This tutorial is for the basics of the k1lib.bioinfo.cli module (docs at https://k1lib.github.io/latest/cli.html). As a quick reminder, this module allows you to use common cli tools from the linux cli inside of Python. The idea for this module came across while I was reading over the Biostar Handbook. They used a lot of cli tools, but all of them are sort of weird, unintuitive, not powerful, and just painful to work with. That's why I made this module to move everything to regular Python.
We're going to go over the multilanguage names dataset from a PyTorch RNN tutorial. The data folder is at cli_name_languages btw. My advice is to read this along with the docs page, and see the sources of functions that you're interested in.
from k1lib.imports import *
import unicodedata, string
namesFolder = "cli_name_languages/names"
nameFiles = glob.glob(f"{namesFolder}/*.txt")
withBareNames = insertColumn(*(nameFiles | op().split("/")[-1].all() | op().split(".")[0].all())) | display(None)
nameFiles[:3], len(nameFiles)
(['cli_name_languages/names/Korean.txt', 'cli_name_languages/names/Spanish.txt', 'cli_name_languages/names/Greek.txt'], 18)
So, we have 18 files in total. Let's look over a few of them:
cat(nameFiles[0]) | headOut(3)
Ahn Baik Bang
You can also pipe the file name in btw, like this:
nameFiles[0] | cat() | headOut(3)
Ahn Baik Bang
Let's convert all unicode chars to regular ascii (taken from the PyTorch doc):
letters = string.ascii_letters + ".,;'"
def unicodeToAscii(s, notIn=False):
if notIn: # debug case
return "".join(c for c in unicodedata.normalize("NFD", s) if unicodedata.category(c) != "Mn" and c not in letters)
else: # "right" case
return "".join(c for c in unicodedata.normalize("NFD", s) if unicodedata.category(c) != "Mn" and c in letters)
How many names in total across files?
nameFiles | cat().all() | joinStreams() | shape(0)
20074
How many names with weird unicode characters?
def unicodes(): return nameFiles | cat().all() | joinStreams() | apply(partial(unicodeToAscii, notIn=True))
unicodes() | count() | display(None)
19962 99% 47 0% 3 0% 21 - 0% 2 -- 0% 1 0% 23 0% 1 / 0% 3 1 0% 9 ß 0% 1 ł 0% 1 : 0%
See over https://k1lib.github.io/latest/cli/streams for more info about how stuff like cat() and joinStreams() work. Also, partial is a pretty awesome function I might add, look over it at Python functools docs. There're lots of empty names here, so let's get rid of them
unicodes() | op().strip().all() | filt(op() != "") | count() | display()
21 - 55% 2 -- 5% 1 / 3% 3 1 8% 9 ß 24% 1 ł 3% 1 : 3%
Here, we're just stripping white spaces at both ends of each name (strip()) and filters them out (filt(op() != "")). How many duplicate names are there in a file?
nameFiles | cat().all() | (count() | filt(op() != "1", 0) | shape(0)).all() | unsqueeze(1) | withBareNames
Korean 94 Spanish 296 Greek 193 Irish 226 Scottish 100 Portuguese 74 Russian 9342 Czech 503 French 273 German 706 Japanese 990 Polish 138 Arabic 108 English 3668 Chinese 246 Dutch 286 Italian 701 Vietnamese 71
Okay yeah there's a lot. Let's see how many unique names (of each file) that appear in other files:
nameFiles | cat().all() | toSet().all() | joinStreams() | (identity() & toSet()) | shape(0).all() | deref()
[18015, 17458]
Let's see what are the actual Korean names that appear in other files:
nameFiles | AA_(0) | ((cat() | toList() | repeat()) + cat().all()) | transpose() | intersection().all()\
| insertColumn(*list(nameFiles | op().split("/")[-1].all() | op().split(".")[0].all())[1:]) | display(None)
Spanish Greek Irish Scottish Portuguese Russian Li Han Czech French German Wang Japanese Ko Jo Seo Polish Arabic English Yang Lee Wang Chong Moon Chung Chinese Kang Yang Chou Chi Chin Han Yim Wang Sun You Woo Yun Chu Chong Hong Song Chang Koo Dutch Italian Vietnamese Han Kim Chu Ho Ha Ma Chung
cat() | toList() | repeat()'s branch essentially creates Iterator[File], and each File is actually just Iterator[str]. Result of cat().all() is also Iterator[File]. We want to place these 2 lists' elements on each row, so we can actually operate on them. joinColumns() will output Iterator[(File, File)]. First file is the Korean one, second file is every other file. intersection() will find the common names between the 2 files, and insertColumn() just to have some nice formatting.
How about we do this for every file and record how many names in that that is in other files:
analyze2Files = intersection() | shape(0) # takes 2 files, and squish them into 1 value
analyze1Combo = ((cat() | toList() | repeat()) + cat().all()) | transpose() | analyze2Files.all() | toSum() # summing all common values
nameFiles | AA_() | analyze1Combo.all() | unsqueeze(1) | withBareNames
Korean 37 Spanish 104 Greek 1 Irish 78 Scottish 115 Portuguese 57 Russian 74 Czech 41 French 102 German 148 Japanese 9 Polish 24 Arabic 5 English 381 Chinese 52 Dutch 58 Italian 54 Vietnamese 20
Nice. Anyway, hope you are as thrilled as I am about this. Really complicated loops and whatnot can be explored quite quickly without actually writing any loops, and that helps with bringing down iteration time.
While developing this module, I thought I'd have to drop down to C level for it to be fast enough to process anything at all. However, time and time again, it seems like Python is good enough for most things. Any Python operation is around 1.5 orders of magnitude slower than 1ns, so 30ns. Also means that flops rate should be around 7-7.5 orders of magnitude, while we should expect 8-8.5 out of C code. Let's see:
%%time
range(400) | repeatFrom() | apply(lambda x: x+2) | batched(1000) | toSum().all() | ~head(10000) | headOut()
181500 221500 181500 221500 181500 221500 181500 221500 181500 221500 CPU times: user 1.19 s, sys: 0 ns, total: 1.19 s Wall time: 1.19 s
This is just taking an infinite list of numbers, add 2 to it, batches every 1000 numbers, summing over each row, and do that 10000 times. So 10M ops in around 1 second. Right around the 6.8-6.9 (nice haha) orders of magnitude flop rate. Is this good enough though?
Lots of ppl reported the builtin module csv can parse around 50MB/s. Let's say there're 10 columns, and each column has 10 characters, which equals to 100 bytes/row. So, the throughput should be 500k rows/s, well below what we have here. Even if you assume it's costly to operate on a table, so the figure 5M table elements/s, then that's still lower than what cli tools can achieve. So no need to worry about this.
A lot of time, I was worried about the performance of .all() operation. But turns out, applyS(f).all() has roughly the same performance as apply(f), so don't worry about it:
%%time
range(int(1e6)) | applyS(lambda x: x / 2).all() | ignore()
CPU times: user 72.9 ms, sys: 0 ns, total: 72.9 ms Wall time: 71.7 ms
%%time
range(int(1e6)) | apply(lambda x: x / 2) | ignore()
CPU times: user 72.3 ms, sys: 0 ns, total: 72.3 ms Wall time: 71.3 ms
%%time
range(int(1e6)) | apply(applyS(lambda x: x / 2)) | ignore()
CPU times: user 73.4 ms, sys: 0 ns, total: 73.4 ms Wall time: 72.3 ms