+++ /dev/null
-#!/usr/bin/env python
-
-"""
-lightning gvcf2numpy -tag-library ~/keep/by_id/su92l-4zz18-92bx4zjg5hgs3yc/tagset.fa.gz -ref ./hg38.fa.gz ~/keep/by_id/su92l-4zz18-s3e6as6uzsoocsb > example.npy
-example-1k-pca.py example.npy
-example-1k-plot.py example.npy.pca.npy sample_info.csv ~/keep/by_id/su92l-4zz18-s3e6as6uzsoocsb
-ls -l example.npy.pca.npy.png
-"""
-
-import sys
-infile = sys.argv[1]
-
-import scipy
-X = scipy.load(infile)
-
-from sklearn.decomposition import PCA
-pca = PCA(n_components=4)
-X = pca.fit_transform(X)
-scipy.save(infile+".pca.npy", X)
+++ /dev/null
-#!/usr/bin/env python
-
-import csv
-import os
-import scipy
-import sys
-
-infile = sys.argv[1]
-X = scipy.load(infile)
-
-colors = None
-if len(sys.argv) > 2:
- labels = {}
- for fnm in os.listdir(sys.argv[3]):
- if '.2.fasta' not in fnm:
- labels[fnm] = '---'
- if len(labels) != len(X):
- raise "len(inputdir) != len(inputarray)"
- with open(sys.argv[2], 'rb') as csvfile:
- for row in csv.reader(csvfile):
- ident=row[0]
- label=row[1]
- for fnm in labels:
- if row[0] in fnm:
- labels[fnm] = row[1]
- colors = []
- labelcolors = {
- 'PUR': 'firebrick',
- 'CLM': 'firebrick',
- 'MXL': 'firebrick',
- 'PEL': 'firebrick',
- 'TSI': 'green',
- 'IBS': 'green',
- 'CEU': 'green',
- 'GBR': 'green',
- 'FIN': 'green',
- 'LWK': 'coral',
- 'MSL': 'coral',
- 'GWD': 'coral',
- 'YRI': 'coral',
- 'ESN': 'coral',
- 'ACB': 'coral',
- 'ASW': 'coral',
- 'KHV': 'royalblue',
- 'CDX': 'royalblue',
- 'CHS': 'royalblue',
- 'CHB': 'royalblue',
- 'JPT': 'royalblue',
- 'STU': 'blueviolet',
- 'ITU': 'blueviolet',
- 'BEB': 'blueviolet',
- 'GIH': 'blueviolet',
- 'PJL': 'blueviolet',
- }
- for fnm in sorted(labels.keys()):
- colors.append(labelcolors[labels[fnm]])
-
-from matplotlib.figure import Figure
-from matplotlib.patches import Polygon
-from matplotlib.backends.backend_agg import FigureCanvasAgg
-fig = Figure()
-ax = fig.add_subplot(111)
-ax.scatter(X[:,0], X[:,1], c=colors, s=60, marker='o', alpha=0.5)
-canvas = FigureCanvasAgg(fig)
-canvas.print_figure(infile+".png", dpi=80)
--- /dev/null
+#!/bin/bash
+
+go run . build-docker-image
+arv keep docker lightning-runtime
+
+project=su92l-j7d0g-jzei0m9yvgauhjf
+gvcf=su92l-4zz18-ykpcoea5nisz74f
+fasta=su92l-4zz18-s3e6as6uzsoocsb
+tags=su92l-4zz18-92bx4zjg5hgs3yc
+
+go run . import -project ${project} \
+ -tag-library ~/keep/by_id/${tags}/tagset.fa.gz \
+ ~/keep/by_id/${fasta}
+go run . filter -project ${project} \
+ -i ~/keep/by_id/su92l-4zz18-fcyucnod8y4515p/library.gob \
+ -min-coverage 0.9 -max-variants 30
+go run . export-numpy -project ${project} \
+ -i ~/keep/by_id/su92l-4zz18-l40xcd2l6dmphaj/library.gob
+go run . pca -project ${project} \
+ -i ~/keep/by_id/su92l-4zz18-i6fzfoxpdh38yk4/library.npy
+go run . plot -project ${project} \
+ -i ~/keep/by_id/su92l-4zz18-zqfo7qc3tadh6zb/pca.npy \
+ -labels-csv ~/keep/by_id/${gvcf}/sample_info.csv \
+ -sample-fasta-dir ~/keep/by_id/${fasta}