geney 1.3.79__py2.py3-none-any.whl → 1.4.0__py2.py3-none-any.whl

geney/_graphic_utils.py

@@ -0,0 +1,269 @@
+import matplotlib.pyplot as plt
+from matplotlib.patches import Rectangle
+import seaborn as sns
+from collections import namedtuple
+from geney.utils import unload_pickle, contains, unload_json, dump_json
+
+
+### 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/_gtex_utils.py

@@ -0,0 +1,68 @@
+import pandas as pd
+from tqdm import tqdm
+
+# Set pandas display options (if necessary)
+pd.options.display.max_rows = 999
+
+# Read metadata
+metadata = pd.read_csv('GTEx_Analysis_v8_Annotations_SampleAttributesDS.txt', delimiter='\t')
+metadata_tissue_mapper = metadata[['SAMPID', 'SMTS']].drop_duplicates().set_index('SAMPID').to_dict()['SMTS']
+
+# Initialize an empty DataFrame for combined results
+combined_df = pd.DataFrame()
+
+# Define chunk size
+tpm_mean = []
+# Process the main data file in chunks
+for chunk in tqdm(pd.read_csv('GTEx_Analysis_2017-06-05_v8_RSEMv1.3.0_transcript_tpm.gct', header=2, chunksize=1000,
+                              delimiter='\t')):
+    # Perform the same operations on the chunk
+    chunk = chunk.set_index(['transcript_id', 'gene_id']).rename(columns=metadata_tissue_mapper)
+    # Append the processed chunk to the combined DataFrame
+    tpm_mean.append(chunk.T.groupby(by=chunk.columns).mean().T)
+
+# Compute the mean TPM per tissue
+tpm_mean = pd.concat(tpm_mean)
+
+
+cancer_projects = {
+    "Adrenal Gland": "ACC",
+    "Bladder": "BLCA",
+    "Brain": ["GBM", "LGG"],  # Note: Brain maps to two projects
+    "Breast": "BRCA",
+    "Colon": "COAD",
+    "Esophagus": "ESCA",
+    "Kidney": ["KICH", "KIRC", "KIRP"],  # Note: Kidney maps to three projects
+    "Liver": "LIHC",
+    "Lung": "LUNG",
+    "Ovary": "OV",
+    "Pancreas": "PAAD",
+    "Prostate": "PRAD",
+    "Skin": "SKCM",
+    "Stomach": "STAD",
+    "Testis": "TGCT",
+    "Uterus": "UCS"
+}
+
+tissue_projects = {
+    "ACC": "Adrenal Gland",
+    "BLCA": "Bladder",
+    "GBM": "Brain",
+    "LGG": "Brain",
+    "BRCA": "Breast",
+    "COAD": "Colon",
+    "ESCA": "Esophagus",
+    "KICH": "Kidney",
+    "KIRC": "Kidney",
+    "KIRP": "Kidney",
+    "LIHC": "Liver",
+    "LUNG": "Lung",
+    "OV": "Ovary",
+    "PAAD": "Pancreas",
+    "PRAD": "Prostate",
+    "SKCM": "Skin",
+    "STAD": "Stomach",
+    "TGCT": "Testis",
+    "UCS": "Uterus"
+}
+

geney/_immune_utils.py

@@ -0,0 +1,125 @@
+import subprocess
+import logging
+import tempfile
+from geney import _config_setup
+import re
+from io import StringIO
+import pandas as pd
+
+
+class NetChop(object):
+    """
+    Wrapper around netChop tool. Assumes netChop is in your PATH.
+    """
+    def predict_epitopes(self, sequences, threshold=0.5, min_len=8):
+        """
+        Return netChop predictions for each position in each sequence.
+
+        Parameters
+        -----------
+        sequences : list of string
+            Amino acid sequences to predict cleavage for
+
+        Returns
+        -----------
+        list of list of float
+
+        The i'th list corresponds to the i'th sequence. Each list gives
+        the cleavage probability for each position in the sequence.
+        """
+        with tempfile.NamedTemporaryFile(dir=config_setup['NETCHOP'], suffix=".fsa", mode="w") as input_fd:
+            for (i, sequence) in enumerate(sequences):
+                _ = input_fd.write("> %d\n" % i)
+                _ = input_fd.write(sequence)
+                _ = input_fd.write("\n")
+            input_fd.flush()
+            try:
+                output = subprocess.check_output(["netchop", str(input_fd.name)])
+            except subprocess.CalledProcessError as e:
+                logging.error("Error calling netChop: %s:\n%s" % (e, e.output))
+                raise
+        parsed = self.parse_netchop(output)
+        # return parsed
+        #
+        assert len(parsed) == len(sequences), \
+            "Expected %d results but got %d" % (
+                len(sequences), len(parsed))
+        assert [len(x) for x in parsed] == [len(x) for x in sequences]
+        filtered_proteosomes = []
+        for scores, seq in list(zip(parsed, sequences)):
+            proteosome = self.chop_protein(seq, [s > threshold for s in scores])
+            filtered_proteosomes.append([e for e in proteosome if len(e) > min_len])
+        return filtered_proteosomes
+    @staticmethod
+    def parse_netchop(netchop_output):
+        """
+        Parse netChop stdout.
+        """
+        line_iterator = iter(netchop_output.decode().split("\n"))
+        scores = []
+        for line in line_iterator:
+            if "pos" in line and 'AA' in line and 'score' in line:
+                scores.append([])
+                if "----" not in next(line_iterator):
+                    raise ValueError("Dashes expected")
+                line = next(line_iterator)
+                while '-------' not in line:
+                    score = float(line.split()[3])
+                    scores[-1].append(score)
+                    line = next(line_iterator)
+        return scores
+    def chop_protein(self, seq, pos):
+        # Generate subsequences using list comprehension and slicing
+        start = 0
+        subsequences = [seq[start:(start := i+1)] for i, marker in enumerate(pos) if marker == 1]
+        # Check if the last part needs to be added
+        if start < len(seq):
+            subsequences.append(seq[start:])
+        return subsequences
+    def generate_cut_sequences(self, char_sequence, cut_probabilities):
+        """
+        Generate all possible cut sequences and their abundance values,
+        considering only those sequences where the probabilities of all cut sites
+        between the two ends are zero.
+
+        :param char_sequence: A string representing the sequence of characters.
+        :param cut_probabilities: A list of probabilities for each position in the sequence.
+        :return: A list of tuples, where each tuple contains a cut sequence and its abundance value.
+        """
+        if len(char_sequence) != len(cut_probabilities):
+            raise ValueError("Character sequence and cut probabilities must have the same length.")
+        cut_sequences = []
+        # Generate all possible cuts
+        for i in range(len(char_sequence)):
+            for j in range(i + 1, len(char_sequence) + 1):
+                # Check if probabilities of all cut sites between i and j are zero
+                if sum(cut_probabilities[i + 1:j - 1]) < 1:
+                    cut_sequence = char_sequence[i:j]
+                    abundance_value = cut_probabilities[i] * cut_probabilities[j - 1] - sum(
+                        cut_probabilities[i + 1:j - 1])
+                    cut_sequences.append({'seq': cut_sequence, 'abundance': abundance_value})
+        return pd.DataFrame(cut_sequences)
+
+
+def run_mhc(sequences):
+    with tempfile.NamedTemporaryFile(dir='/tamir2/nicolaslynn/temp', suffix=".pep", mode="w") as input_fd:
+        for (i, sequence) in enumerate(sequences):
+            _ = input_fd.write(sequence)
+            _ = input_fd.write("\n")
+        input_fd.flush()
+        try:
+            out = subprocess.check_output(
+                ["netMHCpan", "-p", "-BA", str(input_fd.name)])
+        except subprocess.CalledProcessError as e:
+            logging.error("Error calling netChop: %s:\n%s" % (e, e.output))
+            raise
+    out = out.decode('utf-8')
+    out = out.split(
+        '\n---------------------------------------------------------------------------------------------------------------------------\n')
+    out = out[1] + '\n' + out[2]
+    out = re.sub(r'[ ]+', ',', out)
+    out = out.replace('\n,', '\n')
+    return pd.read_csv(StringIO(out)).drop(columns=['Unnamed: 0'])
+
+
+