I'm writing code to find local alignments between two sequences. Here is a minimal, working example I've been working on:
from Bio import pairwise2
from Bio.pairwise2 import format_alignment
seq1 = "GTGGTCCTAGGC"
seq2 = "GCCTAGGACCAC"
# scores for the alignment
match =1
mismatch = -2
gapopen = -2
gapext = 0
# see: http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html
# 'localms' takes <seq1,seq2, match,mismatch,open,extend>
for a in pairwise2.align.localms(seq1,seq2,match,mismatch,gapopen,gapext):
print(format_alignment(*a))
The following code runs with the output
GTGGTCCTAGGC----
|||||
----GCCTAGGACCAC
Score=5
But a score of '6' should be possible, finding the 'C-C' next to the 5 alignments, like so:
GTGGTCCTAGGC----
||||||
----GCCTAGGACCAC
Score=6
Any ideas on what's going on?
This seems to be a bug in the current implementation of local alignments in Biopython's pairwise2 module. There is a recent pull request (#782) on Biopython's GitHub, which should solve your problem:
>>> from Bio import pairwise2 # This is the version from the pull request
>>> seq1 = 'GTGGTCCTAGGC'
>>> seq2 = 'GCCTAGGACCAC'
>>> for a in pairwise2.align.localms(seq1, seq2, 1, -2, -2, 0):
print pairwise2.format_alignment(*a)
GTGGTCCTAGGC----
||||||
----GCCTAGGACCAC
Score=6
If you are working with short sequences only, you can just download
the code for pairwise2.py from the pull request
mentioned above. In addition you need to 'inactivate' the respective
C module (cpairwise2.pyd or
cpairwise2.so), e.g. by renaming it or by removing the
import of the C functions at the end of
pairwise2.py(from .cpairwise import ...).
If your are working with longer sequences, you will need the speed enhancement of the C module. Thus you also have to download
cpairwise2module.c from the pull request and compile it
into cpairwise2.pyd (for Windows systems) or
cpairwise2.so (Unix, Linux).
EDIT: In Biopython 1.68 the problem is solved.
Related
I have this function that I would like to apply to a large dataframe in parallel:
from rdkit import Chem
from rdkit.Chem.MolStandardize import rdMolStandardize
from rdkit import RDLogger
RDLogger.DisableLog('rdApp.*')
def standardize_smiles(smiles):
if smiles is None:
return None
try:
mol = Chem.MolFromSmiles(smiles)
# removeHs, disconnect metal atoms, normalize the molecule, reionize the molecule
clean_mol = rdMolStandardize.Cleanup(mol)
# if many fragments, get the "parent" (the actual mol we are interested in)
parent_clean_mol = rdMolStandardize.FragmentParent(clean_mol)
# try to neutralize molecule
uncharger = rdMolStandardize.Uncharger() # annoying, but necessary as no convenience method exists
uncharged_parent_clean_mol = uncharger.uncharge(parent_clean_mol)
# note that no attempt is made at reionization at this step
# nor at ionization at some pH (rdkit has no pKa caculator)
# the main aim to to represent all molecules from different sources
# in a (single) standard way, for use in ML, catalogue, etc.
te = rdMolStandardize.TautomerEnumerator() # idem
taut_uncharged_parent_clean_mol = te.Canonicalize(uncharged_parent_clean_mol)
return Chem.MolToSmiles(taut_uncharged_parent_clean_mol)
#except:
# return False
standardize_smiles('CCC')
'CCC'
However, neither Dask, nor Swifter, nor Ray can do the job. All frameworks use a single CPU for some reason.
Native Pandas
import pandas as pd
N = 1000
smilest_test = pd.DataFrame({'smiles': ['CCC']*N})
smilest_test
CPU times: user 3.58 s, sys: 0 ns, total: 3.58 s
Wall time: 3.58 s
Swifter 1.3.4
smiles_test['standardized_siles'] = smiles_test.smiles.swifter.allow_dask_on_strings(True).apply(standardize_smiles)
CPU times: user 892 ms, sys: 31.4 ms, total: 923 ms
Wall time: 5.14 s
While this WORKS with the dummy data, it does not with the real data, which looks like this:
The strings are a bit more complicated than the ones in the dummy data.
it seems first swifter needs some time to prepare the parallel execution and only uses one core, but then uses more cores. However, for the real data, it only uses 3 out of 8 cores.
I have the same issue with other frameworks such as dask, ray, modin, swifter.
Is there something that I miss here? Is there a problem when the dataframe contains stings? Why does the parallel execution take so much time even on a single computer (with multiple cores)? Or is there an issue with the RDKit library that I am using that makes it difficult to parallelize the above function?
I am trying to create a table structure through tb.IsDescription class, then create a .h5 file and populate it with a Pandas Dataframe with Datetime index, using TsTables package. I have already tested the Dataframe and the date time Indexing and both seem to be fine. I believe the issue is with the TsTable package, as it remains 'Unused import statement'. The error I get is: " AttributeError: module 'pandas.tseries' has no attribute 'index' ". The reason I am using the TsTAble is that I have heard it is faster than other modules. Any suggestions how to resolve this issue, or any substitute method?
import numpy as np
import pandas as pd
import tables as tb
import datetime as dt
path = r'C:\Users\--------\PycharmProjects\pythonProject2'
no = 5000000 # number of time steps
co = 3 # number of time series
interval = 1. / (12 * 30 * 24 * 60) # the time interval as a year fraction
vol = 0.2 # volatility
rn = np.random.standard_normal((no, co))
rn[0] = 0.0 # sets the initial random numbers to zero
paths = 100 * np.exp(np.cumsum(-0.5 * vol ** 2 * interval + vol * np.sqrt(interval) * rn, axis=0))
# simulation based on an Euler discretization
paths[0] = 100 # Sets the initial values of the paths to 100
dr = pd.date_range('2019-1-1', periods=no, freq='1s')
print(dr[-6:]) # the date range appears fine
df = pd.DataFrame(paths, index=dr, columns=['ts1', 'ts2', 'ts3'])
print(df.info(verbose=True)) # df is pandas Dataframe and appears fine
print(df.head()) # tested a fraction of the data, it is fine
import tstables as tstab # I get Unused import statement
class ts_desc(tb.IsDescription):
timestamp = tb.Int64Col(pos=0) # The column for the timestamps
ts1 = tb.Float64Col(pos=1) # The column to store numerical data
ts2 = tb.Float64Col(pos=2)
ts3 = tb.Float64Col(pos=3)
h5 = tb.open_file(path + 'tstab.h5', 'w')
ts = h5.create_ts('/', 'ts', ts_desc)
ts.append(df) # !!!!! the error I get is from this code line !!!!
# value error raised is: if rows.index.__class__ != pandas.tseries.index.DatetimeIndex:
AttributeError: module 'pandas.tseries' has no attribute 'index' `
I suspect you have run into a version compatibility issue between tstables and your pandas versions (assuming you are running any recent pandas version). Based on the tstables PyPI page, the last release of tstables was in 2015. A check of the tstables github project page shows there was an issue with Pandas 0.20.3 and use of datetime. The error message is the same as yours: module 'pandas.tseries' has no attribute 'index' in tstables See this: tstables breaks down with Pandas 20.3
The issue has a link to another build that works with Pandas 0.20.3. Development notes state "Removed 'convert_datetime64' parameter on line 245". Not sure if it will work with more recent versions, but worth a try. See this: schwed2 tstables build
If that doesn't solve the problem, I suggest running the simple examples provided or run the setup tests. (Note: I could not find the bpi_2014_01.csv file to test the bitcoin/bpi example.)
Good luck.
My problem is as follow:
I have several datasets (900K, 1M7 and 1M7 entries) in csv format which I load into multiple Dask Dataframe.
Then I concatenate them all in one Dask Dataframe that I can feed to my Snorkel Applier, which applies a bunch of Labeling Function to each row of my Dataframe and return a numpy array with as many rows as there are in the Dataframe and as many columns as there are Labeling Functions.
The call to Snorkel Applier seems to take forever when I do that with 3 datasets (more than 2 days...). However if I just run the code with only the first dataset, the call takes around 2 hours. Of course I don't do the concatenation step.
So I was wondering how can this be ? Should I change the number of partitions in the concatenated Dataframe ? Or maybe I'm using Dask badly in the first place ?
Here is the code I'm using:
from snorkel.labeling.apply.dask import DaskLFApplier
import dask.dataframe as dd
import numpy as np
import os
start = time.time()
applier = DaskLFApplier(lfs) # lfs are the function that are going to be applied, one of them featurize one of the column of my Dataframe and apply a sklearn classifier (I put n_jobs to None when loading the model)
# If I have only one CSV to read
if isinstance(PATH_TO_CSV, str):
training_data = dd.read_csv(PATH_TO_CSV, lineterminator=os.linesep, na_filter=False, dtype={'size': 'int32'})
slices = None
# If I have several CSV
elif isinstance(PATH_TO_CSV, list):
training_data_list = [dd.read_csv(path, lineterminator=os.linesep, na_filter=False, dtype={'size': 'int32'}) for path in PATH_TO_CSV]
training_data = dd.concat(training_data_list, axis=0)
# some useful things I do to know where to slice my final result and be sure I can assign each part to each dataset
df_sizes = [len(df) for df in training_data_list]
cut_idx = np.insert(np.cumsum(df_sizes), 0, 0)
slices = list(zip(cut_idx[:-1], cut_idx[1:]))
# The call that lasts forever: I tested all the code above without that line on my 3 datasets and it runs perfectly fine
L_train = applier.apply(training_data)
end = time.time()
print('Time elapsed: {}'.format(timedelta(seconds=end-start)))
If you need more info I will try to get them to you as much as I can.
Thank in you advance for your help :)
It seems that by default applier function is using processes, so does not benefit from additional workers you might have available:
# add this to the beginning of your code
from dask.distributed import Client
client = Client()
# you can see the address of the client by typing `client` and opening the dashboard
# skipping your other code
# you need to pass the client explicitly to the applier
# after launching this open the dashboard and watch the workers work :)
L_train = applier.apply(training_data, scheduler=client)
I have a long-ish dask chained pipeline, and one of the last bits is a string of dask.dataframe.from_delayed calls like below. That line is extremely slow - many minutes per call. It take 1-2 hours to just setup the pipeline.
When I debug the problem, I pull out the relevant code and pass in arrays with the same shape. It runs instantly.
Is this because my real life pipeline has an upstream graph that it's contending with? My solution is going to be to split my pipeline into two and see if that solves it. Anything else that could be going on here?
import dask
import dask.array as da
import dask.dataframe as dd
import numpy as np
import pandas as pd
image = da.zeros((100, 8192, 8192), chunks=(100,256,256))
labels = da.zeros((100, 8192, 8192), chunks=(100,256,256))
image_chunks = image.to_delayed().ravel()
labels_chunks = labels.to_delayed().ravel()
results = []
for image_chunk, labels_chunk in zip(image_chunks, labels_chunks):
offsets = np.array(image_chunk.key[1:]) * np.array(image.chunksize)
result = dask.delayed(lambda x,y,z: None)(image_chunk, labels_chunk, offsets)
results.append(result)
df_meta = pd.DataFrame(columns=['a', 'b'], dtype=np.float64)
df_meta = df_meta.astype({'a': np.int64})
# This line takes forever in actual use, but is instantaneous in this example.
df = dd.from_delayed(results, meta=df_meta)
The code that you have posted works great for me (as you predicted). Without knowing more I don't know how to help. In your situation I would slowly add back in parts of your actual pipeline and see when things get slow. That should help you to isolate the problem.
I want to multiple pairwise comparisons for every protein sequence contained in a FASTA file and then print the percentage sequence similarity (either an average or individually). I think I need to use itertools to create all of the combinations, align them and then probably divide the number of matches by the aligned sequence length to get the % sequence similarity but I am having trouble with the specific script I need to do this, preferably in biopython if possible. Any help is appreciated.
My answer does not involve Biopython, but since no other answer has been posted yet, I will post it anyway:
The bioinformatics package Biotite (https://www.biotite-python.org/), a package I am currently developing, would solve your problem using the following script:
import numpy as np
import biotite
import biotite.sequence as seq
import biotite.sequence.io.fasta as fasta
import biotite.sequence.align as align
import biotite.database.entrez as entrez
# 5 example sequences (bacterial luciferase variants)
uids = [
'Q7N575', 'P19839', 'P09140', 'P07740', 'P24113'
]
# Download these sequences as one file from NCBI
file_name = entrez.fetch_single_file(
uids, biotite.temp_file("fasta"), db_name="protein", ret_type="fasta"
)
# Read each sequence in the file as 'ProteinSequence' object
fasta_file = fasta.FastaFile()
fasta_file.read(file_name)
sequences = list(fasta.get_sequences(fasta_file).values())
# BLOSUM62
substitution_matrix = align.SubstitutionMatrix.std_protein_matrix()
# Matrix that will be filled with pairwise sequence identities
identities = np.ones((len(sequences), len(sequences)))
# Iterate over sequences
for i in range(len(sequences)):
for j in range(i):
# Align sequences pairwise
alignment = align.align_optimal(
sequences[i], sequences[j], substitution_matrix
)[0]
# Calculate pairwise sequence identities and fill matrix
identity = align.get_sequence_identity(alignment)
identities[i,j] = identity
identities[j,i] = identity
print(identities)
The output:
[[1. 0.97214485 0.62921348 0.84225352 0.59776536]
[0.97214485 1. 0.62359551 0.85352113 0.60055866]
[0.62921348 0.62359551 1. 0.61126761 0.85393258]
[0.84225352 0.85352113 0.61126761 1. 0.59383754]
[0.59776536 0.60055866 0.85393258 0.59383754 1. ]]