Merge pull request #4 from druvus/master

Packing the code

README.md

@@ -1,13 +1,18 @@
 # Getting Recycler
 You can download Recycler [here](https://github.com/Shamir-Lab/Recycler/releases/download/Recycler-v0.6/Recycler-0.6.zip) or clone it via the link below. In case you download the zip, unzip the file before following the instructions below (ignoring the 'git clone' line)
 
+# Installation
+To install Recycler and scripts follow the following instructions.
+
+    git clone https://github.com/rozovr/Recycler.git
+    python setup.py install
+
+
 # Quick start
 
 Assuming we have prepared a filtered BAM file (aln-pe.bam) prepared as described [below](#bam-prep) and an isolate assembly graph (e.g., assembly_graph.fastg from [SPAdes 3.6+](http://bioinf.spbau.ru/en/spades)), and that 55 was the maximum k-mer length used by the assembler, 
 
-    git clone https://github.com/rozovr/Recycler.git
-    cd Recycler
-    python recycle.py -g assembly_graph.fastg -k 55 -b aln-pe.bam -i True
+    recycle.py -g assembly_graph.fastg -k 55 -b aln-pe.bam -i True
 
 For metagenome/plasmidome assemblies, we remove the final ("-i") parameter, which has a default False value.
 
@@ -33,7 +38,7 @@ Recommended for generating inputs (as used during testing):
 
 # Detailed usage
 
-python recycle.py -g GRAPH -k MAX_K -b BAM [-l LENGTH] [-m MAX_CV] [-i ISO]
+recycle.py -g GRAPH -k MAX_K -b BAM [-l LENGTH] [-m MAX_CV] [-i ISO]
 
 ### required arguments:
 
@@ -60,7 +65,7 @@ python recycle.py -g GRAPH -k MAX_K -b BAM [-l LENGTH] [-m MAX_CV] [-i ISO]
 
 Recycler uses paired-end alignments of the reads originally assembled to the output assembly graph to filter and select amongst candidate circular sequences. In order to do so, it requires as input a BAM file containing the set of best alignment hits for each read pair. We recommend the following steps (tested on BWA 0.7.5 and samtools 1.19) to prepare the BAM file:
 
-    python make_fasta_from_fastg.py -g assembly_graph.fastg
+    make_fasta_from_fastg.py -g assembly_graph.fastg
 
     bwa index assembly_graph.nodes.fasta
 

get_simple_cycs.py → bin/get_simple_cycs.py

@@ -1,3 +1,5 @@
+#!/usr/bin/env python
+
 # gets simple (single contig) cycles from 
 # (usually plasmid) metagenomes, leaves rest of 
 # graph as is

make_fasta_from_fastg.py → bin/make_fasta_from_fastg.py

@@ -1,3 +1,4 @@
+#!/usr/bin/env python
 import re, argparse, os
 from recycle.utils import readfq
 

recycle.py → bin/recycle.py

@@ -1,9 +1,8 @@
-
 #!/usr/bin/env python
 
 import argparse, os
-from recycle.utils import *
-
+from recycle import *
+import pysam
 
 def parse_user_input():
     parser = argparse.ArgumentParser(

setup.py

@@ -0,0 +1,18 @@
+from setuptools import setup
+
+setup(name='recycler',
+      version='0.6',
+      description='Recycler: an algorithm for detecting plasmids from de novo assembly graphs',
+      url='https://github.com/Shamir-Lab/Recycler',
+      author='Roye Rozov',
+      author_email = '',
+      license='BSD-3-Clause',
+      scripts = ['bin/recycle.py', 'bin/make_fasta_from_fastg.py', 'bin/get_simple_cycs.py'],
+      packages = ['recycle'],
+      requires=['python (<3.0)'],
+      install_requires=[
+        'networkx',
+        'pysam',
+        'nose',
+        'numpy']
+      )