adamrp

#!/usr/bin/env python

from sys import argv

with open(argv[1], 'U') as input_f, open(argv[2], 'w') as output_f:
    for line in input_f:
        # Write comment/header line(s) to output file unmodified
        if line.startswith('#'):
            output_f.write(line)
            continue

adamrp

#!/usr/bin/env python

from sys import argv

prefixes = ['k__', 'p__', 'c__', 'o__', 'f__', 'g__', 's__']

with open(argv[1], 'U') as input_f, open(argv[2], 'w') as output_f:
    for line in input_f:
        otu_id, tax, p = line.strip().split('\t')
        tax = '; '.join([''.join(x) for x in zip(prefixes, tax.split(';'))])

adamrp

#!/usr/bin/env python

import binascii
import os

from amgut import db_conn


def iter_old_surveys():
    sql = """select * from ag_human_survey"""

adamrp

#!/usr/bin/env python

from datetime import datetime

from data_access_connections import data_access_factory
from enums import ServerConfig, DataAccessType

from amgut import db_conn

data_access = data_access_factory(ServerConfig.data_access_type,

adamrp

#!/usr/bin/env python

from datetime import datetime
from os.path import join

import click

from data_access_connections import data_access_factory
from enums import ServerConfig, DataAccessType
from qiita_db.study import StudyPerson

adamrp

#!/usr/bin/env python

from amgut.lib.human_survey_supp import (
    question_map, responses_map, key_map, question_group, group_order,
    supplemental_map, question_type)
from amgut.lib.locale_data.american_gut import _HUMAN_SURVEY
from amgut.lib.data_access.sql_connection import SQLConnectionHandler

conn = SQLConnectionHandler()

adamrp

#!/usr/bin/env python

from sys import argv

from skbio.parse.sequences.fasta import parse_fasta

def calculate_gc_content(input_fasta):
    gc = 0
    total_length = 0

adamrp

#!/usr/bin/env python

from argparse import ArgumentParser
from numpy import array

from biom import load_table, Table

__author__ = "Adam Robbins-Pianka"
__copyright__ = "Copyright 2013"
__credits__ = ["Adam Robbins-Pianka"]