change genome specifications

Author: maxibor

.travis.yml

@@ -7,4 +7,4 @@ install:
     - pip install scipy
     - pip install requests
 # command to run tests
-script: python adrsm -d ./data/genomes -t 1 ./data/short_genome_list.csv
+script: python adrsm -t 1 ./data/short_genome_list.csv

README.md

@@ -35,37 +35,35 @@ You can cite ADRSM like this:
 # Help
 
     $ adrsm --help
-    usage: ADRSM v0.7 [-h] [-d DIRECTORY] [-r READLENGTH] [-n NBINOM]
-                      [-fwd FWDADAPT] [-rev REVADAPT] [-e ERROR] [-p GEOM_P]
-                      [-m MIN] [-M MAX] [-o OUTPUT] [-q QUALITY] [-s STATS]
-                      [-se SEED] [-t THREADS]
-                      confFile
+    usage: ADRSM v0.8 [-h] [-r READLENGTH] [-n NBINOM] [-fwd FWDADAPT]
+                  [-rev REVADAPT] [-e ERROR] [-p GEOM_P] [-m MIN] [-M MAX]
+                  [-o OUTPUT] [-q QUALITY] [-s STATS] [-se SEED] [-t THREADS]
+                  confFile
 
     Ancient DNA Read Simulator for Metagenomics
 
     positional arguments:
-      confFile       path to configuration file
+    confFile       path to configuration file
 
     optional arguments:
-      -h, --help     show this help message and exit
-      -d DIRECTORY   path to genome directory. Default = .
-      -r READLENGTH  Average read length. Default = 76
-      -n NBINOM      n parameter for Negative Binomial insert length distribution.
-                     Default = 8
-      -fwd FWDADAPT  Forward adaptor. Default = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
-                     NNNNNNATCTCGTATGCCGTCTTCTGCTTG
-      -rev REVADAPT  Reverse adaptor. Default =
-                     AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
-      -e ERROR       Illumina sequecing error. Default = 0.01
-      -p GEOM_P      Geometric distribution parameter for deamination. Default =
-                     0.5
-      -m MIN         Deamination substitution base frequency. Default = 0.001
-      -M MAX         Deamination substitution max frequency. Default = 0.3
-      -o OUTPUT      Output file basename. Default = ./metagenome.*
-      -q QUALITY     Base quality encoding. Default = d (PHRED+64)
-      -s STATS       Statistic file. Default = stats.csv
-      -se SEED       Seed for random generator. Default = 7357
-      -t THREADS     Number of threads for parallel processing. Default = 2
+    -h, --help     show this help message and exit
+    -r READLENGTH  Average read length. Default = 76
+    -n NBINOM      n parameter for Negative Binomial insert length distribution.
+                    Default = 8
+    -fwd FWDADAPT  Forward adaptor. Default = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+                    NNNNNNATCTCGTATGCCGTCTTCTGCTTG
+    -rev REVADAPT  Reverse adaptor. Default =
+                    AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+    -e ERROR       Illumina sequecing error. Default = 0.01
+    -p GEOM_P      Geometric distribution parameter for deamination. Default =
+                    0.5
+    -m MIN         Deamination substitution base frequency. Default = 0.001
+    -M MAX         Deamination substitution max frequency. Default = 0.3
+    -o OUTPUT      Output file basename. Default = ./metagenome.*
+    -q QUALITY     Base quality encoding. Default = d (PHRED+64)
+    -s STATS       Statistic file. Default = stats.csv
+    -se SEED       Seed for random generator. Default = 7357
+    -t THREADS     Number of threads for parallel processing. Default = 2
 
 ## Genome directory
 
@@ -78,8 +76,8 @@ Example [short_genome_list.csv](./data/short_genome_list.csv):
 
 | genome(mandatory)            | insert_size(mandatory) | coverage(mandatory) | deamination(mandatory) | mutation_rate(optional) | age(optional) |
 | ---------------------------- | ---------------------- | ------------------- | ---------------------- | ----------------------- | ------------- |
-| Agrobacterium_tumefaciens.fa | 47                     | 0.1                 | yes                    | 10e-8                   | 10000         |
-| Bacillus_anthracis.fa        | 48                     | 0.2                 | no                     |                         |               |
+| ./data/genomes/Agrobacterium_tumefaciens.fa | 47                     | 0.1                 | yes                    | 10e-8                   | 10000         |
+| ./data/genomes/Bacillus_anthracis.fa        | 48                     | 0.2                 | no                     |                         |               |
 
 ## Note on Coverage
 

adrsm

@@ -10,13 +10,16 @@ def _get_args():
     '''This function parses and return arguments passed in'''
     parser = argparse.ArgumentParser(
         prog='ADRSM v' + str(version),
-        description='Ancient DNA Read Simulator for Metagenomics')
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        description='''
+==================================================\n
+ADRSM: Ancient DNA Read Simulator for Metagenomics\n
+Author: Maxime Borry\n
+Contact: <borry[at]shh.mpg.de>\n
+Homepage & Documentation: github.com/maxibor/adrsm
+==================================================
+        ''')
     parser.add_argument('confFile', help="path to configuration file")
-    parser.add_argument(
-        '-d',
-        dest="directory",
-        default=".",
-        help="path to genome directory. Default = .")
     parser.add_argument(
         '-r',
         dest='readLength',
@@ -86,7 +89,6 @@ def _get_args():
     args = parser.parse_args()
 
     infile = args.confFile
-    gendir = args.directory
     readlen = int(args.readLength)
     nbinom = int(args.nbinom)
     a1 = args.fwdAdapt
@@ -101,10 +103,10 @@ def _get_args():
     seed = int(args.seed)
     threads = int(args.threads)
 
-    return(infile, gendir, readlen, nbinom, a1, a2, err, geom_p, themin, themax, outfile, quality, stats, seed, threads)
+    return(infile, readlen, nbinom, a1, a2, err, geom_p, themin, themax, outfile, quality, stats, seed, threads)
 
 
-def read_config(infile, gendir):
+def read_config(infile):
     """
     READS CONFIG FILE AND RETURNS CONFIG DICT
     """
@@ -128,20 +130,20 @@ def read_config(infile, gendir):
                 mutrate = 0
                 age = 0
 
-            genomes[gendir + "/" + agenome] = {'size': ainsert,
-                                               'cov': acov, 'deam': deamination, 'mutate': mutate, 'mutrate': mutrate, 'age': age}
+            genomes[agenome] = {'size': ainsert,
+                                'cov': acov, 'deam': deamination, 'mutate': mutate, 'mutrate': mutrate, 'age': age}
     return(genomes)
 
 
 if __name__ == "__main__":
-    version = 0.7
-    INFILE, GENDIR, READLEN, NBINOM, A1, A2, ERR, GEOM_P, THEMIN, THEMAX, OUTFILE, QUALITY, STATS, SEED, PROCESS = _get_args()
+    version = 0.8
+    INFILE, READLEN, NBINOM, A1, A2, ERR, GEOM_P, THEMIN, THEMAX, OUTFILE, QUALITY, STATS, SEED, PROCESS = _get_args()
 
     MINLENGTH = 20
     npr.seed(SEED)
     genome_dict = {}
     stat_dict = {}
-    all_genomes = read_config(INFILE, GENDIR)
+    all_genomes = read_config(INFILE)
     for agenome in all_genomes.keys():
         stat_and_run = ad.run_read_simulation_multi(INFILE=agenome,
                                                     COV=all_genomes[agenome]['cov'],

data/short_genome_list.csv

@@ -1,3 +1,3 @@
 genome(mandatory), insert_size(mandatory), coverage(mandatory), deamination(mandatory), mutation_rate(optional), age(optional)
-Agrobacterium_tumefaciens.fa, 47 , 0.1, yes, 10e-7, 10000
-Bacillus_anthracis.fa, 48, 0.2, no
+./data/genomes/Agrobacterium_tumefaciens.fa, 47 , 0.1, yes, 10e-7, 10000
+./data/genomes/Bacillus_anthracis.fa, 48, 0.2, no