mgnify-pipelines-toolkit 1.1.2__py3-none-any.whl → 1.2.1__py3-none-any.whl

mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py

@@ -1,214 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Copyright 2024-2025 EMBL - European Bioinformatics Institute
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import argparse
-
-from Bio.Seq import Seq
-import numpy as np
-import pandas as pd
-
-from mgnify_pipelines_toolkit.analysis.amplicon.amplicon_utils import (
-    get_read_count,
-    build_cons_seq,
-    build_mcp_cons_dict_list,
-    fetch_mcp,
-)
-from mgnify_pipelines_toolkit.constants.thresholds import MCP_MAX_LINE_COUNT
-
-
-def parse_args():
-
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(
-        "-i",
-        "--input",
-        required=True,
-        type=str,
-        help="Path to fastq file to choose inflection point",
-    )
-    parser.add_argument(
-        "-p", "--points", required=True, type=str, help="Path to inflection points file"
-    )
-    parser.add_argument("-s", "--sample", required=True, type=str, help="Sample ID")
-    parser.add_argument("-o", "--output", required=True, type=str, help="Output path")
-
-    args = parser.parse_args()
-
-    path = args.input
-    points = args.points
-    sample = args.sample
-    output = args.output
-
-    return path, points, sample, output
-
-
-def assess_inflection_point_mcp_for_sample(path, inf_point_list, rev=False):
-    """
-    Assess inflection point list, selecting one for automatic primer trimming.
-
-    Takes as input a fastq file and a list of inflection points generated by "find_mcp_inflection_points.py".
-    Computes the average conservation of mcp before inflection point and after.
-    Gets the difference in avg. conservation between the pre- and post- points.
-    Selects the inflection point with the maximum difference as the cutoff.
-    If an inf point has a similar difference and is earlier than the max, we make a 'conservative' choice and
-    replace it with the earlier cutoff.
-
-    Returns the cutoff point and the consensus sequence 'forming' the automatically predicted primer
-    """
-
-    # TODO error handle for empty inflection point list
-
-    start_confs = []  # pre-inf point conservations
-    end_confs = []  # post-inf point conservations
-    start_cons_lens = []  # list for storing lengths of pre-inflection point sequences
-    cons_seq_list = []  # list for storing consensus sequences pre-inflection points
-
-    do_not_include_list = [
-        i + 5 for i in inf_point_list
-    ]  # ignore conservation of inflection point in calculation
-
-    read_count = get_read_count(path)  # get readcount from fastq
-
-    max_line_count = None
-    if read_count > MCP_MAX_LINE_COUNT:
-        max_line_count = MCP_MAX_LINE_COUNT
-
-    n_prop = 0.8
-
-    for start in inf_point_list:  # Looping through the pre-inflection point mcps
-        mcp_len = start + 4  # length of pre-inf mcps is inflection point + 4
-
-        mcp_count_dict = fetch_mcp(
-            path, mcp_len, rev=rev, max_line_count=max_line_count
-        )  # get MCP count dict
-        mcp_cons_list = build_mcp_cons_dict_list(
-            mcp_count_dict, mcp_len
-        )  # list of base conservation dicts for mcps
-        cons_seq, cons_confs = build_cons_seq(
-            mcp_cons_list,
-            read_count,
-            n_prop,
-            do_not_include_list,
-            max_line_count=max_line_count,
-        )  # get list of max base conservations for each index
-        # also get consensus sequence
-        cons_seq_list.append(cons_seq)
-        start_confs.append(np.mean(cons_confs))
-        start_cons_lens.append(len(cons_seq))
-
-    for i, end in enumerate(
-        inf_point_list
-    ):  # Looping through the post-inflection point mcps
-        mcp_len = end + 5  # length of pre-inf mcps is inflection point + 5
-        subs_len = start_cons_lens[i]  # length of respective pre-inf point sequence
-        l = mcp_len + subs_len - 1  # final index of MCP
-
-        mcp_count_dict = fetch_mcp(
-            path, l, mcp_len, rev=rev, max_line_count=max_line_count
-        )
-        mcp_cons_list = build_mcp_cons_dict_list(mcp_count_dict, subs_len)
-        cons_seq, cons_confs = build_cons_seq(
-            mcp_cons_list,
-            read_count,
-            n_prop,
-            do_not_include_list,
-            subs_len,
-            max_line_count=max_line_count,
-        )
-
-        end_confs.append(np.mean(cons_confs))
-
-    diff_res = [
-        start_confs[i] - end_confs[i] for i in range(len(start_confs))
-    ]  # get differences between pre- and -post avg conservation values
-    diff_res_sorted = sorted(
-        diff_res, reverse=True
-    )  # sort differences from highest to lowest
-
-    ini_max_res = diff_res_sorted[0]  # maximum differences
-    curr_max_index = diff_res.index(ini_max_res)  # index of maximum differences
-
-    for res in diff_res_sorted[1:]:  # Loop through the rest of the differences
-        curr_res_index = np.where(diff_res == res)[0][0]
-
-        index_diff = inf_point_list[curr_max_index] - inf_point_list[curr_res_index]
-
-        # if difference between the max and the current is negligible and the index of the current is earlier then..
-        if ini_max_res - res < 0.05 and (index_diff <= 3 and index_diff > 0):
-            curr_max_index = (
-                curr_res_index  # replace the selected index with the current one
-            )
-
-    cutoff = (
-        inf_point_list[curr_max_index] + 5
-    )  # cutoff is the inflection point index + 5
-    primer = cons_seq_list[
-        curr_max_index
-    ]  # grab the correct consensus sequence as primer
-
-    # if the requested strand is reverse..
-    if rev:
-        primer = str(
-            Seq(primer).complement()
-        )  # ..get the complement of consensus sequence
-
-    return cutoff, primer
-
-
-def main():
-
-    path, points, sample, output = parse_args()
-    inf_df = pd.read_csv(points, sep="\t")
-
-    f_slice = inf_df[inf_df.strand == "F"]  # get forward inflection points
-    r_slice = inf_df[inf_df.strand == "R"]  # get reverse inflection points
-    r_slice = r_slice.reset_index(drop=True)
-
-    f_cutoff = ""
-    r_cutoff = ""
-    f_primer = ""
-    r_primer = ""
-
-    if not f_slice.empty:  # if there is a forward inflection point..
-        inf_list = f_slice.inf_point.tolist()
-        f_cutoff, f_primer = assess_inflection_point_mcp_for_sample(
-            path, inf_list
-        )  # .. assess and select
-
-    if not r_slice.empty:  # if there is a reverse inflection point..
-        inf_list = r_slice.inf_point.tolist()
-        r_cutoff, r_primer = assess_inflection_point_mcp_for_sample(
-            path, inf_list, rev=True
-        )  # .. assess and select
-
-    # Output cutoff point(s) to .txt file
-    with open(f"{output}/{sample}_cutoff.txt", "w") as fw:
-        if f_cutoff != "":
-            fw.write(f"F: {f_cutoff}\n")
-        if r_cutoff != "":
-            fw.write(f"R: {r_cutoff}\n")
-
-    # Output consensus primer sequence(s) to .fasta file
-    with open(f"{output}/{sample}_auto_primers.fasta", "w") as fw:
-        if f_cutoff != "":
-            fw.write(f">F_auto\n{f_primer}\n")
-        if r_cutoff != "":
-            fw.write(f">R_auto\n{r_primer}\n")
-
-
-if __name__ == "__main__":
-    main()

mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py

@@ -1,175 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Copyright 2024-2025 EMBL - European Bioinformatics Institute
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-import argparse
-from collections import defaultdict
-
-import pandas as pd
-import numpy as np
-
-from mgnify_pipelines_toolkit.analysis.amplicon.amplicon_utils import (
-    get_read_count,
-    build_cons_seq,
-    build_mcp_cons_dict_list,
-    fetch_mcp,
-)
-from mgnify_pipelines_toolkit.constants.thresholds import MCP_MAX_LINE_COUNT
-
-
-def parse_args():
-
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(
-        "-i",
-        "--input",
-        required=True,
-        type=str,
-        help="Path to fastq file to assess mcps",
-    )
-    parser.add_argument("-s", "--sample", required=True, type=str, help="Sample ID")
-    parser.add_argument(
-        "-st",
-        "--strand",
-        required=True,
-        choices=["FR", "F", "R"],
-        help="F: Forward, R: Reverse",
-    )
-    parser.add_argument("-o", "--output", required=True, type=str, help="Output path")
-
-    args = parser.parse_args()
-
-    path = args.input
-    sample = args.sample
-    strand = args.strand
-    output = args.output
-
-    return path, sample, strand, output
-
-
-def find_mcp_props_for_sample(path, rev=False):
-    """
-    Generate mcp proportions in a stepwise and windowed manner for a fastq file.
-
-    For a continuous range of starting indices (2 to 25), generate mcps of window size of 5 bases.
-    Calculate the average conservation of the most common base at each index of a window.
-    The resulting list of mcp conservations can be considered a conservation curve and used to
-    identify inflection points where the conservation suddenly changes.
-
-    Output a dictionary where:
-        key -> an index starting point e.g. base 10
-        val -> the average conservation of the most common base for the mcp window goign from base 10 to 15 (inclusive)
-    """
-
-    res_dict = defaultdict(float)
-    start_range = range(2, 25, 1)  # Range of starting indices
-
-    print(f"Processing {path}")
-
-    mcp_len = 5  # length of generated mcps
-
-    for start in start_range:
-
-        end = (
-            start + mcp_len - 1
-        )  # compute the final index for the mcp (inclusive). Indices are of base 1 not 0.
-
-        read_count = get_read_count(
-            path, file_type="fastq"
-        )  # get read count for fastq file
-
-        max_line_count = None
-        if read_count > MCP_MAX_LINE_COUNT:
-            max_line_count = MCP_MAX_LINE_COUNT
-
-        mcp_count_dict = fetch_mcp(
-            path, end, start, rev, max_line_count
-        )  # get MCP count dict
-        mcp_cons_list = build_mcp_cons_dict_list(
-            mcp_count_dict, mcp_len
-        )  # list of base conservation dicts for mcps
-        cons_seq, cons_conf = build_cons_seq(
-            mcp_cons_list, read_count, max_line_count=max_line_count
-        )  # get list of max base conservations for each index
-
-        res_dict[start] = np.mean(cons_conf)  # compute the mean
-
-    return res_dict
-
-
-def concat_out(fwd_out="", rev_out=""):
-    """
-    Generate Pandas dataframe out of mcp dictionary.
-
-    Output looks like this (when both F and R are requested):
-        2	3	4
-    F	0.7814975041597337	0.8736772046589019	0.9434276206322796
-    R	0.9010981697171381	0.9082861896838601	0.90369384359401
-
-    Columns are the starting indices. Row labels are the strand.
-    """
-
-    total_res_dict = defaultdict(list)
-    df_ind = []
-
-    # Check if fwd strand was requested
-    if fwd_out != "":
-        [total_res_dict[key].append(fwd_out[key]) for key in fwd_out.keys()]
-        df_ind.append("F")
-
-    # Check if rev strand was requested
-    if rev_out != "":
-        [total_res_dict[key].append(rev_out[key]) for key in rev_out.keys()]
-        df_ind.append("R")
-
-    res_df = pd.DataFrame.from_dict(total_res_dict)
-    res_df.index = df_ind
-
-    return res_df
-
-
-def main():
-
-    path, sample, strand, output = parse_args()
-
-    res_df = ""
-
-    # TODO: match-case statement is python 3.10>. We are currently locking the version
-    # at version 3.9. The day we bump the version we should replace these if statements
-    # with a match-case block.
-
-    if strand == "FR":
-        fwd_out = find_mcp_props_for_sample(path)
-        rev_out = find_mcp_props_for_sample(path, rev=True)
-        res_df = concat_out(fwd_out, rev_out)
-    elif strand == "F":
-        fwd_out = find_mcp_props_for_sample(path)
-        res_df = concat_out(fwd_out)
-    elif strand == "R":
-        rev_out = find_mcp_props_for_sample(path, rev=True)
-        res_df = concat_out(rev_out=rev_out)
-    else:
-        print(
-            "Incorrect strand input. Should be F for forward, R for reverse, or FR for both."
-        )
-        exit(1)
-
-    # Save resulting dataframe to a tsv file
-    res_df.to_csv(f"{output}/{sample}_mcp_cons.tsv", sep="\t")
-
-
-if __name__ == "__main__":
-    main()

mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py

@@ -1,111 +0,0 @@
-#!/usr/bin/env python
-# -*- coding: utf-8 -*-
-
-# Copyright 2024-2025 EMBL - European Bioinformatics Institute
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an "AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
-
-from collections import defaultdict
-import argparse
-
-import pandas as pd
-import numpy as np
-
-
-def parse_args():
-
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(
-        "-i",
-        "--input",
-        required=True,
-        type=str,
-        help="Path to mcp tsv file to find inflection points",
-    )
-    parser.add_argument("-s", "--sample", required=True, type=str, help="Sample ID")
-    parser.add_argument("-o", "--output", required=True, type=str, help="Output path")
-
-    args = parser.parse_args()
-
-    path = args.input
-    sample = args.sample
-    output = args.output
-
-    return path, sample, output
-
-
-def find_mcp_inf_points(mcp_df):
-    """
-    Find inflection points from an mcp_df file output by "assess_mcp_proportions_MERGED.py"
-
-    Takes the list of average mcp conservations and gets the derivative of the curve
-    Keep any points of the derivative where value is above the 80th percentile
-
-    Outputs a dictionary with key-val pairs where vals are lists:
-        'strand' -> strand list
-        'inf_point' -> inf_point list
-
-    """
-
-    inf_point_dict = defaultdict(list)
-    start_indices = [int(i) for i in mcp_df.columns.tolist()]
-
-    for i in range(len(mcp_df)):  # Loop through both possible strands of the mcp_df
-        strand = mcp_df.index[i]
-        props = mcp_df.iloc[i].tolist()
-        props = [-val for val in props]
-
-        prop_diff = np.diff(props) / np.diff(start_indices)  # Get the derivative
-        infl_points = np.where(prop_diff > np.percentile(prop_diff, 80))[
-            0
-        ]  # Grab points above 80th percentile
-
-        for ind in infl_points:
-            inf_point = start_indices[ind]
-
-            if (
-                inf_point < 10 or inf_point > 20
-            ):  # Rule to facilitate results - won't accept
-                continue  # points below index 10 or above index 20
-                # 10 means a cutoff of 15 and 20 a cutoff of 25
-                # literature points to no primers existing that are
-                # shorter or bigger  than these lengths
-
-            inf_point_dict["strand"].append(strand)
-            inf_point_dict["inf_point"].append(inf_point)
-
-    return inf_point_dict
-
-
-def main():
-
-    path, sample, output = parse_args()
-
-    mcp_df = pd.read_csv(path, sep="\t", index_col=0)  # Read mcp_df
-    inf_point_dict = find_mcp_inf_points(mcp_df)  # Generate inflection points dict
-
-    if len(inf_point_dict) > 0:  # If the inf_point_dict isn't empty..
-        inf_point_df = pd.DataFrame.from_dict(
-            inf_point_dict
-        )  # .. turn it into a dataframe
-        inf_point_df.to_csv(
-            f"{output}/{sample}_inf_points.tsv", sep="\t", index=False
-        )  # ..save it to a .tsv file
-
-    else:  # If it is empty..
-        fw = open(f"{output}/{sample}_inf_points.tsv", "w")  # ..make an empty file
-        fw.close()
-
-
-if __name__ == "__main__":
-    main()