nickloman

from Bio import SeqIO
import sys

seq_number = 1
for rec in SeqIO.parse(open(sys.argv[1]), "fasta"):
        cols = rec.name.split("_")
        count = int(cols[3])

        for n in xrange(count):
                print ">%s_%s_%s read%s" % (cols[0], cols[1], seq_number, seq_number)

nickloman

## little tweet ripper, run python get.py ABPH11

import operator
import sys
import urllib
import json

url = "http://search.twitter.com/search.json"
u_hash = {}

nickloman

import sys
from copy import copy

used_keys = ['DP', 'AF1', 'CI95', 'DP4', 'MQ', 'PV4', 'INDEL']
initial_dict = dict([(k, '') for k in used_keys])

for ln in sys.stdin:
    d = copy(initial_dict)

    cols = ln.rstrip().split("\t")

nickloman

# Usage python filter.py <read1.gz> <read2.gz>

from Bio import SeqIO
import itertools
import sys
import gzip
import os.path

f1 = gzip.open(sys.argv[1], "r")
f2 = gzip.open(sys.argv[2], "r")

nickloman

from Bio import SeqIO
import sys
import glob

def system(cmd):
    print >>sys.stderr, cmd
    os.system(cmd)

# dodir_pyro.py directory

nickloman

import os
import sys
import glob

def system(cmd):
    print >>sys.stderr, cmd
    os.system(cmd)

# dodir_pyro.py directory

nickloman

import os
import sys
import glob

def system(cmd):
    print >>sys.stderr, cmd
    os.system(cmd)

# dodir_pyro.py directory

nickloman

import os
import sys
import glob

TRUNCATE_LENGTH = int(sys.argv[2])

def system(cmd):
    print >>sys.stderr, cmd
    os.system(cmd)

nickloman

# requires biopython
# run like:
#   genbank_to_tbl.py "my organism name" "my strain ID" "ncbi project id" < my_sequence.gbk
#   writes seq.fsa, seq.tbl as output

import sys
from copy import copy
from Bio import SeqIO

def find_gene_entry(features, locus_tag):

nickloman

--- lib/qiime/assign_taxonomy.py        2011-09-11 20:53:06.000000000 +0100
+++ ../16s/Qiime-1.2.1/build/lib/qiime/assign_taxonomy.py       2011-02-22 21:00:06.000000000 +0000
@@ -89,7 +89,7 @@
         """ Initialize the object
         """
         _params = {
-            'Min percent identity': 90,
+            'Min percent identity': 0.90,
             'Max E value': 1e-30,
             'Application': 'blastn/megablast'