laserson

diff --git a/Bio/GenBank/Scanner.py b/Bio/GenBank/Scanner.py
index cc72e7f..18d2551 100644
--- a/Bio/GenBank/Scanner.py
+++ b/Bio/GenBank/Scanner.py
@@ -161,9 +161,17 @@ class InsdcScanner:
                 while line[:self.FEATURE_QUALIFIER_INDENT] == self.FEATURE_QUALIFIER_SPACER:
                     line = self.handle.readline()
             else:
-                #Build up a list of the lines making up this feature:
-                feature_key = line[2:self.FEATURE_QUALIFIER_INDENT].strip()

laserson

diff --git a/Bio/GenBank/Scanner.py b/Bio/GenBank/Scanner.py
index cc72e7f..dd9d7f0 100644
--- a/Bio/GenBank/Scanner.py
+++ b/Bio/GenBank/Scanner.py
@@ -1183,7 +1183,69 @@ class GenBankScanner(InsdcScanner):
             return
         except StopIteration:
             raise ValueError("Problem in misc lines before sequence")
+
+class ImgtScanner(EmblScanner):

laserson

import sys
import re

rev_gr_re = re.compile(r'([0-9]+)>{1}')
correct = lambda s: rev_gr_re.sub(r'>\1',s) + '\n'

if len(sys.argv) == 3:
    ip = open(sys.argv[1],'r')
    op = open(sys.argv[2],'w')
else:

laserson

ar: adding 50 object files to build/temp.macosx-10.4-x86_64-2.7/libarpack.a
/usr/bin/ranlib: archive member: build/temp.macosx-10.4-x86_64-2.7/libarpack.a(cgetv0.o) cputype (7) does not match previous archive members cputype (16777223) (all members must match)
/usr/bin/ranlib: archive member: build/temp.macosx-10.4-x86_64-2.7/libarpack.a(cnaitr.o) cputype (7) does not match previous archive members cputype (16777223) (all members must match)
/usr/bin/ranlib: archive member: build/temp.macosx-10.4-x86_64-2.7/libarpack.a(cnapps.o) cputype (7) does not match previous archive members cputype (16777223) (all members must match)
/usr/bin/ranlib: archive member: build/temp.macosx-10.4-x86_64-2.7/libarpack.a(cnaup2.o) cputype (7) does not match previous archive members cputype (16777223) (all members must match)
/usr/bin/ranlib: archive member: build/temp.macosx-10.4-x86_64-2.7/libarpack.a(cnaupd.o) cputype (7) does not match previous archive members cputype (16777223) (all members must match)
/usr/bin/ranlib: archiv

laserson

diff --git a/make.osx b/make.osx
index d3093a7..42a4852 100644
--- a/make.osx
+++ b/make.osx
@@ -1,10 +1,11 @@
 # build mpl into a local install dir with
 # PREFIX=/Users/jdhunter/dev make -f make.osx fetch deps mpl_install
 MPLVERSION=1.0rc1
-PYVERSION=2.6
+PYVERSION=2.7

laserson

import numpy as np

def multinomial_sample(n,p):
    """Return sample variates from multinomial.
    
    In contrast with `numpy`'s multinomial sampler, this will return the actual
    samples, rather than the summed results. In other words, the result of
    `numpy`'s sampler is the same length as `p`, while the result of this
    sampler is of length `n`.
    

laserson

#! /usr/bin/env python

import os
import datetime
import optparse

import lsf

option_parser = optparse.OptionParser()
option_parser.add_option('-m','--make_jobs',action='store_true')

laserson

require 'formula'

class Exonerate <Formula
  url 'http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0.tar.gz'
  homepage 'http://www.ebi.ac.uk/~guy/exonerate/'
  md5 'ad3f7fc413376201c4631687b2e0ae89'
  depends_on 'glib'
  
  def install
    ENV.j1

laserson

laserson@hobbes:~$ brew install -v exonerate
==> Build Environment
CC: /usr/bin/cc => /usr/bin/gcc-4.2
CXX: /usr/bin/c++ => /usr/bin/c++-4.2
LD: /usr/bin/cc => /usr/bin/gcc-4.2
CFLAGS: -O3 -march=core2 -w -pipe
CXXFLAGS: -O3 -march=core2 -w -pipe
MACOSX_DEPLOYMENT_TARGET: 10.6
MAKEFLAGS: -j2
==> Downloading http://www.ebi.ac.uk/~guy/exonerate/exonerate-2.2.0.tar.gz

laserson

# Based on http://code.activestate.com/recipes/576633/
# which is based on:
# Reference: 'Stacked graphs- geometry & aesthetics' by Byron and Wattenberg
# http://www.leebyron.com/else/streamgraph/download.php?file=stackedgraphs_byron_wattenberg.pdf

import numpy as np
import matplotlib as mpl
# mpl.use('Agg')
import matplotlib.pyplot as plt