Python read_txt Examples

Example #1

File: medians_by_otu.py Project: TankMermaid/otu_scripts

#!/usr/bin/env python

'''
author: scott w olesen ([email protected])

this script grabs medians from an otu table
'''

import pysurvey as ps, numpy as np, pandas as pd
import argparse

if __name__ == '__main__':
	p = argparse.ArgumentParser(description='get medians by otu')
	p.add_argument('table', help='input otu table')
	p.add_argument('out', help='output medians list')
	args = p.parse_args()

	table = ps.read_txt(args.table, verbose=False)
	medians = pd.DataFrame({'median': table.apply(np.median)}).T
	ps.write_txt(medians, args.out)

Example #2

File: filter_by_maximum.py Project: TankMermaid/otu_scripts

import pysurvey as ps, numpy as np
import argparse

if __name__ == '__main__':
    p = argparse.ArgumentParser(
        description='filter otus based on their maximum abundance')
    p.add_argument('table', help='input otu table')
    p.add_argument('-o', '--output', help='output otu table', required=True)
    g = p.add_mutually_exclusive_group(required=True)
    g.add_argument('-l',
                   '--log',
                   type=float,
                   help='minimum max (negative log10)')
    g.add_argument('-m', '--min', type=float, help='minimum max (raw value)')
    args = p.parse_args()

    # load up the table
    table = ps.read_txt(args.table)

    # convert to raw minimum median
    if args.log:
        args.min = 10.0**(-args.log)

    # filter columns if the maximum is below the specified min
    criterion = (np.max, lambda x, y: x > y, args.min)
    table = ps.filter_by_vals(table, criterion)

    # write out the filtered table
    ps.write_txt(table, args.output)

Example #3

#!/usr/bin/env python
'''
author: scott w olesen ([email protected])

combine two otu tables, etc.
'''

import pysurvey as ps, numpy as np, pandas as pd
import argparse

if __name__ == '__main__':
    p = argparse.ArgumentParser(description='get medians')
    p.add_argument('table1', help='input otu table')
    p.add_argument('table2', help='other input otu table')
    p.add_argument('out', help='output table')
    args = p.parse_args()

    # read tables. don't transpose, since that would cause joining samples, not OTU IDs
    table1 = ps.read_txt(args.table1, verbose=False, T=False)
    table2 = ps.read_txt(args.table2, verbose=False, T=False)

    table = table1.join(table2, how='outer').fillna(0)

    ps.write_txt(table, args.out, T=False)