wasade

#!/bin/bash

OLD_VERSION=$1
NEW_VERSION=$2

cd trunk/examples
sed -ie "s/Biological Observation Matrix $OLD_VERSION/Biological Observation Matrix $NEW_VERSION/" *.biom

cd ../scripts
sed -ie "s/^__version__ = \"$OLD_VERSION\"/__version__ = \"$NEW_VERSION\"/" *.py

wasade

#!/usr/bin/env python
r"""Cluster submission

Light helper script for submitting jobs to a cluster. For instance, to submit
a job that calls the command hostname, just use:

    $ sub hostname

Additionally, you can specify the name of the job:

wasade

#!/bin/sh

# get notes by ID

if [ ! -e SUB.notes ]
then
    echo "Cannot find SUB.notes!"
    exit 1
fi

wasade

#!/bin/env python
#cluster_jobs.py
"""
Simple helper script to make pbs jobs and submit to the cluster 

Will only work if run on bmf or hemisphere

Can run from command line or import into python code.

Author: Micah Hamady

wasade

wasade

wasade

#!/usr/bin/env python

__author__ = "Daniel McDonald"
__copyright__ = "Copyright 2013, The QIIME Project"
__credits__ = ["Daniel McDonald", "Greg Caporaso", "Doug Wendel",
               "Jai Ram Rideout"]
__license__ = "GPL"
__version__ = "0.1.0-dev"
__maintainer__ = "Daniel McDonald"
__email__ = "[email protected]"

wasade

#!/usr/bin/env python

from qcli.command import CLInterface, Command, \
        FilterSamplesFromOTUTable, CLOption

usage_examples = [("Abundance filtering (low coverage)","Filter samples with fewer than 150 observations from the otu table.","%prog -i otu_table.biom -o otu_table_no_low_coverage_samples.biom -n 150"),
                ("Abundance filtering (high coverage)","Filter samples with greater than 149 observations from the otu table.","%prog -i otu_table.biom -o otu_table_no_high_coverage_samples.biom -x 149"),
                ("Metadata-based filtering (positive)","Filter samples from the table, keeping samples where the value for 'Treatment' in the mapping file is 'Control'","%prog -i otu_table.biom -o otu_table_control_only.biom -m map.txt -s 'Treatment:Control'"),
                ("Metadata-based filtering (negative)","Filter samples from the table, keeping samples where the value for 'Treatment' in the mapping file is not 'Control'","%prog -i otu_table.biom -o otu_table_not_control.biom -m map.tx

wasade

#!/usr/bin/env python

from qcli.command import CLInterface, Command, \
        FilterSamplesFromOTUTable, CLOption

usage_examples = [("Abundance filtering (low coverage)","Filter samples with fewer than 150 observations from the otu table.","%prog -i otu_table.biom -o otu_table_no_low_coverage_samples.biom -n 150"),
                ("Abundance filtering (high coverage)","Filter samples with greater than 149 observations from the otu table.","%prog -i otu_table.biom -o otu_table_no_high_coverage_samples.biom -x 149"),
                ("Metadata-based filtering (positive)","Filter samples from the table, keeping samples where the value for 'Treatment' in the mapping file is 'Control'","%prog -i otu_table.biom -o otu_table_control_only.biom -m map.txt -s 'Treatment:Control'"),
                ("Metadata-based filtering (negative)","Filter samples from the table, keeping samples where the value for 'Treatment' in the mapping file is not 'Control'","%prog -i otu_table.biom -o otu_table_not_control.biom -m map.tx

wasade

from qcli.interface.cli import CLOption, UsageExample, ParameterConversion

usage_examples = [
        UsageExample(ShortDesc="Abundance filtering (low coverage)",
                     LongDesc="Filter samples with fewer than 150 observations from the otu table.",
                     Ex="%prog -i otu_table.biom -o otu_table_no_low_coverage_samples.biom -n 150"),
        UsageExample(ShortDesc="Abundance filtering (high coverage)",
                     LongDesc="Filter samples with fewer than 150 observations from the otu table.",
                     Ex="%prog -i otu_table.biom -o otu_table_no_high_coverage_samples.biom -x 149")
        ]