ipyrad testing

In [1]:
import ipyrad as ip      ## for RADseq assembly
print ip.__version__     ## print version
0.1.26
In [2]:
## clear test directory if it already exists
import shutil
import os
if os.path.exists("./test_pairgbs"):
    shutil.rmtree("./test_pairgbs")

Getting started -- Assembly objects

The first step is to create an Assembly object. It takes an optional argument that provides it with an internal name. We could imagine that we planned to assemble and later combine data from multiple sequencing runs, but before combining them each group of samples has to be analyzed under a different set of parameters. As an example, we could call this data set "2014_data_set" and another "2015_data_set".

In [3]:
## create an Assembly object called data1. 
## It takes an 'test'
data1 = ip.Assembly('test_pairgbs')
  New Assembly: test_pairgbs
In [5]:
data1.set_params("project_dir", "./test_pairgbs")
data1.set_params("raw_fastq_path", "./data/sim_pairgbs_*.gz")
data1.set_params("barcodes_path", "./data/sim_pairgbs_barcodes.txt")
data1.set_params("datatype", "pairgbs")
#data1.set_params(17, 0)
#data1.set_params(19, 1)
In [6]:
data1.get_params()
  1   project_dir           ./test_pairgbs                               
  2   raw_fastq_path              ./data/sim_pairgbs_*.gz                      
  3   barcodes_path               ./data/sim_pairgbs_barcodes.txt              
  4   sorted_fastq_path                                                        
  5   assembly_method             denovo                                       
  6   reference_sequence                                                       
  7   datatype                    pairgbs                                      
  8   restriction_overhang        ('TGCAG', '')                                
  9   max_low_qual_bases          5                                            
  10  phred_Qscore_offset         33                                           
  11  mindepth_statistical        6                                            
  12  mindepth_majrule            6                                            
  13  maxdepth                    1000                                         
  14  clust_threshold             0.85                                         
  15  max_barcode_mismatch        1                                            
  16  filter_adapters             0                                            
  17  filter_min_trim_len         35                                           
  18  max_alleles_consens         2                                            
  19  max_Ns_consens              (5, 5)                                       
  20  max_Hs_consens              (8, 8)                                       
  21  min_samples_locus           4                                            
  22  max_SNPs_locus              (100, 100)                                   
  23  max_Indels_locus            (5, 99)                                      
  24  max_shared_Hs_locus         0.25                                         
  25  edit_cutsites               (0, 0)                                       
  26  trim_overhang               (1, 2, 2, 1)                                 
  27  output_formats              *                                            
  28  pop_assign_file                                                          
  29  excludes                                                                 
  30  outgroups                                                                

Step 1: Demultiplex the raw data files

This demultiplexes, and links the new fastq data files as Samples to the Assembly object.

In [8]:
## demultiplex the raw_data files
## set step1 to only go if no samples are present...
data1.step1() #append=True)

print data1.stats
     state  reads_raw
1A0      1       4000
1B0      1       4000
1C0      1       4000
1D0      1       4000
2E0      1       4000
2F0      1       4000
2G0      1       4000
2H0      1       4000
3I0      1       4000
3J0      1       4000
3K0      1       4000
3L0      1       4000
In [ ]:
#data1.set_params(4, "./test_pairgbs/fastq/*")
#data1.link_fastqs()

Step 2: Filter reads

If for some reason we wanted to execute on just a subsample of our data, we could do this by selecting only certain samples to call the step2 function on. Because step2 is a function of data, it will always execute with the parameters that are linked to data.

In [9]:
data1.step2(force=True) #["1A0","1B0"])#

print data1.stats
     state  reads_raw  reads_filtered
1A0      2       4000            4000
1B0      2       4000            4000
1C0      2       4000            4000
1D0      2       4000            4000
2E0      2       4000            4000
2F0      2       4000            4000
2G0      2       4000            4000
2H0      2       4000            4000
3I0      2       4000            4000
3J0      2       4000            4000
3K0      2       4000            4000
3L0      2       4000            4000

We can access the name and fname of the Sample objects and edit them as desired without affecting the original data files. The name identifier is equal to the filename (fname) by default, but is the name used in the final output files, and thus it may be desirable to reduce it to something more readable, like below.

In [1]:
import ipyrad as ip
data1 = ip.load.load_assembly("test_pairgbs/test_pairgbs.assembly")
  loading Assembly: test_pairgbs [test_pairgbs/test_pairgbs.assembly]
In [11]:
data1.step3()
In [3]:
print data1.stats
     state  reads_raw  reads_filtered  reads_merged  clusters_total  \
1A0      3       4000            4000          4000             200   
1B0      3       4000            4000          4000             200   
1C0      3       4000            4000          4000             200   
1D0      3       4000            4000          4000             200   
2E0      3       4000            4000          4000             200   
2F0      3       4000            4000          4000             200   
2G0      3       4000            4000          4000             200   
2H0      3       4000            4000          4000             200   
3I0      3       4000            4000          4000             200   
3J0      3       4000            4000          4000             200   
3K0      3       4000            4000          4000             200   
3L0      3       4000            4000          4000             200   

     clusters_hidepth  
1A0               200  
1B0               200  
1C0               200  
1D0               200  
2E0               200  
2F0               200  
2G0               200  
2H0               200  
3I0               200  
3J0               200  
3K0               200  
3L0               200  
In [2]:
data1.step4()
print data1.stats
[3:apply]: 
---------------------------------------------------------------------------ValueError                                Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
    255                                             (bfreqs, ustacks, counts),
    256                                              disp=False,
--> 257                                              full_output=False)
    258     return [sample.name, hetero, errors]
    259 
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
    375             'return_all': retall}
    376 
--> 377     res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
    378     if full_output:
    379         retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
    433     if retall:
    434         allvecs = [sim[0]]
--> 435     fsim[0] = func(x0)
    436     nonzdelt = 0.05
    437     zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
    283     def function_wrapper(*wrapper_args):
    284         ncalls[0] += 1
--> 285         return function(*(wrapper_args + args))
    286 
    287     return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
     94     else:
     95         ## get likelihood for all sites
---> 96         lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
     97         lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
     98         liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
     46     ## make sure base_frequencies are in the right order
     47     #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48     totals = np.array([ustacks.sum(axis=1)]*4).T
     49     prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
     50     return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
     30 
     31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32     return umr_sum(a, axis, dtype, out, keepdims)
     33 
     34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds

[0:apply]: 
---------------------------------------------------------------------------ValueError                                Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
    255                                             (bfreqs, ustacks, counts),
    256                                              disp=False,
--> 257                                              full_output=False)
    258     return [sample.name, hetero, errors]
    259 
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
    375             'return_all': retall}
    376 
--> 377     res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
    378     if full_output:
    379         retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
    433     if retall:
    434         allvecs = [sim[0]]
--> 435     fsim[0] = func(x0)
    436     nonzdelt = 0.05
    437     zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
    283     def function_wrapper(*wrapper_args):
    284         ncalls[0] += 1
--> 285         return function(*(wrapper_args + args))
    286 
    287     return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
     94     else:
     95         ## get likelihood for all sites
---> 96         lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
     97         lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
     98         liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
     46     ## make sure base_frequencies are in the right order
     47     #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48     totals = np.array([ustacks.sum(axis=1)]*4).T
     49     prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
     50     return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
     30 
     31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32     return umr_sum(a, axis, dtype, out, keepdims)
     33 
     34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds

[1:apply]: 
---------------------------------------------------------------------------ValueError                                Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
    255                                             (bfreqs, ustacks, counts),
    256                                              disp=False,
--> 257                                              full_output=False)
    258     return [sample.name, hetero, errors]
    259 
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
    375             'return_all': retall}
    376 
--> 377     res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
    378     if full_output:
    379         retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
    433     if retall:
    434         allvecs = [sim[0]]
--> 435     fsim[0] = func(x0)
    436     nonzdelt = 0.05
    437     zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
    283     def function_wrapper(*wrapper_args):
    284         ncalls[0] += 1
--> 285         return function(*(wrapper_args + args))
    286 
    287     return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
     94     else:
     95         ## get likelihood for all sites
---> 96         lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
     97         lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
     98         liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
     46     ## make sure base_frequencies are in the right order
     47     #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48     totals = np.array([ustacks.sum(axis=1)]*4).T
     49     prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
     50     return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
     30 
     31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32     return umr_sum(a, axis, dtype, out, keepdims)
     33 
     34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds

[2:apply]: 
---------------------------------------------------------------------------ValueError                                Traceback (most recent call last)<string> in <module>()
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in optim(args)
    255                                             (bfreqs, ustacks, counts),
    256                                              disp=False,
--> 257                                              full_output=False)
    258     return [sample.name, hetero, errors]
    259 
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in fmin(func, x0, args, xtol, ftol, maxiter, maxfun, full_output, disp, retall, callback)
    375             'return_all': retall}
    376 
--> 377     res = _minimize_neldermead(func, x0, args, callback=callback, **opts)
    378     if full_output:
    379         retlist = res['x'], res['fun'], res['nit'], res['nfev'], res['status']
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in _minimize_neldermead(func, x0, args, callback, xtol, ftol, maxiter, maxfev, disp, return_all, **unknown_options)
    433     if retall:
    434         allvecs = [sim[0]]
--> 435     fsim[0] = func(x0)
    436     nonzdelt = 0.05
    437     zdelt = 0.00025
/home/deren/anaconda/lib/python2.7/site-packages/scipy/optimize/optimize.pyc in function_wrapper(*wrapper_args)
    283     def function_wrapper(*wrapper_args):
    284         ncalls[0] += 1
--> 285         return function(*(wrapper_args + args))
    286 
    287     return ncalls, function_wrapper
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in get_diploid_lik(pstart, bfreqs, ustacks, counts)
     94     else:
     95         ## get likelihood for all sites
---> 96         lik1 = (1.-hetero)*likelihood1(errors, bfreqs, ustacks)
     97         lik2 = (hetero)*likelihood2(errors, bfreqs, ustacks)
     98         liks = lik1+lik2
/home/deren/Documents/ipyrad/ipyrad/assemble/jointestimate.pyc in likelihood1(errors, bfreqs, ustacks)
     46     ## make sure base_frequencies are in the right order
     47     #print uniqstackl.sum()-uniqstack, uniqstackl.sum(), 0.001
---> 48     totals = np.array([ustacks.sum(axis=1)]*4).T
     49     prob = scipy.stats.binom.pmf(totals-ustacks, totals, errors)
     50     return np.sum(bfreqs*prob, axis=1)
/home/deren/anaconda/lib/python2.7/site-packages/numpy/core/_methods.pyc in _sum(a, axis, dtype, out, keepdims)
     30 
     31 def _sum(a, axis=None, dtype=None, out=None, keepdims=False):
---> 32     return umr_sum(a, axis, dtype, out, keepdims)
     33 
     34 def _prod(a, axis=None, dtype=None, out=None, keepdims=False):
ValueError: 'axis' entry is out of bounds

... 8 more exceptions ...
In [ ]:
data1.step5(["1A0"])
In [ ]:
#data1.step5(["1A0"])  ## better filters for -N-
In [ ]:
 

Quick parameter explanations are always on-hand

In [ ]:
ip.get_params_info(10)

Log history

A common problem after struggling through an analysis is that you find you've completely forgotten what parameters you used at what point, and when you changed them. The log history time stamps all calls to set_params(), as well as calls to step methods. It also records copies/branching of data objects.

In [ ]:
for i in data.log:
    print i

Saving Assembly objects

Assembly objects can be saved and loaded so that interactive analyses can be started, stopped, and returned to quite easily. The format of these saved files is a serialized 'pickle' object used by Python. Individual Sample objects are saved within Assembly objects. While it is important to remember that some of the information in Assembly objects is in their links to data files, most of the useful information that we would want to analyze post assembly is stored in the object itself. Thus these objects will be useful for making plots and tables of assembly statistics later.

In [ ]:
## save assembly object
#ip.save_assembly("data1.p")

## load assembly object
#data = ip.load_assembly("data1.p")
#print data.name

figureing out insert

In [ ]:
indels = []
catg = []
In [ ]:
arcatg = np.array([[5, 0, 0, 0],
                   [0, 5, 0, 0],
                   [0, 0, 5, 0],
                   [0, 0, 0, 5]],
                  [[5, 0, 0, 0],
                   [0, 5, 0, 0],
                   [0, 0, 5, 0],
                   [0, 0, 0, 5]], dtype=uint32)
In [ ]:
arcatg