int ,
59+ show_default = True ,
60+ help = 'Seed for random generator generator' )
61+ @click .option ('-t' ,
62+ '--threads' ,
63+ default = 2 ,
64+ type = click .IntRange (min = 1 , max = 1024 ),
65+ show_default = True ,
66+ help = 'Number of threads for parallel processing' )
67+ @click .option ('-o' ,
68+ '--output' ,
69+ default = './metagenome' ,
70+ type = click .Path (file_okay = True , writable = True , resolve_path = True ),
71+ show_default = True ,
72+ help = 'Fastq output file basename' )
73+ @click .option ('-s' ,
74+ '--stats' ,
75+ default = './stats.csv' ,
76+ type = click .Path (file_okay = True , writable = True , resolve_path = True ),
77+ show_default = True ,
78+ help = 'Summary statistics file' )
79+
80+
81+ def cli (no_args_is_help = True , ** kwargs ):
82+ """\b
83+ ==================================================
84+ ADRSM: Ancient DNA Read Simulator for Metagenomics
85+ Author: Maxime Borry
86+ Contact: <borry[at]shh.mpg.de>
87+ Homepage & Documentation: github.com/maxibor/adrsm
88+
89+ CONFFILE: path to ADRSM configuration file
90+ """
91+ main (** kwargs )
92+
93+ def read_config (infile ):
94+ """
95+ READS CONFIG FILE AND RETURNS CONFIG DICT
96+ """
97+ genomes = {}
98+ with open (infile , "r" ) as f :
99+ next (f )
100+ for line in f :
101+ line = line .rstrip ()
102+ splitline = line .split ("," )
103+ agenome = splitline [0 ].replace (" " , "" )
104+ ainsert = int (splitline [1 ].replace (" " , "" ))
105+ acov = float (splitline [2 ].replace (" " , "" ))
106+ deambool = str (splitline [3 ].replace (" " , "" ))
107+ deamination = ad .parse_yes_no (deambool )
108+ if len (splitline ) > 4 and float (splitline [4 ].replace (" " , "" )) != 0.0 :
109+ mutate = True
110+ mutrate = float (splitline [4 ].replace (" " , "" ))
111+ age = float (splitline [5 ].replace (" " , "" ))
112+ else :
113+ mutate = False
114+ mutrate = 0
115+ age = 0
116+
117+ genomes [agenome ] = {'size' : ainsert ,
118+ 'cov' : acov , 'deam' : deamination , 'mutate' : mutate , 'mutrate' : mutrate , 'age' : age }
119+ return (genomes )
120+
121+
122+ def main (conffile , readlength , nbinom , fwdadapt , revadapt , geom_p , mind , maxd , seed , threads , output , stats ):
123+ MINLENGTH = 20
124+ npr .seed (seed )
125+ fastq_list = []
126+ stat_dict = {}
127+ all_genomes = read_config (conffile )
128+ for agenome in all_genomes .keys ():
129+ stat_and_run = ad .run_read_simulation_multi (INFILE = agenome ,
130+ COV = all_genomes [agenome ]['cov' ],
131+ READLEN = readlength ,
132+ INSERLEN = all_genomes [agenome ]['size' ],
133+ NBINOM = nbinom ,
134+ A1 = fwdadapt ,
135+ A2 = revadapt ,
136+ MINLENGTH = MINLENGTH ,
137+ MUTATE = all_genomes [agenome ]['mutate' ],
138+ MUTRATE = all_genomes [agenome ]['mutrate' ],
139+ AGE = all_genomes [agenome ]['age' ],
140+ DAMAGE = all_genomes [agenome ]['deam' ],
141+ GEOM_P = geom_p ,
142+ THEMIN = mind ,
143+ THEMAX = maxd ,
144+ PROCESS = threads ,
145+ FASTQ_OUT = output )
146+ stat_dict [ad .get_basename (agenome )] = stat_and_run
147+
148+ ad .write_stat (stat_dict = stat_dict , stat_out = stats )
149+ print ("\n -- ADRSM v" + __version__ +
150+ " finished generating this mock metagenome --" )
151+ print ("-- FASTQ files written to " + output +
152+ ".1.fastq and " + output + ".2.fastq --" )
153+ print ("-- Statistic file written to " + stats + " --" )
154+
155+ if __name__ == "__main__" :
156+ cli ()
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