new release

Author: Dom Laetsch

scripts/__init__.py __init__.py

@@ -0,0 +1 @@
+blobtools.py

bam2cov.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+"""
+usage: blobtools <command> [<args>...] [--help]
+
+commands:
+  version       print version number
+
+  create        create a BlobDB
+  view          print BlobDB as a table
+  blobplot      plot BlobDB as a blobplot
+  covplot       compare BlobDB cov(s) to additional cov file
+
+  bam2cov       generate cov file from bam file
+  sumcov        sum coverage from multiple COV files
+  seqfilter     filter FASTA sequences based on header in list
+  taxify        assign taxids to blast-results based on list
+
+-h --help    show this
+
+"""
+
+from __future__ import division
+import sys
+from subprocess import call
+from os.path import join, dirname
+from docopt import docopt
+
+__version__ = "blobtools v0.9.18"
+MAINDIR = join(dirname(__file__), '')
+DATADIR = join(MAINDIR, 'data/')
+SRCDIR = join(MAINDIR, 'src/')
+LIBDIR = join(MAINDIR, 'lib/')
+
+if __name__ == '__main__':
+    args = docopt(__doc__,
+                  version=__version__,
+                  options_first=True)
+
+    argv = [args['<command>']] + args['<args>']
+    if args['<command>'] == 'create':
+        exit(call(['python', SRCDIR + 'create.py'] + argv))
+    elif args['<command>'] == 'view':
+        exit(call(['python', SRCDIR + 'view.py'] + argv))
+    elif args['<command>'] == 'blobplot' or args['<command>'] == 'plot':
+        argv[0] = "blobplot"
+        exit(call(['python', SRCDIR + 'blobplot.py'] + argv))
+    elif args['<command>'] == 'bam2cov':
+        exit(call(['python', SRCDIR + 'bam2cov.py'] + argv))
+    elif args['<command>'] == 'covplot' or args['<command>'] == 'comparecov':
+        argv[0] = "covplot"
+        exit(call(['python', SRCDIR + 'covplot.py'] + argv))
+    elif args['<command>'] == 'sumcov':
+        exit(call(['python', SRCDIR + 'sumcov.py'] + argv))
+    elif args['<command>'] == 'seqfilter':
+        exit(call(['python', SRCDIR + 'seqfilter.py'] + argv))
+    elif args['<command>'] == 'taxify':
+        exit(call(['python', SRCDIR + 'taxify.py'] + argv))
+    else:
+        exit("%r is not a blobtools command. See 'blobtools -h'." % args['<command>'])

blobtools

@@ -1,11 +1,11 @@
-#48a365=Nematoda
-#d0694a=Arthropoda
-#ffb917=Proteobacteria
-#926eb3=Actinobacteria
-#a6cee3=Ascomycota
-#d3d3d3=no-hit
-#ec84ba=Chordata
-#e0d799=Cnidaria
-#b89c75=Platyhelminthes
-#fdb761=Bacteriodetes
-#ffffff=other
+Nematoda    #48a365
+Arthropoda  #d0694a
+Proteobacteria  #ffb917
+Actinobacteria  #926eb3
+Ascomycota  #a6cee3
+no-hit  #d3d3d3
+Chordata    #ec84ba
+Cnidaria    #e0d799
+Platyhelminthes #b89c75
+Bacteriodetes   #fdb761
+other   #ffffff