adding documentation and renaming

README.md

@@ -1,2 +1,60 @@
-# adrsm
-Ancient DNA Read Simulator for Metagenomic 
+<img src="./img/logo_adrsm.png" width="300">
+
+# Introduction
+ADRSM (Ancient DNA Read Simulator for Metagenomics) is a tool designed to simulate the paired-end sequencing of a metagenomic community. ADRSM allows you to control precisely the amount of DNA from each organism in the community, which can be used to benchmark different metagenomics methods.
+
+# Dependencies
+- [Conda](https://conda.io/miniconda.html)  
+
+# Installation
+
+```
+conda install -c maxibor adrsm
+```
+
+# Usage
+
+```
+adrsm -d path/to/genome/directory configFile.txt
+```
+
+# Help
+
+```
+maxime@gph:~$ adrsm --help
+usage: ADRSM [-h] [-d DIRECTORY] [-r READLENGTH] [-l LENSTDEV] [-fwd FWDADAPT]
+             [-rev REVADAPT] [-e ERROR] [-o OUTPUT] [-s STATS]
+             confFile
+
+Ancient DNA Read Simulator for Metagenomics
+
+positional arguments:
+  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
+  -l LENSTDEV    Insert length standard deviation. Default = 10
+  -fwd FWDADAPT  Forward adaptor. Default = AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
+                 NNNNNNATCTCGTATGCCGTCTTCTGCTTG
+  -rev REVADAPT  Reverse adaptor. Default =
+                 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+  -e ERROR       Illumina sequecing error. Default = 0.01
+  -o OUTPUT      Output file basename. Default = ./metagenome.*
+  -s STATS       Statistic file. Default = stats.csv
+
+```
+
+## Genome directory
+Each genome `fasta` file must be names after the name of the organism. (ex: `Bacillus_anthracis_genome.fa`)
+
+## Configuration file (`confFile`)
+The configuration file is a `.csv` file describing, one line per genome, the mean insert size, and the expected genome coverage.
+Example [short_genome_list.csv](./short_genome_list.csv):
+
+```
+genome, insert_size, coverage
+Agrobacterium_tumefaciens_genome.fa, 47 , 0.1
+Bacillus_anthracis_genome.fa, 48, 0.2
+```

adrsm_multi.py → adrsm

@@ -8,8 +8,8 @@
 def _get_args():
     '''This function parses and return arguments passed in'''
     parser = argparse.ArgumentParser(
-    prog='MetaBenReadSim',
-    description='Metagenomic Benchmarking Read Simulator for ancient DNA')
+    prog='ADRSM',
+    description='Ancient DNA Read Simulator for Metagenomics')
     parser.add_argument('confFile', help="path to configuration file")
     parser.add_argument(
     '-d',

adrsm_single.py → adrsm_single

@@ -9,8 +9,8 @@
 def _get_args():
     '''This function parses and return arguments passed in'''
     parser = argparse.ArgumentParser(
-    prog='MetaBenReadSim',
-    description='Metagenomic Benchmarking Read Simulator for ancient DNA')
+    prog='ADRSM',
+    description='Ancient DNA Read Simulator for Metagenomics')
     parser.add_argument('infile', help="path to reference fasta file")
     parser.add_argument(
     '-n',