From 1168972b00566eafd56a04cc15b7ab36049fe1e8 Mon Sep 17 00:00:00 2001
From: HarshitGupta11 <50410275+HarshitGupta11@users.noreply.github.com>
Date: Sat, 22 Jun 2019 20:41:40 +0530
Subject: [PATCH] Delete prepare_train_data.py

---
 prepare_train_data.py | 98 -------------------------------------------
 1 file changed, 98 deletions(-)
 delete mode 100644 prepare_train_data.py

diff --git a/prepare_train_data.py b/prepare_train_data.py
deleted file mode 100644
index 953522d..0000000
--- a/prepare_train_data.py
+++ /dev/null
@@ -1,98 +0,0 @@
-import pandas as pd
-import numpy as np
-def create_branch_length_padding(bl):
-    maxlen=0
-    for x in bl:
-        if len(x)>maxlen:
-            maxlen=len(x)
-
-    for x in bl:
-        for i in range(len(x),maxlen):
-            x.append(0)
-
-def train_data(indexes,synteny_matrices_global,synteny_matrices_local,df,branch_length_species,branch_length_homology_species,distance,dist_p_s,dist_p_hs,gene_sequences):
-    """
-    homology_type_counts=dict(df.homology_type.value_counts())
-    homology_species_counts=dict(df.homology_species.value_counts())
-
-    #limits for each species and homology type in the trainig data so that the dataset is balanced
-    max_species_count=10000
-    max_homology_type_count=25000
-    for species in homology_species_counts:
-        homology_species_counts[species]=0
-
-    for homology_type in homology_type_counts:
-        homology_type_counts[homology_type]=0
-    """
-    labels=dict(ortholog_one2one=0,other_paralog=1,ortholog_one2many=2,ortholog_many2many=3,within_species_paralog=4)
-
-    train_data_dataframe=pd.DataFrame()
-    train_labels=[]
-    train_indexes=[]
-    train_mean_gene_length=[]
-    for i in range(len(indexes)):
-        row=df.loc[indexes[i]]
-        if row["homology_type"]=="within_species_paralog":
-            continue
-        train_data_dataframe=train_data_dataframe.append(row)
-        train_indexes.append(i)
-        train_labels.append(labels[row["homology_type"]])
-        train_mean_gene_length.append((len(gene_sequences[row["gene_stable_id"]])+len(gene_sequences[row["homology_gene_stable_id"]]))/2)
-
-    train_synteny_matrices_global=synteny_matrices_global[train_indexes]
-    train_synteny_matrices_local=synteny_matrices_local[train_indexes]
-    train_distance=distance[train_indexes]
-    train_dist_p_s=dist_p_s[train_indexes]
-    train_dist_p_hs=dist_p_hs[train_indexes]    
-    train_branch_length_species=branch_length_species[train_indexes]
-    train_branch_length_homology_species=branch_length_homology_species[train_indexes]
-
-    create_branch_length_padding(train_branch_length_species)
-    train_branch_length_species=np.array(train_branch_length_species)
-    create_branch_length_padding(train_branch_length_homology_species)
-    train_branch_length_homology_species=np.array(train_branch_length_homology_species)
-
-    #renormalize the train_mean_gene_length by (x-mean)/std
-    train_mean_gene_length=(train_mean_gene_length-np.mean(train_mean_gene_length))/np.std(train_mean_gene_length)
-
-    #create a random array of permutations to shuffle the indices
-    shi=np.random.permutation(len(train_labels))
-
-    train_branch_length_species=train_branch_length_species[shi]
-    print(train_branch_length_species.shape)
-
-    train_branch_length_homology_species=train_branch_length_homology_species[shi]
-    print(train_branch_length_homology_species.shape)
-
-    train_dist_p_s=np.array(train_dist_p_s)
-    train_dist_p_s=train_dist_p_s[shi]
-    print(train_dist_p_s.shape)
-
-    train_dist_p_hs=np.array(train_dist_p_hs)
-    train_dist_p_hs=train_dist_p_hs[shi]
-    print(train_dist_p_hs.shape)
-
-    train_synteny_matrices_global=train_synteny_matrices_global[shi]
-    print(train_synteny_matrices_global.shape)
-
-    train_synteny_matrices_local=train_synteny_matrices_local[shi]
-    print(train_synteny_matrices_local.shape)
-
-    train_indexes=np.array(train_indexes)
-    train_indexes=train_indexes[shi]
-    print(train_indexes.shape)
-
-    train_labels=np.array(train_labels)
-    train_labels=train_labels[shi]
-    print(train_labels.shape)
-
-    train_mean_gene_length=np.array(train_mean_gene_length)
-    train_mean_gene_length=train_mean_gene_length[shi]
-    print(train_mean_gene_length.shape)
-
-    train_distance=np.array(train_distance)
-    train_distance=train_distance[shi]
-    train_distance=(train_distance-np.mean(train_distance))/np.std(train_distance)
-    train_distance.shape
-
-    return train_synteny_matrices_global,train_synteny_matrices_local,train_branch_length_species,train_branch_length_homology_species,train_mean_gene_length,train_dist_p_s,train_dist_p_hs,train_distance,train_labels