Carlos-Francisco Méndez-Cruz / deep-learning-workshop

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Carlos-Francisco Méndez-Cruz
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Deep Learning Workshop

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...@@ -11,23 +11,25 @@ ...@@ -11,23 +11,25 @@
11 # Start End Sequence Feature 11 # Start End Sequence Feature
12 12
13 # Run: 13 # Run:
14 -# c:\Anaconda3\python get-hga-data-set.py 14 +# c:\Anaconda3\python get-hga-data-set-py27.py
15 # --feature gene 15 # --feature gene
16 # --outputFile hga-sequences-toy.txt 16 # --outputFile hga-sequences-toy.txt
17 # --outputPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation 17 # --outputPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation
18 # --hgaFile some-rows-example-human-genome-annotation.csv 18 # --hgaFile some-rows-example-human-genome-annotation.csv
19 # --hgaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation 19 # --hgaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation
20 # --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files 20 # --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files
21 -# c:\Anaconda3\python get-hga-data-set.py --feature gene --outputFile hga-sequences-toy.txt --outputPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --hgaFile some-rows-example-human-genome-annotation.csv --hgaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files 21 +# c:\Anaconda3\python get-hga-data-set-py27.py --feature gene --outputFile hga-sequences-toy.txt --outputPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --hgaFile some-rows-example-human-genome-annotation.csv --hgaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files
22 22
23 -# python3 get-hga-sequences.py 23 +# LAVIS
24 +# qlogin
25 +# python get-hga-sequences-py27.py
24 # --feature gene 26 # --feature gene
25 # --outputFile hga-sequences-toy.txt 27 # --outputFile hga-sequences-toy.txt
26 -# --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 28 +# --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
27 # --hgaFile Homo_sapiens.GRCh38.92.csv 29 # --hgaFile Homo_sapiens.GRCh38.92.csv
28 -# --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 30 +# --hgaPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
29 -# --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna 31 +# --fastaPath /mnt/Genoma/amedina/cmendez/data-FASTA-Homo_sapiens.GRCh38.dna
30 -# python3 get-hga-sequences.py --feature gene --outputFile hga-sequences.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --hgaFile Homo_sapiens.GRCh38.92.csv --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna 32 +# python get-hga-sequences-py27.py --feature gene --outputFile hga-sequences.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --hgaFile Homo_sapiens.GRCh38.92.csv --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna
31 33
32 import argparse 34 import argparse
33 # from Bio import SeqIO 35 # from Bio import SeqIO
......
...@@ -20,14 +20,15 @@ ...@@ -20,14 +20,15 @@
20 # --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files 20 # --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files
21 # c:\Anaconda3\python get-hga-data-set.py --feature gene --outputFile hga-sequences-toy.txt --outputPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --hgaFile some-rows-example-human-genome-annotation.csv --hgaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files 21 # c:\Anaconda3\python get-hga-data-set.py --feature gene --outputFile hga-sequences-toy.txt --outputPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --hgaFile some-rows-example-human-genome-annotation.csv --hgaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\human-genome-annotation --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files
22 22
23 -# python3 get-hga-sequences.py 23 +# Sinik
24 +# python3 get-hga-sequences-py3.py
24 # --feature gene 25 # --feature gene
25 # --outputFile hga-sequences-toy.txt 26 # --outputFile hga-sequences-toy.txt
26 # --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 27 # --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
27 # --hgaFile Homo_sapiens.GRCh38.92.csv 28 # --hgaFile Homo_sapiens.GRCh38.92.csv
28 # --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 29 # --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
29 # --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna 30 # --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna
30 -# python3 get-hga-sequences.py --feature gene --outputFile hga-sequences.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --hgaFile Homo_sapiens.GRCh38.92.csv --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna 31 +# python3 get-hga-sequences-py3.py --feature gene --outputFile hga-sequences.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --hgaFile Homo_sapiens.GRCh38.92.csv --hgaPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --fastaPath /home/cmendezc/data-FASTA-Homo_sapiens.GRCh38.dna
31 32
32 import argparse 33 import argparse
33 # from Bio import SeqIO 34 # from Bio import SeqIO
......
1 # Get training and test data set for deep learning from sequence data set 1 # Get training and test data set for deep learning from sequence data set
2 -# obtained from FASTA and HGA data sets (see script get-hga-sequences.py) 2 +# obtained from FASTA and HGA data sets (see script get-hga-sequences-py3.py)
3 3
4 # Input tab-separated format: 4 # Input tab-separated format:
5 # Sequences: hga-sequences-toy.txt 5 # Sequences: hga-sequences-toy.txt
...@@ -8,22 +8,23 @@ ...@@ -8,22 +8,23 @@
8 # Each sequence as a one-hot encoding WHAT array or matrix 8 # Each sequence as a one-hot encoding WHAT array or matrix
9 9
10 # Run: 10 # Run:
11 -# python3 get-hga-training-test.py 11 +# python3 get-hga-training-test-py27.py
12 # --inputFile hga-sequences-toy.txt 12 # --inputFile hga-sequences-toy.txt
13 # --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 13 # --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
14 # --outputTraining hga-sequences-training.txt 14 # --outputTraining hga-sequences-training.txt
15 # --outputTest hga-sequences-test.txt 15 # --outputTest hga-sequences-test.txt
16 # --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 16 # --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
17 -# python get-hga-training-test.py --inputFile hga-sequences-1000.txt --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 17 +# python get-hga-training-test-py3.py --inputFile hga-sequences-1000.txt --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
18 18
19 # LAVIS 19 # LAVIS
20 -# python get-hga-training-test.py 20 +# qlogin
21 -# --inputFile hga-sequences-toy.txt 21 +# python get-hga-training-test-py27.py
22 +# --inputFile hga-sequences-1000.txt
22 # --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 23 # --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
23 # --outputTraining hga-sequences-training.txt 24 # --outputTraining hga-sequences-training.txt
24 # --outputTest hga-sequences-test.txt 25 # --outputTest hga-sequences-test.txt
25 # --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 26 # --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
26 -# python3 get-hga-training-test.py --inputFile hga-sequences-toy.txt --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 27 +# python get-hga-training-test-py27.py --inputFile hga-sequences-toy.txt --inputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
27 28
28 import argparse 29 import argparse
29 import pandas as pd 30 import pandas as pd
......
1 # Get training and test data set for deep learning from sequence data set 1 # Get training and test data set for deep learning from sequence data set
2 -# obtained from FASTA and HGA data sets (see script get-hga-sequences.py) 2 +# obtained from FASTA and HGA data sets (see script get-hga-sequences-py3.py)
3 3
4 # Input tab-separated format: 4 # Input tab-separated format:
5 # Sequences: hga-sequences-toy.txt 5 # Sequences: hga-sequences-toy.txt
...@@ -8,13 +8,13 @@ ...@@ -8,13 +8,13 @@
8 # Each sequence as a one-hot encoding WHAT array or matrix 8 # Each sequence as a one-hot encoding WHAT array or matrix
9 9
10 # Run: 10 # Run:
11 -# python3 get-hga-training-test.py 11 +# python3 get-hga-training-test-py3.py
12 # --inputFile hga-sequences-toy.txt 12 # --inputFile hga-sequences-toy.txt
13 # --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 13 # --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
14 # --outputTraining hga-sequences-training.txt 14 # --outputTraining hga-sequences-training.txt
15 # --outputTest hga-sequences-test.txt 15 # --outputTest hga-sequences-test.txt
16 # --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 16 # --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
17 -# python get-hga-training-test.py --inputFile hga-sequences-1000.txt --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation 17 +# python get-hga-training-test-py3.py --inputFile hga-sequences-1000.txt --inputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation --outputTraining hga-sequences-training.txt --outputTest hga-sequences-test.txt --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
18 18
19 import argparse 19 import argparse
20 import pandas as pd 20 import pandas as pd
......