add setuptools stuff

README.md

@@ -25,25 +25,33 @@ could be improvements.
 QuickStart
 ==========
 
+Without installation, you can use as `python bwameth.py` with install, the
+command is `bwa-meth`.
+
 The commands:
 
-    python bwa-meth.py index $REF
-    python bwa-meth.py --reference $REF some_R1.fastq.gz some_R2.fastq.gz --prefix some.output
+    bwa-meth index $REF
+    bwa-meth --reference $REF some_R1.fastq.gz some_R2.fastq.gz --prefix some.output
 
 will create `some.output.bam` and `some.output.bam.bai`
 
 Installation
 ============
 
-`bwa-meth.py` depends on 
+`bwa-meth` depends on 
 
  + python 2.7 
    - `toolshed` library. can be installed with: 
       * `easy_install toolshed` or
       * `pip install toolshed`
 
+   - or run: `python setup.py install` from this directory
+
  + samtools command on the `$PATH` (https://github.com/samtools/samtools)
 
+
+
+
 usage
 =====
 
@@ -52,15 +60,15 @@ Index
 
 One time only, you need to index a reference sequence.
 
-    python bwa-meth.py index $REFERENCE
+    bwa-meth index $REFERENCE
 
 If your reference is `some.fasta`, this will create `some.c2t.fasta`
 and all of the bwa indexes associated with it.
 
 Align
 -----
 
-    python bwa-meth.py --threads 16 \
+    bwa-meth --threads 16 \
          --prefix $PREFIX \
          --reference $REFERENCE \
          $FQ1 $FQ2
@@ -75,10 +83,10 @@ or not.
 The command above will be sent to BWA to do the work as something like:
 
     bwa mem -L 25 -pCM -t 15  $REFERENCE.c2t.fa \
-            '<python bwa-meth.py c2t $FQ1 $FQ2'
+            '<python bwa-meth c2t $FQ1 $FQ2'
 
 So the converted reads are streamed directly to bwa and **never written
-to disk**. The output from that is modified by `bwa-meth.py` and streamed
+to disk**. The output from that is modified by `bwa-meth` and streamed
 straight to a bam file.
 
 Tabulate
@@ -89,7 +97,7 @@ for SNPs.
 
 E.g.:
 
-    bwa-meth.py tabulate \
+    bwa-meth tabulate \
                 --trim 3,3 \
                 --map-q 60 \
                 --bissnp BisSNP-0.82.2.jar \

bwa-meth.py → bwameth.py

@@ -429,7 +429,7 @@ def tabulate_main(args):
             print >>fhs[sample], fmt.format(**d)
 
 
-def main(args):
+def main(args=sys.argv[1:]):
 
     if len(args) > 0 and args[0] == "index":
         sys.exit(bwa_index(convert_fasta(args[1])))