Deep Learning Workshop

@@ -11,23 +11,25 @@
 # Start End Sequence Feature
 
 # Run:
-# c:\Anaconda3\python get-hga-data-set.py
+# 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
-# 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
+# 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
 
-# python3 get-hga-sequences.py
+# LAVIS
+# qlogin
+# python get-hga-sequences-py27.py
 # --feature gene
 # --outputFile hga-sequences-toy.txt
-# --outputPath /home/cmendezc/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
+# --outputPath /mnt/Genoma/amedina/cmendez/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
-# 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
+# --hgaPath /mnt/Genoma/amedina/cmendez/gitlab-deep-learning-workshop/data-sets/human-genome-annotation
+# --fastaPath /mnt/Genoma/amedina/cmendez/data-FASTA-Homo_sapiens.GRCh38.dna
+# 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
 
 import argparse
 # from Bio import SeqIO

@@ -20,14 +20,15 @@
 # --fastaPath C:\Users\cmendezc\Documents\GENOMICAS\DEEP_LEARNING\gitlab-deep-learning-workshop\data-sets\fasta-files
 # 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
 
-# python3 get-hga-sequences.py
+# Sinik
+# python3 get-hga-sequences-py3.py
 # --feature gene
 # --outputFile hga-sequences-toy.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
-# 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
+# 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
 
 import argparse
 # from Bio import SeqIO

 # Get training and test data set for deep learning from sequence data set
-# obtained from FASTA and HGA data sets (see script get-hga-sequences.py)
+# obtained from FASTA and HGA data sets (see script get-hga-sequences-py3.py)
 
 # Input tab-separated format:
 # Sequences: hga-sequences-toy.txt
@@ -8,22 +8,23 @@
 # Each sequence as a one-hot encoding WHAT array or matrix
 
 # Run:
-# python3 get-hga-training-test.py
+# python3 get-hga-training-test-py27.py
 # --inputFile hga-sequences-toy.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
-# 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
+# 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
 
 # LAVIS
-# python get-hga-training-test.py
-# --inputFile hga-sequences-toy.txt
+# qlogin
+# python get-hga-training-test-py27.py
+# --inputFile hga-sequences-1000.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
-# 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
+# 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
 
 import argparse
 import pandas as pd

 # Get training and test data set for deep learning from sequence data set
-# obtained from FASTA and HGA data sets (see script get-hga-sequences.py)
+# obtained from FASTA and HGA data sets (see script get-hga-sequences-py3.py)
 
 # Input tab-separated format:
 # Sequences: hga-sequences-toy.txt
@@ -8,13 +8,13 @@
 # Each sequence as a one-hot encoding WHAT array or matrix
 
 # Run:
-# python3 get-hga-training-test.py
+# python3 get-hga-training-test-py3.py
 # --inputFile hga-sequences-toy.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
-# 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
+# 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
 
 import argparse
 import pandas as pd