Merge pull request #1 from maxibor/dev

Reorganizing to use setupTools

.github/workflows/publish_conda.yml

@@ -0,0 +1,14 @@
+name: publish_conda
+
+on: [release]
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v1
+    - name: publish-to-conda
+      uses: maxibor/[email protected]
+      with:
+        subDir: 'conda'
+        AnacondaToken: ${{ secrets.ANACONDA_TOKEN }}

.gitignore

@@ -5,3 +5,7 @@ r1.fq
 r2.fq
 metagenome.*
 stats.csv
+adrsm.egg-info
+__pycache__
+.ipynb_checkpoints
+dist

.travis.yml

@@ -6,5 +6,8 @@ install:
     - pip install numpy
     - pip install scipy
     - pip install requests
+    - pip install click
 # command to run tests
-script: python adrsm -p 0.5 -m 0.001 -M 0.3 -t 2 ./data/short_genome_list.csv
+script: 
+  - python setup.py install
+  - adrsm -p 0.5 -m 0.001 -M 0.3 -t 2 ./test/data/short_genome_list.csv

adrsm/__init__.py

@@ -0,0 +1 @@
+__version__ = "0.9.4"

adrsm/adrsm.py

@@ -0,0 +1,156 @@
+#!/usr/bin/env python
+
+from numpy import random as npr
+from .lib import adrsmlib as ad
+from . import __version__
+import click
+
+@click.command()
+@click.version_option(__version__)
+@click.argument('confFile', type=click.Path(exists=True, 
+                                            readable=True, 
+                                            resolve_path=True))
+@click.option('-r',
+              '--readLength',
+              default='76',
+              type=int,
+              show_default=True,
+              help='Average read length')
+@click.option('-n',
+              '--nbinom',
+              default=8,
+              type=int,
+              show_default=True,
+              help='n parameter for Negative Binomial insert length distribution')
+@click.option('-fwd',
+              '--fwdAdapt',
+              default='AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG',
+              type=str,
+              show_default=True,
+              help='Forward adaptor sequence')
+@click.option('-rev',
+              '--revAdapt',
+              default='AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT',
+              type=str,
+              show_default=True,
+              help='Reverse adaptor sequence')
+@click.option('-p', 
+              '--geom_p',
+              default=0.5,
+              type=click.FloatRange(min=0.0, max=1.0),
+              show_default=True,
+              help='Geometric distribution parameter for deamination')
+@click.option('-m',
+              '--minD',
+              default=0.01,
+              type=click.FloatRange(min=0.0, max=1.0),
+              show_default=True,
+              help='Deamination substitution base frequency')   
+@click.option('-M',
+              '--maxD',
+              default=0.3,
+              type=click.FloatRange(min=0.0, max=1.0),
+              show_default=True,
+              help='Deamination substitution max frequency')
+@click.option('-s',
+              '--seed',
+              default=42,
+              type=int,
+              show_default=True,
+              help='Seed for random generator generator')
+@click.option('-t',
+              '--threads',
+              default=2,
+              type=click.IntRange(min=1, max=1024),
+              show_default=True,
+              help='Number of threads for parallel processing')
+@click.option('-o',
+              '--output',
+              default='./metagenome',
+              type=click.Path(file_okay=True, writable=True, resolve_path=True),
+              show_default=True,
+              help='Fastq output file basename')
+@click.option('-s',
+              '--stats',
+              default='./stats.csv',
+              type=click.Path(file_okay=True, writable=True, resolve_path=True),
+              show_default=True,
+              help='Summary statistics file')
+
+
+def cli(no_args_is_help=True, **kwargs):
+    """\b
+    ==================================================
+    ADRSM: Ancient DNA Read Simulator for Metagenomics
+    Author: Maxime Borry
+    Contact: <borry[at]shh.mpg.de>
+    Homepage & Documentation: github.com/maxibor/adrsm
+
+    CONFFILE: path to ADRSM configuration file
+    """
+    main(**kwargs)
+
+def read_config(infile):
+    """
+    READS CONFIG FILE AND RETURNS CONFIG DICT
+    """
+    genomes = {}
+    with open(infile, "r") as f:
+        next(f)
+        for line in f:
+            line = line.rstrip()
+            splitline = line.split(",")
+            agenome = splitline[0].replace(" ", "")
+            ainsert = int(splitline[1].replace(" ", ""))
+            acov = float(splitline[2].replace(" ", ""))
+            deambool = str(splitline[3].replace(" ", ""))
+            deamination = ad.parse_yes_no(deambool)
+            if len(splitline) > 4 and float(splitline[4].replace(" ", "")) != 0.0:
+                mutate = True
+                mutrate = float(splitline[4].replace(" ", ""))
+                age = float(splitline[5].replace(" ", ""))
+            else:
+                mutate = False
+                mutrate = 0
+                age = 0
+
+            genomes[agenome] = {'size': ainsert,
+                                'cov': acov, 'deam': deamination, 'mutate': mutate, 'mutrate': mutrate, 'age': age}
+    return(genomes)
+
+
+def main(conffile, readlength, nbinom, fwdadapt, revadapt, geom_p, mind, maxd, seed, threads, output, stats):
+    MINLENGTH = 20
+    npr.seed(seed)
+    fastq_list = []
+    stat_dict = {}
+    all_genomes = read_config(conffile)
+    for agenome in all_genomes.keys():
+        stat_and_run = ad.run_read_simulation_multi(INFILE=agenome,
+                                                    COV=all_genomes[agenome]['cov'],
+                                                    READLEN=readlength,
+                                                    INSERLEN=all_genomes[agenome]['size'],
+                                                    NBINOM=nbinom,
+                                                    A1=fwdadapt,
+                                                    A2=revadapt,
+                                                    MINLENGTH=MINLENGTH,
+                                                    MUTATE=all_genomes[agenome]['mutate'],
+                                                    MUTRATE=all_genomes[agenome]['mutrate'],
+                                                    AGE=all_genomes[agenome]['age'],
+                                                    DAMAGE=all_genomes[agenome]['deam'],
+                                                    GEOM_P=geom_p,
+                                                    THEMIN=mind,
+                                                    THEMAX=maxd,
+                                                    PROCESS=threads,
+                                                    FASTQ_OUT=output)
+        stat_dict[ad.get_basename(agenome)] = stat_and_run
+
+    ad.write_stat(stat_dict=stat_dict, stat_out=stats)
+    print("\n-- ADRSM v" + __version__ +
+          " finished generating this mock metagenome --")
+    print("-- FASTQ files written to " + output +
+          ".1.fastq and " + output + ".2.fastq --")
+    print("-- Statistic file written to " + stats + " --")
+
+if __name__ == "__main__":
+    cli()

lib/adrsmlib.py → adrsm/lib/adrsmlib.py

@@ -8,6 +8,7 @@
 import multiprocessing
 import pickle
 from functools import partial
+from pkg_resources import resource_filename
 from . import sequencefunctions as sf
 from . import markov as mk
 
@@ -95,10 +96,7 @@ def get_fwd_qual():
         ret = pickle.load(open("data/quality/fwd_qual.p", 'rb'))
         return(ret)
     except FileNotFoundError:
-        cmd = "which adrsm"
-        res = subprocess.check_output(cmd, shell=True)
-        res = res.decode('utf-8').rstrip()
-        path = "/".join(res.split("/")[:-2])+"/data/quality/fwd_qual.p"
+        path = resource_filename('adrsm', '/data/quality/fwd_qual.p')
         ret = pickle.load(open(path, 'rb'))
         return(ret)
 
@@ -108,10 +106,7 @@ def get_rev_qual():
         ret = pickle.load(open("data/quality/fwd_qual.p", 'rb'))
         return(ret)
     except FileNotFoundError:
-        cmd = "which adrsm"
-        res = subprocess.check_output(cmd, shell=True)
-        res = res.decode('utf-8').rstrip()
-        path = "/".join(res.split("/")[:-2])+"/data/quality/rev_qual.p"
+        path = resource_filename('adrsm', '/data/quality/rev_qual.p')
         ret = pickle.load(open(path, 'rb'))
         return(ret)