merged

Changelog.txt

@@ -1,3 +1,44 @@
+Moa 0.11.4 / 2012-10-16
+==========================
+  * Minor fix with installation
+
+Moa 0.11.3 / 2012-10-16
+==========================
+
+  * fix to work with /usr/local/share/moa for moa data
+  * improved docs
+
+Moa 0.11.2 / 2012-10-15
+==========================
+
+  * some code cleanup
+  * improved installer (that might even work)
+
+Moa 0.11.1 / 2012-10-14
+==========================
+
+  * lots of (pep8) cleanup
+  * git repositories as templates
+  * reworked templates/providers
+  * new moa.cli for all CLI code
+  * allowing a default title
+  * fixed a few unittests
+  * started using pelican for static website generation - in progress
+  * reworked changelogs & blog messages - now stored in ./doc/*
+  * better openlava actor
+  * Not using os.getcwd - prevent dereferencing of symlinks
+  * uses TTYtter to send tweets
+  * better autogenerated changelog messages
+  * writes exec scripts to ./.moa/tmp now - easier to track
+  * retains title when running moa new
+  * better plugin structure - distinguish between job & system plugins
+  * start drawing images of moa workflows
+  * track versioning
+  * moved `fileset` code to the core
+  * moa mv now works
+  * new argparse structure - better command line interface
+  * remoteLogger logs to mysql
+
 Moa 0.10.15 / 2012-01-30
 ==========================
 
@@ -87,7 +128,7 @@ Moa 0.10.10 / 2011-05-10
 ==========================
 
   * jinja2 version of the ncbi template
-  * recursively defined variables are adapted if they appear to be 
+  * recursively defined variables are adapted if they appear to be
     a relative path
   * rearranged plugin management
   * many small fixes improving recursive & multithreaded operation
@@ -125,7 +166,7 @@ Moa 0.10.7 / 2011-04-27
 
   * fixed a bug confusing the ~/.moa config dir with a proper moa job
 
-Moa 0.10.6 / 2011-04-27 
+Moa 0.10.6 / 2011-04-27
 =======================
 
   * debian pacakaging is deprecated

MANIFEST.in

@@ -1,25 +1,25 @@
-exclude .*
 include VERSION
 include README
 include COPYING
+include Changelog.txt
 include etc/bash_completion.d/moa
 include etc/config
 
-recursive-include bin/ *
-recursive-include template2 *.mk *.moa *.jinja2
+include bin/moa
+include bin/moar
+include bin/moainit
 
-recursive-include lib/jinja2/ *.jinja2
-recursive-include lib/ruff/ *.jinja2
-recursive-include lib/gnumake/ *.mk
+recursive-include template2 *.moa *.jinja2
 
-include lib/gnumake/util/__gmsl
-include lib/gnumake/util/gmsl
+recursive-include lib/jinja2 *jinja2
 
-recursive-include share/ *.fq *fasta
+recursive-include share/test *.fq *fasta
+
+include etc/config
+include etc/bash_completion.d/moa
+include etc/profile.d/moa.sh
+
+include share/logo/moa.logo.txt
 
-recursive-include etc *.mk *.conf *.jinja2
-recursive-include share/ *.txt
-recursive-include www/ *.html *.js *.css *.png *.gif *.jpg *.css *.cgi
 
 
-

README

@@ -1,9 +1,8 @@
 Moa - lightweight workflows in bioinformatics.
 
-For installation & operation please read the manual:
-
+For information on how to install and operate Moa, please refer to
 http://mfiers.github.com/Moa/
-
+f
 or try:
 
 moa --help

VERSION

@@ -1 +1 @@
-0.11.0
+0.11.4

bin/fastq2contigs

@@ -0,0 +1,44 @@
+#!/usr/bin/env python
+
+import os
+import re
+import sys
+import argparse
+
+parser = argparse.ArgumentParser()
+parser.add_argument('fastq')
+parser.add_argument('output')
+parser.add_argument('-n', dest='non', help='nubmer NNNs to cut a fastq file',
+                    type=int, default=10)
+
+args = parser.parse_args()
+
+F =  open(args.fastq)
+G = open(args.output, 'w')
+
+splitter = re.compile('n{'+str(args.non)+',}', re.I)
+
+header = F.readline()
+assert(header[0] == '@')
+header = header[1:].split()[0]
+print 'header', header
+
+seq = []
+for line in F:
+    if line[0] == '+': break
+    seq.append(line.strip())
+seq = "".join(seq)
+print 'read %d nt' % len(seq)
+
+contigs = splitter.split(seq)
+for i, c in enumerate(contigs):
+    G.write(">%s_%s\n" % (header, i))
+    while c:
+        G.write("%s\n" % c[:80])
+        c = c[80:]
+
+print "wrote %d contigs to %s" %  (len(contigs), sys.argv[2])
+
+F.close()
+G.close()
+