assemstats3.py

#! /usr/bin/env python
# This file is part of khmer, https://github.com/dib-lab/khmer/, and is
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# Contact: khmer-project@idyll.org
'''
assemstats.py

Uses screed to calculate various assembly statistics.

You can obtain screed by running
   pip install screed
'''

import screed
import sys
import glob
import os

def trimLens(lens, minLen):
    '''
    Eliminates any reads below a certain threshold.
    Function assumes that input list lens is sorted smallest to largest.
    '''

    index = 0

    for i in range(len(lens)):
        if lens[i] < minLen:
            index += 1
        else:
            break

    return lens[index:len(lens)]


def getLens(filename):
    '''
    Parses FASTA file using screed to create a sorted list of contig lengths.
    '''
    lens = []

    fa_instance = screed.open(filename)
    for record in fa_instance:
        lens.append(len(record['sequence']))

    return sorted(lens)


def calcNXX(lens, percent):
    '''
    Calculates any NXX (e.g. N50, N90) statistic.
    '''

    lenSum = sum(lens)
    threshold = (float(percent) / 100) * lenSum

    runningSum = 0
    nxx = 0
    nxxLen = 0

    for i in range(len(lens) - 1, -1, -1):
        myLen = lens[i]
        nxx += 1
        runningSum += myLen

        if runningSum >= threshold:
            nxxLen = myLen
            break

    return nxx, nxxLen


def main():
    '''
    Outputs assembly statistics for provided FASTA files.
    '''
    totalN = 0
    totalSum = 0

    if len(sys.argv) < 3:
        print("Usage: python assemstats.py <min contig length> [ FASTA files ]")
        return

    try:
        minLen = int(sys.argv[1])
    except ValueError:
        print("Minimum contig length must be an integer.")
        return

    print('** cutoff:', minLen)
    print("N\tsum\tmax\tfilename")

    for filename in sys.argv[2:]:
        if not os.path.exists(filename):
            print("WARNING: file %s does not exist." % filename, file=sys.stderr)
            continue

        lens = getLens(filename)
        trimmedLens = trimLens(lens, minLen)

        if trimmedLens:
            statTrimmedN = len(trimmedLens)
            statSum = sum(trimmedLens)
            statMax = max(trimmedLens)
        else:
            statTrimmedN = 0
            statSum = 0
            statMax = 0

        totalN += statTrimmedN
        totalSum += statSum

        print("%d\t%d\t%d\t%s" % (statTrimmedN, statSum, statMax, filename))

    if len(sys.argv) > 3 and totalN:
        print('--')
        print('TOTAL: %g in %d contigs (mean size %d)' % (
            totalSum, totalN, totalSum / totalN + .5))

main()

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