<reponame>apcamargo/inStrain
'''
This file contains the API-like elements that are called from the outside
'''

import inStrain.profile.profile_controller

def profile_bam(bam, fasta_db, sR2M, ISP_loc, **kwargs):
    '''
    Profile a bam file with inStrain

    arguments:
        bam = location of .bam file
        Fdb = dictionary listing fasta locations to profile
        sR2M = dictionary of scaffold -> read pair -> number of mm
        ISP_loc = location of inStrain profile to store results
    '''
    return inStrain.profile.profile_controller.BamProfileController(
                                        bam, fasta_db, sR2M, ISP_loc, **kwargs).main()

'''
This file contains the API-like elements that are called from the outside
'''

import inStrain.profile.profile_controller

def profile_bam(bam, fasta_db, sR2M, ISP_loc, **kwargs):
    '''
    Profile a bam file with inStrain

    arguments:
        bam = location of .bam file
        Fdb = dictionary listing fasta locations to profile
        sR2M = dictionary of scaffold -> read pair -> number of mm
        ISP_loc = location of inStrain profile to store results
    '''
    return inStrain.profile.profile_controller.BamProfileController(
                                        bam, fasta_db, sR2M, ISP_loc, **kwargs).main()
This file contains the API-like elements that are called from the outside Profile a bam file with inStrain      arguments:         bam = location of .bam file         Fdb = dictionary listing fasta locations to profile         sR2M = dictionary of scaffold -> read pair -> number of mm         ISP_loc = location of inStrain profile to store results