From 2417a6b7603524dc5cd30d29b153f91024b9443d Mon Sep 17 00:00:00 2001 From: Mitja Felicijan Date: Wed, 1 Nov 2023 22:54:27 +0100 Subject: Move to Jekyll --- assets/posts/dna-sequence/benchmarks.csv | 7 + assets/posts/dna-sequence/chart-size.py | 28 + assets/posts/dna-sequence/chart-size.svg | 1553 ++++++++++++++++++++++ assets/posts/dna-sequence/chart-speed.py | 23 + assets/posts/dna-sequence/chart-speed.svg | 1416 ++++++++++++++++++++ assets/posts/dna-sequence/dna-basics.jpg | Bin 0 -> 165883 bytes assets/posts/dna-sequence/quote.png | Bin 0 -> 1068 bytes assets/posts/dna-sequence/sample-binary-file.png | Bin 0 -> 66417 bytes assets/posts/dna-sequence/sample.png | Bin 0 -> 65930 bytes 9 files changed, 3027 insertions(+) create mode 100644 assets/posts/dna-sequence/benchmarks.csv create mode 100644 assets/posts/dna-sequence/chart-size.py create mode 100644 assets/posts/dna-sequence/chart-size.svg create mode 100644 assets/posts/dna-sequence/chart-speed.py create mode 100644 assets/posts/dna-sequence/chart-speed.svg create mode 100755 assets/posts/dna-sequence/dna-basics.jpg create mode 100755 assets/posts/dna-sequence/quote.png create mode 100755 assets/posts/dna-sequence/sample-binary-file.png create mode 100755 assets/posts/dna-sequence/sample.png (limited to 'assets/posts/dna-sequence') diff --git a/assets/posts/dna-sequence/benchmarks.csv b/assets/posts/dna-sequence/benchmarks.csv new file mode 100644 index 0000000..8645d5e --- /dev/null +++ b/assets/posts/dna-sequence/benchmarks.csv @@ -0,0 +1,7 @@ +Packages,Encode to FASTA (ms),FASTA file size (KB),FASTA gzipped (KB) +1KB,5.625224,4.1,1.4 +10KB,32.679975,40.7,13 +100KB,112.864416,406.7,121 +1MB,872.887675,4100,1200 +10MB,8472.693202,40700,12000 +100MB,85525.178217,406700,118000 diff --git a/assets/posts/dna-sequence/chart-size.py b/assets/posts/dna-sequence/chart-size.py new file mode 100644 index 0000000..4fc408d --- /dev/null +++ b/assets/posts/dna-sequence/chart-size.py @@ -0,0 +1,28 @@ +import csv + +import matplotlib.pyplot as plt +import pandas as pd + +# Read the data +df = pd.read_csv("benchmarks.csv") + +# Settings +plt.title("Encode to FASTA out filesize") +plt.tight_layout(pad=2) +fig = plt.gcf() +fig.set_size_inches(10, 4) + +# Plotting +plt.plot(df["Packages"], df["FASTA file size (KB)"], label = "Raw", color="black", linestyle="-") +plt.plot(df["Packages"], df["FASTA gzipped (KB)"], label = "Gzipped", color="black", linestyle="--") + +# Adding x and y axis labels +plt.xlabel("Size of an input file", fontstyle="italic") +plt.ylabel("File size (KB)", fontstyle="italic") + +# Legend +legend = plt.legend() +legend.get_frame().set_linewidth(0) + +# Export as SVG +plt.savefig("chart-size.svg", format="svg") diff --git a/assets/posts/dna-sequence/chart-size.svg b/assets/posts/dna-sequence/chart-size.svg new file mode 100644 index 0000000..1a2d127 --- /dev/null +++ b/assets/posts/dna-sequence/chart-size.svg @@ -0,0 +1,1553 @@ + + + + + + + + 2023-08-05T13:29:17.701350 + image/svg+xml + + + Matplotlib v3.5.2, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/assets/posts/dna-sequence/chart-speed.py b/assets/posts/dna-sequence/chart-speed.py new file mode 100644 index 0000000..c07b057 --- /dev/null +++ b/assets/posts/dna-sequence/chart-speed.py @@ -0,0 +1,23 @@ +import csv + +import matplotlib.pyplot as plt +import pandas as pd + +# Read the data +df = pd.read_csv("benchmarks.csv") + +# Settings +plt.title("Encode to FASTA speed over time") +plt.tight_layout(pad=2) +fig = plt.gcf() +fig.set_size_inches(10, 4) + +# Plotting +plt.plot(df["Packages"], df["Encode to FASTA (ms)"], label = "ALB", color="black", linestyle="--") + +# Adding x and y axis labels +plt.xlabel("Size of an input file", fontstyle="italic") +plt.ylabel("Encoding time (ms)", fontstyle="italic") + +# Export as SVG +plt.savefig("chart-speed.svg", format="svg") diff --git a/assets/posts/dna-sequence/chart-speed.svg b/assets/posts/dna-sequence/chart-speed.svg new file mode 100644 index 0000000..7bb0c29 --- /dev/null +++ b/assets/posts/dna-sequence/chart-speed.svg @@ -0,0 +1,1416 @@ + + + + + + + + 2023-08-05T13:29:20.420382 + image/svg+xml + + + Matplotlib v3.5.2, https://matplotlib.org/ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/assets/posts/dna-sequence/dna-basics.jpg 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