geney 1.2.21__py2.py3-none-any.whl → 1.2.23__py2.py3-none-any.whl

geney/__init__.py

@@ -1,6 +1,18 @@
 from .config_setup import get_config
-config_setup = get_config()
-print("Hello Geney.")
+config = get_config()
+from .Fasta_segment import Fasta_segment
+from .utils import *
+
+mut_id = 'KRAS:12:25227343:G:T'
+epistasis_id = 'KRAS:12:25227343:G:T|KRAS:12:25227344:A:T'
+
+def available_genes(organism='hg38'):
+    import os
+    for file in os.listdir(config[organism]['MRNA_PATH'] / 'protein_coding'):
+        gene = file.split('_')[-1].strip('.pkl')
+        yield gene
+
+
 # import os
 # import json
 # from pathlib import Path

geney/data_setup.py

@@ -234,7 +234,7 @@ def main():
         config_data = unload_json(config_file)
         overwrite = 'y'
         if args.organism in config_data:
-            overwrite = input("Organism {args.organism} already configured... Overwrite? (y/n)")
+            overwrite = input(f"Organism {args.organism} already configured... Overwrite? (y/n)")
 
         if overwrite == 'y':
             config_data[args.organism] = config_paths

geney/graphic_utils.py

@@ -0,0 +1,270 @@
+
+import matplotlib.pyplot as plt
+from matplotlib.patches import Rectangle
+import seaborn as sns
+from collections import namedtuple
+from geney.utils import find_files_by_gene_name, reverse_complement, unload_pickle, contains, unload_json, dump_json #, is_monotonic
+
+
+### Graphical Stuff
+def create_figure_story(epistasis, to_file=None):
+    g = epistasis.split(':')[0]
+    out = oncosplice(epistasis, annotate=True)
+    out = out[out.cons_available==1]
+
+    for _, row in out.iterrows():
+        max_length = 0
+        pos = 0
+        for i, k in row.deletions.items():
+            if len(k) > max_length:
+                pos = i
+                max_length = len(k)
+
+        if max_length > 5:
+            del_reg = [pos, pos + max_length]
+        else:
+            del_reg = None
+
+        if row.oncosplice_score == 0:
+            mutation_loc = None
+        else:
+            mutation_loc = pos
+
+        plot_conservation(tid=row.transcript_id,
+                          gene=f'{g}, {row.transcript_id}.{row.isoform}',
+                          mutation_loc=mutation_loc,
+                          target_region=del_reg, mut_name='Epistasis',
+                          domain_annotations=get_annotations(row.transcript_id, 300),
+                          to_file=to_file)
+
+
+
+def plot_conservation(gene_name, tid, gene='', mutation_loc=None, target_region=None, mut_name='Mutation', domain_annotations=[]):
+    """
+    Plots conservation vectors with protein domain visualization and Rate4Site scores.
+
+    Parameters:
+    tid (str): Transcript identifier.
+    gene (str): Gene name.
+    mutation_loc (int): Position of the mutation.
+    target_region (tuple): Start and end positions of the target region.
+    mut_name (str): Name of the mutation.
+    domain_annotations (list): List of tuples for domain annotations (start, end, label).
+    """
+    # Access conservation data
+    _, cons_vec = unload_pickle(gene_name)['tid']['cons_vector']
+
+    if not cons_vec:
+        raise ValueError("The conservation vector is empty.")
+
+    sns.set_theme(style="white")
+    fig, ax = plt.subplots(figsize=(max(15, len(cons_vec)/10), 3))  # Dynamic figure size
+
+    # Plotting the conservation vectors in the main plot
+    plot_conservation_vectors(ax, cons_vec)
+
+    # Setting up primary axis for the main plot
+    setup_primary_axis(ax, gene, len(cons_vec))
+
+    # Create a separate axes for protein domain visualization
+    domain_ax = create_domain_axes(fig, len(cons_vec))
+
+    # Draw protein domains
+    plot_protein_domains(domain_ax, domain_annotations, len(cons_vec))
+
+    # Plotting Rate4Site scores on secondary y-axis
+    plot_rate4site_scores(ax, cons_vec)
+
+    # Plotting mutation location and target region, if provided
+    plot_mutation_and_target_region(ax, mutation_loc, target_region, mut_name)
+
+    plt.show()
+
+def plot_conservation_vectors(ax, cons_vec):
+    """Plots transformed conservation vectors."""
+    temp = transform_conservation_vector(cons_vec, 76)  # Larger window
+    temp /= max(temp)
+    ax.plot(list(range(len(temp))), temp, c='b', label='Estimated Functional Residues')
+
+    temp = transform_conservation_vector(cons_vec, 6)   # Smaller window
+    temp /= max(temp)
+    ax.plot(list(range(len(temp))), temp, c='k', label='Estimated Functional Domains')
+
+def setup_primary_axis(ax, gene, length):
+    """Configures the primary axis of the plot."""
+    ax.set_xlabel(f'AA Position - {gene}', weight='bold')
+    ax.set_xlim(0, length)
+    ax.set_ylim(0, 1)
+    ax.set_ylabel('Relative Importance', weight='bold')
+    ax.tick_params(axis='y')
+    ax.spines['right'].set_visible(False)
+    ax.spines['top'].set_visible(False)
+
+def create_domain_axes(fig, length):
+    """Creates an axis for protein domain visualization."""
+    domain_ax_height = 0.06
+    domain_ax = fig.add_axes([0.125, 0.95, 0.775, domain_ax_height])
+    domain_ax.set_xlim(0, length)
+    domain_ax.set_xticks([])
+    domain_ax.set_yticks([])
+    for spine in domain_ax.spines.values():
+        spine.set_visible(False)
+    return domain_ax
+
+def plot_protein_domains(ax, domain_annotations, length):
+    """Plots protein domain annotations."""
+    ax.add_patch(Rectangle((0, 0), length, 0.9, facecolor='lightgray', edgecolor='none'))
+    for domain in domain_annotations:
+        start, end, label = domain
+        ax.add_patch(Rectangle((start, 0), end - start, 0.9, facecolor='orange', edgecolor='none', alpha=0.5))
+        ax.text((start + end) / 2, 2.1, label, ha='center', va='center', color='black', size=8)
+
+def plot_rate4site_scores(ax, cons_vec):
+    """Plots Rate4Site scores on a secondary y-axis."""
+    ax2 = ax.twinx()
+    c = np.array(cons_vec)
+    c = c + abs(min(c))
+    c = c/max(c)
+    ax2.set_ylim(min(c), max(c)*1.1)
+    ax2.scatter(list(range(len(c))), c, color='green', label='Rate4Site Scores', alpha=0.4)
+    ax2.set_ylabel('Rate4Site Normalized', color='green', weight='bold')
+    ax2.tick_params(axis='y', labelcolor='green')
+    ax2.spines['right'].set_visible(True)
+    ax2.spines['top'].set_visible(False)
+
+def plot_mutation_and_target_region(ax, mutation_loc, target_region, mut_name):
+    """Highlights mutation location and target region, if provided."""
+    if mutation_loc is not None:
+        ax.axvline(x=mutation_loc, ymax=1, color='r', linestyle='--', alpha=0.7)
+        ax.text(mutation_loc, 1.04, mut_name, color='r', weight='bold', ha='center')
+
+    if target_region is not None:
+        ax.add_patch(Rectangle((target_region[0], 0), target_region[1] - target_region[0], 1, alpha=0.25, facecolor='gray'))
+        center_loc = target_region[0] + 0.5 * (target_region[1] - target_region[0])
+        ax.text(center_loc, 1.04, 'Deleted Region', ha='center', va='center', color='gray', weight='bold')
+
+
+def merge_overlapping_regions(df):
+    """
+    Merges overlapping regions in a DataFrame.
+
+    Parameters:
+    df (pd.DataFrame): DataFrame with columns 'start', 'end', 'name'
+
+    Returns:
+    List: List of merged regions as namedtuples (start, end, combined_name)
+    """
+    if df.empty:
+        return []
+
+    Region = namedtuple('Region', ['start', 'end', 'combined_name'])
+    df = df.sort_values(by='start')
+    merged_regions = []
+    current_region = None
+
+    for _, row in df.iterrows():
+        start, end, name = row['start'], row['end'], row['name'].replace('_', ' ')
+        if current_region is None:
+            current_region = Region(start, end, [name])
+        elif start <= current_region.end:
+            current_region = Region(current_region.start, max(current_region.end, end), current_region.combined_name + [name])
+        else:
+            merged_regions.append(current_region._replace(combined_name=', '.join(current_region.combined_name)))
+            current_region = Region(start, end, [name])
+
+    if current_region:
+        merged_regions.append(current_region._replace(combined_name=', '.join(current_region.combined_name)))
+
+    # Assuming split_text is a function that splits the text appropriately.
+    merged_regions = [Region(a, b, split_text(c, 35)) for a, b, c in merged_regions]
+    return merged_regions
+
+
+def split_text(text, width):
+    """
+    Splits a text into lines with a maximum specified width.
+
+    Parameters:
+    text (str): The text to be split.
+    width (int): Maximum width of each line.
+
+    Returns:
+    str: The text split into lines of specified width.
+    """
+    lines = re.findall('.{1,' + str(width) + '}', text)
+    return '\n'.join(lines)
+
+def get_annotations(target_gene, w=500):
+    PROTEIN_ANNOTATIONS = {}
+    temp = PROTEIN_ANNOTATIONS[(PROTEIN_ANNOTATIONS['Transcript stable ID'] == PROTEIN_ANNOTATIONS[target_gene]) & (PROTEIN_ANNOTATIONS.length < w)].drop_duplicates(subset=['Interpro Short Description'], keep='first')
+    return merge_overlapping_regions(temp)
+
+
+# def plot_conservation(tid, gene='', mutation_loc=None, target_region=None, mut_name='Mutation', domain_annotations=[], to_file=None):
+#     _, cons_vec = access_conservation_data(tid)
+#
+#     sns.set_theme(style="white")
+#     fig, ax = plt.subplots(figsize=(15, 3))  # Adjusted figure size for better layout
+#
+#     # Plotting the conservation vectors in the main plot
+#     temp = transform_conservation_vector(cons_vec, 76)
+#     temp /= max(temp)
+#     ax.plot(list(range(len(temp))), temp, c='b', label='Estimated Functional Residues')
+#     temp = transform_conservation_vector(cons_vec, 6)
+#     temp /= max(temp)
+#     ax.plot(list(range(len(temp))), temp, c='k', label='Estimated Functional Domains')
+#
+#     # Setting up primary axis for the main plot
+#     ax.set_xlabel(f'AA Position - {gene}', weight='bold')
+#     ax.set_xlim(0, len(cons_vec))
+#     ax.set_ylim(0, 1)  # Set y-limit to end at 1
+#     ax.set_ylabel('Relative Importance', weight='bold')
+#     ax.tick_params(axis='y')
+#     ax.spines['right'].set_visible(False)
+#     ax.spines['top'].set_visible(False)
+#
+#     # Create a separate axes for protein domain visualization above the main plot
+#     domain_ax_height = 0.06  # Adjust for thinner protein diagram
+#     domain_ax = fig.add_axes([0.125, 0.95, 0.775, domain_ax_height])  # Position higher above the main plot
+#     domain_ax.set_xlim(0, len(cons_vec))
+#     domain_ax.set_xticks([])
+#     domain_ax.set_yticks([])
+#     domain_ax.spines['top'].set_visible(False)
+#     domain_ax.spines['right'].set_visible(False)
+#     domain_ax.spines['left'].set_visible(False)
+#     domain_ax.spines['bottom'].set_visible(False)
+#
+#     # Draw the full-length protein as a base rectangle
+#     domain_ax.add_patch(Rectangle((0, 0), len(cons_vec), 0.9, facecolor='lightgray', edgecolor='none'))
+#
+#     # Overlay domain annotations
+#     for domain in domain_annotations:
+#         start, end, label = domain
+#         domain_ax.add_patch(Rectangle((start, 0), end - start, 0.9, facecolor='orange', edgecolor='none', alpha=0.5))
+#         domain_ax.text((start + end) / 2, 2.1, label, ha='center', va='center', color='black', size=8)
+#
+#     # Plotting Rate4Site scores on secondary y-axis
+#     ax2 = ax.twinx()
+#     c = np.array(cons_vec)
+#     c = c + abs(min(c))
+#     c = c/max(c)
+#     ax2.set_ylim(min(c), max(c)*1.1)
+#     ax2.scatter(list(range(len(c))), c, color='green', label='Rate4Site Scores', alpha=0.4)
+#     ax2.set_ylabel('Rate4Site Normalized', color='green', weight='bold')
+#     ax2.tick_params(axis='y', labelcolor='green')
+#     ax2.spines['right'].set_visible(True)
+#     ax2.spines['top'].set_visible(False)
+#
+#     # Plotting mutation location and target region
+#     if mutation_loc is not None:
+#         ax.axvline(x=mutation_loc, ymax=1,color='r', linestyle='--', alpha=0.7)
+#         ax.text(mutation_loc, 1.04, mut_name, color='r', weight='bold', ha='center')
+#
+#     if target_region is not None:
+#         ax.add_patch(Rectangle((target_region[0], 0), target_region[1] - target_region[0], 1, alpha=0.25, facecolor='gray'))
+#         center_loc = target_region[0] + 0.5 * (target_region[1] - target_region[0])
+#         ax.text(center_loc, 1.04, 'Deleted Region', ha='center', va='center', color='gray', weight='bold')
+#
+#     plt.show()
+#
+

geney/mutation_utils.py

@@ -0,0 +1,56 @@
+from .seqmat_utils import *
+import numpy as np
+
+class Allele(SeqMat):
+    def __init__(self, alt, pos1, pos2, rev):
+        super().__init__(alt, pos1, pos2)
+        self.position = min(pos1)
+        if rev:
+            self.reverse_complement()
+
+    # def _continuous(self, ind):
+    #     return True
+
+
+class SNP(Allele):
+    def __init__(self, alt, pos1, pos2):
+        super().__init__(alt, pos1, pos2)
+        pass
+
+class INDEL(Allele):
+    def __init__(self, alt, pos):
+        super().__init__(alt, pos)
+        pass
+
+class INS(Allele):
+    def __init__(self, alt, pos):
+        super().__init__()
+        pass
+
+class DEL(Allele):
+    def __init__(self, alt, pos):
+        super().__init__()
+        pass
+
+def get_mutation(mut_id, rev=False):
+    _, _, i, r, a = mut_id.split(':')
+    i = int(i)
+
+    if len(a) == len(r) == 1 and a != '-' and r != '-':
+        return Allele(a, [i], [0], rev)
+
+    elif a == '-' and r != '-':
+        return Allele('-' *len(r), np.arange(i, i+ len(r), dtype=np.int32), [0] * len(r), rev)
+
+    elif r == '-' and a != '-':
+        # print(a, np.full(len(a), int(i)), np.arange(1, len(a)+1),)
+        return Allele(a, np.full(len(a), int(i)), np.arange(1, len(a)+1), rev)
+
+    elif a != '-' and r != '-':
+        ind1 = np.concatenate(
+            [np.arange(i, i + len(r), dtype=np.int32), np.full(len(a), len(r) + i - 1, dtype=np.int32)])
+        ind2 = np.concatenate([np.zeros(len(r), dtype=np.int32), np.arange(1, len(a) + 1, dtype=np.int32)])
+        return Allele('-' * len(r) + a, ind1, ind2, rev)
+
+
+