helen | Homopolymer Encoded Long-read Error | Genomics library
kandi X-RAY | helen Summary
kandi X-RAY | helen Summary
HELEN uses a Recurrent-Neural-Network (RNN) based Multi-Task Learning (MTL) model that can predict a base and a run-length for each genomic position using the weights generated by MarginPolish. 2020 Kishwar Shafin, Trevor Pesout, Benedict Paten. Computational Genomics Lab (CGL), University of California, Santa Cruz.
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Top functions reviewed by kandi - BETA
- Call consensus
- Predict the transducer
- Call the prediction method on GPU
- Get file paths from a directory
- Adds common arguments to the given parser
- Add polar arguments to the given parser
- Adds training arguments to the given parser
- Performs aitch on the input directory
- Calculate the alignment for the given sequences
- Given a cigar string return all the positions in the alignment
- Create a consensus sequence for a contig
- Stitch the given contig
- Convert a medaka h5py h5py5 file into a pandas h5py h5py h5py h5py h5py
- Wishes a genome
- Perform a Stitch on the input directory
- Perform pairwise alignment
- Add test arguments to the given parser
- Run CMake
- Load a pre - trained model
- Read a QUAST file
- Analyze Tensor
- Count the number of misassemblies not overlays that are not overlapping
- Add command line arguments to the parser
- Train the interface
- Read a h5py hdf5 file
- Save a checkpoint checkpoint
- Run the hyperband
helen Key Features
helen Examples and Code Snippets
Lines of Code : 39License : Permissive (MIT)
Copysudo apt-get -y install git cmake make gcc g++ autoconf bzip2 lzma-dev zlib1g-dev \
libcurl4-openssl-dev libpthread-stubs0-dev libbz2-dev liblzma-dev libhdf5-dev \
python3-pip python3-virtualenv virtualenv
git clone https://github.com/kishwarshafin/ minimap2 -ax map-ont -t 32 shasta_assembly.fa reads.fq | samtools view -hb -F 0x904 > unsorted.bam;
samtools sort -@32 -o reads_2_assembly.0x904.bam unsorted.bam;
samtools index -@32 reads_2_assembly.0x904.bam
helen download_models \
--output_dir Community Discussions
Trending Discussions on helen
QUESTION
So I have this problem in SQL where the question is this: List the sId and name of students that applied to “WSU” But not “U of O”. and my attempt was this:
ANSWER
Answered 2022-Feb-23 at 19:53You don't need a join. You want to see students? So, select from the students table. They shall meet criteria? Use a where clause. Straight-forward with IN clauses:
QUESTION
I am attempting to insert data from one table into another in SQL. my solution is as follows:
...ANSWER
Answered 2022-Feb-23 at 08:21You need to specify the colage with a prefix, so that mysql knows whch colage name it should use
QUESTION
I have a file with lines, each line is split on "|", I want to compare arguments 5 from each line and if intersect, then proceed. This gets to a second part:
- first arguments1,2 are compared by dictionary, and if they are same AND
- if arguments5,6 are overlapping, then those lines get concatenated.
How to compare intersection of values under the same key? The code below works cross-key but not within same key:
...ANSWER
Answered 2022-Jan-31 at 08:47from itertools import zip_longest
data = """\
text1|text2|text3|text4 text 5| text 6| text 7 text 8|
text1|text2|text12|text4 text 5| text 6| text 7| text9|text10|text3|text4 text 5| text 11| text 12 text 8|
"""
lines = tuple(line.split('|') for line in data.splitlines())
number_of_lines = len(lines)
print(f"number of lines : {number_of_lines}")
print(f"number of cells in line 1 : {len(lines[0])}")
print(f"number of cells in line 2 : {len(lines[1])}")
print(f"{lines[0]=}")
print(f"{lines[1]=}")
result = []
# we want to compare each line with each other :
for line_a_index, line_a in enumerate(lines):
for line_b_index, line_b in enumerate(lines[line_a_index+1:]):
assert len(line_a) >= 5, f"not enough cells ({len(line_a)}) in line {line_a_index}"
assert len(line_b) >= 5, f"not enough cells ({len(line_b)}) in line {line_b_index}"
assert all(isinstance(cell, str) for cell in line_a)
assert all(isinstance(cell, str) for cell in line_b)
if line_a[0] == line_b[0] and line_a[1] == line_b[1] and (
line_a[5] in line_b[5] or line_a[6] in line_b[6] # A in B
or line_b[5] in line_a[5] or line_b[6] in line_a[6] # B in A
):
result.append(tuple(
((cell_a or "") + (";" if (cell_a or cell_b) else "") + (cell_b or "")) if cell_a != cell_b else cell_a
for cell_a, cell_b in zip_longest(line_a[:5+1], line_b[:5+1]) # <-- here I truncated the lines
))
# I decided to have a fancy output, but I made some simplifying assumptions to make it simple
if len(result) > 1:
raise NotImplementedError
widths = tuple(max(len(a) if a is not None else 0, len(b) if b is not None else 0, len(c) if c is not None else 0)
for a, b, c in zip_longest(lines[0], lines[1], result[0]))
length = max(len(lines[0]), len(lines[1]), len(result[0]))
for line in (lines[0], lines[1], result[0]):
for index, cell in zip_longest(range(length), line):
if cell:
print(cell.ljust(widths[index]), end='|')
print("", end='\n') # explicit newline
original_expected_output = "text1|text2|text3;text12|text4;text5;text4;text5|text6;text7 text8;text6"
print(f"{original_expected_output} <-- expected")
lenormju_expected_output = "text1|text2|text3;text12|text4 text 5| text 6| text 7 text 8; text 7"
print(f"{lenormju_expected_output} <-- fixed")
QUESTION
I am querying one file with the other file and have them as following:
File1:
...ANSWER
Answered 2022-Jan-30 at 15:00With your shown samples please try following. You were on right track, you need to do 2 things, 1st: take whole line as an index in array a while reading file2.txt and set field seapeator to | before awk starts reading file1
QUESTION
I have a dataframe that has multiple tables with 1 or 2 empty rows in between. I want to split based on empty rows.
There are 3 tables here. As you can see, row no. 4,5, 13,14 are blank on which the split must happen.
ANSWER
Answered 2022-Jan-26 at 13:46I think in your example the rows are not NaN, it seems they're having an empty string.
Plese try the following code:
QUESTION
I know this code here selects columns from one table and inserts it into another table. However, I have a value that I want to insert into one of the columns, how do I pass in the value?
This selects from on table and inserts into another...
...ANSWER
Answered 2022-Jan-06 at 19:26To achieve that you should do something like this:
QUESTION
I'm currently having a problem with my code specifically the If-else part. If my year-level is 1, the if-else is satisfied but if the year-level I'll input is 2, 3 or 4, the if-else for these are satisfied HOWEVER, it always displays the if-else for yrep1 (It always prints "Year-level Representative: Lady Carmel") except if the year-level is 1.
...ANSWER
Answered 2022-Jan-06 at 10:28The problem is that these variables
QUESTION
I've been trying to solve the following problem : I try to upgrade this Frontend Mentor project https://haydee75.github.io/galleria/ from React Router v5 to v6. I tried to replace the code between with :
...ANSWER
Answered 2021-Dec-09 at 18:01If I'm understanding your question/issue correctly, you want to render the Gallery and Paint components each on their own routes independently, and fix the slideshow linking from painting to painting. For this use the first routing snippet so they are independent routes and not nested.
QUESTION
The goal of the task is to create an unordered HTML list from list of objects given below.
My setup so far:
...ANSWER
Answered 2021-Dec-09 at 09:53If the goal is to create a list of users, where each user only appear once, and all items appear in the same line, you only need a single loop to get the user, and generate the li item.
QUESTION
I'm currently working on a project that cross validate 2 sheets with approx 500 loops.
ROSTER
First Name Last Name DoB Judith Barragan 4/10/1959 Kelly Benitez 9/14/1993 Martha Bustos 1/12/1960 Robyn Carroll 5/9/1954 Janet Chambers 8/27/1949 Nikki Corso 10/25/1957 Angella Decohen 5/23/1988 Damian Delaney 6/26/1961 Anora Denison 4/14/1998 Cristina Dimatulac 7/28/1959 Mercy Erazo 3/14/1959 Michelle Fanara 11/20/1981 Shannon Feldmann 9/10/1986 Alejandra Frutos-Silva 2/14/1978 Rebecka Aceves 7/14/2007 Jarely Aguilera 6/8/2006 Jasmine Aguillon 1/29/2007 Adriana Alaniz 10/4/2007 Blanca Angel 11/3/2007 Francie Arellano 9/11/2007 Molly Barajas 10/1/2007 Emily Barranco 9/12/2007 Valeria Bata 3/29/2007 Sarahi Cabeza 8/8/2007 Carla Cadena 3/31/2006 Emily Cano 1/25/2007 Janet Canul 4/27/2007 Caitlyn Castaneda 3/26/2007 Jacqueline Castillo 1/22/2007 Melanie Colindres 6/8/2007 Nyah Davis 8/8/2007 Karie Delgadillo 2/10/2007 Gabriela Diaz 6/25/2007 Helen Diaz 8/17/2007 Hailey Duran 5/20/2007 Hazel Flores 9/7/2007 Kiherra Gamboa 10/4/2007 Belen Gonzalez 4/23/2007 Samantha Gonzalez 10/16/2007 Ashlee Palacios 8/31/2006 Naomi Papaqui 5/17/2007 Karely Paxtor 10/21/2006 Michelle Paxtor 10/20/2007 Audra Perez 2/24/2007 Josueline Perez 10/30/2006 Yaretzi Pineda 2/17/2007 Zuleyka Portela 9/10/2007 Jacqueline Prudencio 3/1/2007 Destiny Quiroz 5/10/2007 Kelcey Raiz 5/11/2007 Brianna Ramos 8/15/2007 Neydy Renderos 8/26/2007 Daiman Johnson 3/3/1968 Kimberley Rivas 11/2/2007 Michelle Dominguez 5/15/2005 Marleny Rodriguez 7/29/2007 Maria Roman 5/9/2006 Cristal Solis 9/29/2006 Carmela Torralba 6/28/2007 Dora Vasquez 5/14/2007 Cindy Vega 11/20/2007 Jennifer Velasco 6/30/2006 Chloe Wilson 10/8/2007 Melody Zacarias 5/17/2007 Hazel Zamora 1/27/2007 Kayden Alexander 2/6/2006 Yvette Alvarado 3/30/2006 Damian Delaney 6/26/1961 Kimberly Amezcua 7/14/2006 Kimberly Antonio 5/30/2006 Alicia Aquino 6/15/2006 Samantha Aquino 6/27/2006 Destiny Arauz 6/13/2006 Julissa Arroyo 5/26/2006 Cassandra Ayala 8/18/2006 Samantha Ayala 7/2/2006 Eva Azul 2/6/2006 Stacey Bacelis 4/4/2006 America Baires 7/17/2006 Ashley Barajas 6/10/2005 Janet Barrera 10/14/2005 Alisa Benitez 5/26/2006 Sara Bolanos-Mejia 1/12/2006 Ashley Mendez 6/22/2006 Ana Carvente 7/12/2006 Mia Castellanos 6/19/2006 Rosalma Cebreros 3/3/2006 Yosselin Celis 5/25/2005 Jacqueline Lucero 9/2/1974 Evelyn Chamu 1/30/2006 Nataly Chavez 2/27/2006 Juliana Coeto 10/4/2005 Shesith Covarrubias 12/8/2005 Ashley Cruz 7/20/2006 Erin Dakers 8/2/2007 Claudia Lopez 6/16/2007 Cristina Diaz 10/13/2005 Zoe Dighero 4/11/2006 Kaylynn Domingo 10/4/2006 Celeste Dominguez 6/1/2006 Lizzy Escobar 12/14/2005 Lilian Escorza 12/23/2005REGISTRATION
First Name Last Name DoB Jacqueline Lucero 9/2/1974 Ashley Mendez 6/22/2006 Hyobe Namkoong 6/19/2007 Hetzabel Sanchez 4/13/2005 cristal solis 9/29/2006 Briseida Lopez 5/22/2005 Daiman Johnson 3/3/1968 Kayleen Vasquez 12/9/2003 Ashley Aguilar 12/9/2003 Damian Delaney 6/26/1961 Michelle Dominguez 5/15/2005 Martha Bustos 1/12/1960 Jaqueline Granadino 9/6/2004 jacqueline granadino 9/6/2004 Jacqueline granadino 9/6/2004 Maria Gutierrez 11/30/2006 Claudia Lopez 6/16/2007 Kelly Benitez 9/14/1993 Kelly Benitez 9/14/1993RESULT
First Name Last Name DoB Start Code Jacqueline Lucero 9/2/1974 1980001 Ashley Mendez 6/22/2006 1980002 Cristal Solis 9/29/2006 1980003 Daiman Johnson 3/3/1968 1980004 Damian Delaney 6/26/1961 1980005 Michelle Dominguez 5/15/2005 1980006 Martha Bustos 1/12/1960 1980007 Claudia Lopez 6/16/2007 1980008 Kelly Benitez 9/14/1993 1980009Sample Data Sheet my problem is that my script sometimes getting run-time timeout. I am seeing map function but I'm not sure if it's applicable for my current problem.
here are my sheets that is included in my script. sheets are roster, form responses 1, reference, result. roster and registration tab have common columns (First name, Last Name, Date of Birth)
...ANSWER
Answered 2021-Dec-09 at 05:24You could process all the "Roster" data in batches by keeping track of the last row that you have processed with PropertiesService
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