Minor update (#27)

* helper script to index at start of module3..could be use for all modules

* increment version for cmo_index, etc

* initial commit of cmo_index

* logging

* cmo_split_reads now opens and emits gzips..slow bc native python gzip instead of subprocess zcat

* add logger function

* use bufferereader for speed improvement on gzip

* increment version

* version increment AGAIN

* install cmo_fillout

* longer delay for polling

* speed improvement for split_reads...hopefully...

* increment version for release

* fake gz files for trimgalore

* use args.version

Author: lordzappo

bin/cmo_fillout

@@ -32,7 +32,7 @@ else:
 
 ### Path to GetBaseCountsMultiSample
 #should be cmo.util.programs['GetBaseCountsMultiSample]['1.0.0'], but zeng hasn't packaged this for release yet
-gbcmPath = cmo.util.programs['getbasecountsmultisample']['1.2.1']
+gbcmPath = cmo.util.programs['getbasecountsmultisample'][args.version]
 
 
 ### Set genome path

bin/cmo_split_reads

@@ -26,9 +26,10 @@ if __name__ =='__main__':
         fh = io.BufferedReader(gzip.open(fastq, "rb"))
         output_file_count = 0
         output_file_lines = 0
+        #these aren't relaly gz but trimgalore doesnt like files not named gz...great work trimgalore
         filename = output_prefix +  "chunk{:0>3d}".format(output_file_count) +  ".fastq.gz"
         logger.info("Opening %s and writing reads..." % (filename))
-        ofh = io.BufferedWriter(gzip.open(filename, "wb"))
+        ofh = open(filename, "wb")
         lines = list()
         for line in os.popen("zcat " + fastq):
             lines.append(line)
@@ -42,7 +43,7 @@ if __name__ =='__main__':
                     output_file_count +=1
                     filename = output_prefix + "chunk{:0>3d}".format(output_file_count) +  ".fastq.gz"
                     logger.info("Opening %s and writing reads..." % (filename))
-                    ofh = io.BufferedWriter(gzip.open(filename, "wb"))
+                    ofh = open(filename, "wb")
         ofh.write("".join(lines))
         ofh.close()
 

cmo/_version.py

@@ -2,5 +2,4 @@
 # This file is originally generated from Git information by running 'setup.py
 # version'. Distribution tarballs contain a pre-generated copy of this file.
 
-
 __version__ = '1.3.2'