cschin

import gradio as gr
import numpy as np
import wave

def response():
    def streaming():
        f = wave.open("sound.wav", 'rb')
        buffer = f.readframes(f.getnframes())
        data = np.frombuffer(buffer, dtype=f'int{f.getsampwidth()*8}')
        chunks = []

cschin

cschin

[
  "Traceback (most recent call last):",
  "  File \"/home/ubuntu/miniconda3/lib/python3.10/site-packages/urllib3/connectionpool.py\", line 703, in urlopen",
  "    httplib_response = self._make_request(",
  "  File \"/home/ubuntu/miniconda3/lib/python3.10/site-packages/urllib3/connectionpool.py\", line 398, in _make_request",
  "    conn.request(method, url, **httplib_request_kw)",
  "  File \"/home/ubuntu/miniconda3/lib/python3.10/site-packages/urllib3/connection.py\", line 239, in request",
  "    super(HTTPConnection, self).request(method, url, body=body, headers=headers)",
  "  File \"/home/ubuntu/miniconda3/lib/python3.10/http/client.py\", line 1282, in request",
  "    self._send_request(method, url, body, headers, encode_chunked)",

cschin

❯ ./wfa_adapt
s0 len: 16179, s1 len: 16326 Alignment contains 16168 matches 46 mismatches, 149 insertions, and 2 deletions

The alignment length is not consitent with sequence length:

16168 + 46 + 2 = 16216 != 16179
16168 + 46 + 149 = 16363 != 16326

cschin

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cschin

+ bash getStats.sh chm13_pergrine_p_ctg_cns.fasta
Checking attempted with maximum distance from contig end of 1000 bp..Done
******************* BAC SUMMARY ******************
 TOTAL    : 341
 BP       : 51532183
************** Statistics for: chm13_p_ctg_cns.fasta ****************
BACs closed: 321 (94.1349); BACs attempted: 333 %good = 96.3964; BASES 48527269 (94.1689)
Median:          99.9878
MedianQV:        39.1364
Mean:            99.94864

cschin

cschin

from os.path import abspath, expanduser
from io import StringIO
import contextlib
import gzip
import re
import subprocess

##
# Utility functions for FastaReader
##

cschin

```
$ cat Dockerfile
FROM ubuntu
RUN apt-get update -qq && \
apt-get install -qqy tar gzip curl jq  && \
apt-get install -qqy python python-pip vim-tiny less git
RUN pip install httpie requests
RUN apt-get install -qqy curl
RUN mkdir /build &&  cd /build && curl -s https://nim-lang.org/download/nim-0.17.2.tar.xz > nim-0.17.2.tar.xz && \
tar xvf nim-0.17.2.tar.xz && \

cschin

I currently work for PacBio as a bioinformatist developing some methods to handle single molecule data and genome assembly properly. 

Recently, I feel I am so lacking of vision. I have spent most of my time helping to develop methods in hope that they will be useful for the scientific community to use PacBio data. While we were developing those methods, as far as I could tell, many of those ONT fans had zero vision about them. We openly revealed those methods for the benefit to the scientific community to understand the value of PacBio's and PacBio-like data.  We naively assumed ONT would generate some great data with raw single molecule read accuracy > 96% as what Clive presented in 2012 AGBT. If so, those ONT fans would not need to use any of those methods we had developed. After a while, we find out that some of the visionary ONT fans are finally "inspired" to use some of our methods for processing some ONT data and publishing papers to show some values which some of those fan questioned about before. Wit