mgnify-pipelines-toolkit 1.2.0__py3-none-any.whl → 1.2.1__py3-none-any.whl

mgnify_pipelines_toolkit/constants/thresholds.py

@@ -14,9 +14,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-# used by fetch_mcp in analysis.amplicon
-MCP_MAX_LINE_COUNT = 300_000
-
 # used by classify_var_regions in analysis.amplicon
 MIN_OVERLAP = 0.95
 MIN_SEQ_COUNT = 5000
@@ -26,7 +23,6 @@ MAX_INTERNAL_PRIMER_PROPORTION = 0.2
 # used by library_strategy_checker in analysis.shared
 MIN_AMPLICON_STRATEGY_CHECK = 0.30
 
-
 # used by markergene_study_summary in analysis.shared
 MAJORITY_MARKER_PROPORTION = 0.45
 # used by gff_toolkit in analysis.assembly

{mgnify_pipelines_toolkit-1.2.0.dist-info → mgnify_pipelines_toolkit-1.2.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: mgnify_pipelines_toolkit
-Version: 1.2.0
+Version: 1.2.1
 Summary: Collection of scripts and tools for MGnify pipelines
 Author-email: MGnify team <metagenomics-help@ebi.ac.uk>
 License: Apache Software License 2.0
@@ -14,7 +14,6 @@ License-File: LICENSE
 Requires-Dist: biopython>=1.85
 Requires-Dist: numpy<3,>=2.2.4
 Requires-Dist: pandas<3,>=2.2.3
-Requires-Dist: regex>=2024.11.6
 Requires-Dist: requests<3,>=2.32.3
 Requires-Dist: click<9,>=8.1.8
 Requires-Dist: pandera<0.24,>=0.23.1

{mgnify_pipelines_toolkit-1.2.0.dist-info → mgnify_pipelines_toolkit-1.2.1.dist-info}/RECORD

@@ -1,17 +1,11 @@
 mgnify_pipelines_toolkit/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mgnify_pipelines_toolkit/analysis/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py,sha256=8qmb57E2XBrwqo6YcJYyvPyuaIMu82Ifho7yyyUdnSM,6572
-mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py,sha256=2-URxvcl13_8O9bUmoa3-KMPSvdTaLbxfFDY-ycs_4M,5316
-mgnify_pipelines_toolkit/analysis/amplicon/assess_inflection_point_mcp.py,sha256=cRoHPM-VB_L3NWYgkNWuyzqIqhzwHJuU3-6BiiS2lnw,7553
-mgnify_pipelines_toolkit/analysis/amplicon/assess_mcp_proportions.py,sha256=RAdqakH05Qt_LG9jlV7P2M90o5KmlAXmDFQ4X51NIBE,5387
 mgnify_pipelines_toolkit/analysis/amplicon/classify_var_regions.py,sha256=W0ob9z_8sjrB1Ck48Ac-_5Vw2kyoRFalcxhrR6KSXpI,20196
-mgnify_pipelines_toolkit/analysis/amplicon/find_mcp_inflection_points.py,sha256=vC3nKxggnSljfw4HNkugXbXfGvLx7XnryEE7eEGqfqs,3552
 mgnify_pipelines_toolkit/analysis/amplicon/make_asv_count_table.py,sha256=soTewFddtebW-EcejGh9whs3cBLWJrGCYdPc0KukoAw,8756
 mgnify_pipelines_toolkit/analysis/amplicon/mapseq_to_asv_table.py,sha256=BLqhflblUegCvuQic16PrFXfIXlFWmGkmWJyl4wJoLQ,5040
 mgnify_pipelines_toolkit/analysis/amplicon/primer_val_classification.py,sha256=Bmc4Yu8inpT6AVTG1zwxp9F9mknIDLY33-UuFdaZuq0,3756
 mgnify_pipelines_toolkit/analysis/amplicon/remove_ambiguous_reads.py,sha256=Wu4tRtuRkgd3hoeuwPl_E5ghxIW7e_1vrcvFGWv_U4A,3173
 mgnify_pipelines_toolkit/analysis/amplicon/rev_comp_se_primers.py,sha256=yLpzkRJXAeXRUNgz60zopEwHcdprM2UDjquE-GkrFys,1722
-mgnify_pipelines_toolkit/analysis/amplicon/standard_primer_matching.py,sha256=K6gniytuItq5WzHLi1BsaUCOdP4Zm0_ZzW2_ns7-BTI,11114
 mgnify_pipelines_toolkit/analysis/amplicon/study_summary_generator.py,sha256=epVClL10QcllL8yu7YGjx0rXNVHL2GxHi-Ek0MOjsjo,13859
 mgnify_pipelines_toolkit/analysis/assembly/add_rhea_chebi_annotation.py,sha256=NZSNY2bqs_TQyz8riDqiEFPLKcwTgzh1C7DeVHT6V8Q,4366
 mgnify_pipelines_toolkit/analysis/assembly/antismash_gff_builder.py,sha256=vZdDIcG09hulgCp0FylwHXVSGSlwl2RsDU4_xvsrUC0,6732
@@ -40,18 +34,17 @@ mgnify_pipelines_toolkit/analysis/shared/mapseq2biom.py,sha256=7-U0DN1joVu0ifLOo
 mgnify_pipelines_toolkit/analysis/shared/markergene_study_summary.py,sha256=sKAo_rKEyVAZXSaIFMkpSoYZxiWwXMA3XDA6Z-hbHgg,7904
 mgnify_pipelines_toolkit/constants/db_labels.py,sha256=omPINMylAjO2PxeFhSk2MbYNcGZH3P82optSlMey3dw,858
 mgnify_pipelines_toolkit/constants/ncrna.py,sha256=a_5hWp446S7BhRbe_JcydFgZM7sgPLuMlaiBvKWN_XM,1928
-mgnify_pipelines_toolkit/constants/regex_ambiguous_bases.py,sha256=7nEOODQq35y9wx9YnvJuo29oBpwTpXg_kIbf_t7N4TQ,1093
 mgnify_pipelines_toolkit/constants/regex_fasta_header.py,sha256=G-xrc9b8zdmPTaOICD2b3RCVeFAEOVkfRkIfotQ7gek,1193
 mgnify_pipelines_toolkit/constants/tax_ranks.py,sha256=kMq__kOJcbiwsgolkdvb-XLo3WMnJdEXgedjUyMOYjI,1081
-mgnify_pipelines_toolkit/constants/thresholds.py,sha256=V_xDBk0RhS3hHeWqOacKzth2gM6zJABRPgwHy-Ciqfk,1157
+mgnify_pipelines_toolkit/constants/thresholds.py,sha256=1AMBmoHBR0WjXZpkwJ7_Q-gfJtHXuCA4tZ-uvPhF0Xc,1085
 mgnify_pipelines_toolkit/constants/var_region_coordinates.py,sha256=0bM4MwarFiM5yTcp5AbAmQ0o-q-gWy7kknir9zJ9R0A,1312
 mgnify_pipelines_toolkit/schemas/schemas.py,sha256=pyDZvCuWbwccQF0D7c5BN1vv36wQdgcAUXU43_zAu74,18164
 mgnify_pipelines_toolkit/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 mgnify_pipelines_toolkit/utils/fasta_to_delimited.py,sha256=lgYIR1S4crURY7C7nFtgE6QMV4u4zCNsUrVkcRnsEEo,3996
 mgnify_pipelines_toolkit/utils/get_mpt_version.py,sha256=aS9bWrC9CP7tpxoEVg6eEYt18-pmjG7fJl5Mchz4YOU,798
-mgnify_pipelines_toolkit-1.2.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-mgnify_pipelines_toolkit-1.2.0.dist-info/METADATA,sha256=uTDvoF0oYy-1ApjeygcGbjipM9ZLt1tLArKA6xDNyl4,5807
-mgnify_pipelines_toolkit-1.2.0.dist-info/WHEEL,sha256=Nw36Djuh_5VDukK0H78QzOX-_FQEo6V37m3nkm96gtU,91
-mgnify_pipelines_toolkit-1.2.0.dist-info/entry_points.txt,sha256=JSjuxAr71MTeSUPPpno22wmZYgVO-gbsXfDkgWKkF7A,3533
-mgnify_pipelines_toolkit-1.2.0.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
-mgnify_pipelines_toolkit-1.2.0.dist-info/RECORD,,
+mgnify_pipelines_toolkit-1.2.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+mgnify_pipelines_toolkit-1.2.1.dist-info/METADATA,sha256=CIH7XH5WIzQMc0e2MfYFlWCnV1hokgYaQskYsfobzao,5775
+mgnify_pipelines_toolkit-1.2.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+mgnify_pipelines_toolkit-1.2.1.dist-info/entry_points.txt,sha256=d7r4_VUS1hWNMnTJOy8u2kTRSFcy-sDN5NLRUXz-IhU,3041
+mgnify_pipelines_toolkit-1.2.1.dist-info/top_level.txt,sha256=xA_wC7C01V3VwuDnqwRM2QYeJJ45WtvF6LVav4tYxuE,25
+mgnify_pipelines_toolkit-1.2.1.dist-info/RECORD,,

{mgnify_pipelines_toolkit-1.2.0.dist-info → mgnify_pipelines_toolkit-1.2.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.7.1)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{mgnify_pipelines_toolkit-1.2.0.dist-info → mgnify_pipelines_toolkit-1.2.1.dist-info}/entry_points.txt

@@ -2,17 +2,13 @@
 add_rhea_chebi_annotation = mgnify_pipelines_toolkit.analysis.assembly.add_rhea_chebi_annotation:main
 amplicon_study_summary_generator = mgnify_pipelines_toolkit.analysis.amplicon.study_summary_generator:cli
 antismash_gff_builder = mgnify_pipelines_toolkit.analysis.assembly.antismash_gff_builder:main
-are_there_primers = mgnify_pipelines_toolkit.analysis.amplicon.are_there_primers:main
 assembly_study_summary_generator = mgnify_pipelines_toolkit.analysis.assembly.study_summary_generator:cli
-assess_inflection_point_mcp = mgnify_pipelines_toolkit.analysis.amplicon.assess_inflection_point_mcp:main
-assess_mcp_proportions = mgnify_pipelines_toolkit.analysis.amplicon.assess_mcp_proportions:main
 classify_var_regions = mgnify_pipelines_toolkit.analysis.amplicon.classify_var_regions:main
 combined_gene_caller_merge = mgnify_pipelines_toolkit.analysis.assembly.combined_gene_caller_merge:main
 convert_cmscan_to_cmsearch_tblout = mgnify_pipelines_toolkit.analysis.shared.convert_cmscan_to_cmsearch_tblout:main
 dwc_summary_generator = mgnify_pipelines_toolkit.analysis.shared.dwc_summary_generator:main
 fasta_to_delimited = mgnify_pipelines_toolkit.utils.fasta_to_delimited:main
 fastq_suffix_header_check = mgnify_pipelines_toolkit.analysis.shared.fastq_suffix_header_check:main
-find_mcp_inflection_points = mgnify_pipelines_toolkit.analysis.amplicon.find_mcp_inflection_points:main
 generate_gaf = mgnify_pipelines_toolkit.analysis.assembly.generate_gaf:main
 genomes_extract_bacterial_rrnas_as_tsv = mgnify_pipelines_toolkit.analysis.genomes.rna.extract_bacterial_rrnas_as_tsv:main
 genomes_extract_rrnas_as_fasta = mgnify_pipelines_toolkit.analysis.genomes.rna.extract_rrnas_as_fasta:main
@@ -32,7 +28,6 @@ process_dbcan_cazys = mgnify_pipelines_toolkit.analysis.assembly.process_dbcan_r
 process_dbcan_clusters = mgnify_pipelines_toolkit.analysis.assembly.process_dbcan_result_clusters:main
 remove_ambiguous_reads = mgnify_pipelines_toolkit.analysis.amplicon.remove_ambiguous_reads:main
 rev_comp_se_primers = mgnify_pipelines_toolkit.analysis.amplicon.rev_comp_se_primers:main
-standard_primer_matching = mgnify_pipelines_toolkit.analysis.amplicon.standard_primer_matching:main
 summarise_antismash_bgcs = mgnify_pipelines_toolkit.analysis.assembly.summarise_antismash_bgcs:main
 summarise_goslims = mgnify_pipelines_toolkit.analysis.assembly.summarise_goslims:main
 summarise_sanntis_bgcs = mgnify_pipelines_toolkit.analysis.assembly.summarise_sanntis_bgcs:main

mgnify_pipelines_toolkit/analysis/amplicon/amplicon_utils.py

@@ -1,221 +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, Counter
-import logging
-import gzip
-import os
-import pyfastx
-
-from mgnify_pipelines_toolkit.constants.regex_ambiguous_bases import (
-    _AMBIGUOUS_BASES_DICT,
-    _AMBIGUOUS_BASES_DICT_REV,
-)
-
-logging.basicConfig(level=logging.DEBUG)
-
-
-def split_dir_into_sample_paths(dir):
-    file_list = os.listdir(dir)
-    file_list = [
-        file
-        for file in file_list
-        if ".fastq" in file and ("_1" in file or "_2" in file)
-    ]
-    sample_set = set()
-    [sample_set.add(f"{dir}/{file.split('_')[0]}") for file in file_list]
-    sample_list = sorted(list(sample_set))
-
-    return sample_list
-
-
-def get_read_count(read_path: str, file_type: str = "fastq") -> int:
-    """
-    Get the read count of a FASTQ or FASTA file.
-
-    :param read_path: The path to the FASTQ or FASTA file.
-    :type read_path: str
-    :param fasta_type: The type of the file, either "fastq" or "fasta". Defaults to "fastq".
-    :type fasta_type: str
-    :return: The number of reads in the file.
-    :rtype: int
-    :raises ValueError: If the file type is not supported or the read count is not a positive integer.
-    """
-    read_count = 0
-
-    if file_type == "fasta":
-        fasta = pyfastx.Fasta(read_path, build_index=False)
-        read_count = sum(1 for _ in fasta)
-    elif file_type == "fastq":
-        fastq = pyfastx.Fastq(read_path, build_index=False)
-        read_count = sum(1 for _ in fastq)
-    else:
-        raise ValueError(
-            f"Invalid file_type {file_type}, it needs to be either 'fasta' or 'fastq'"
-        )
-
-    if read_count <= 0:
-        raise ValueError(f"Read count is not a positive integer: {read_count}")
-
-    return read_count
-
-
-def build_cons_seq(
-    cons_list,
-    read_count,
-    cons_threshold=0.80,
-    do_not_include=None,
-    counter=1,
-    max_line_count=None,
-):
-    """
-    Generate consensus sequence using a list of base conservation dictionaries most likely
-    generated by the `build_mcp_cons_dict_list()` function.
-    Also returns a list containing the conservation value of the most conserved base at every
-    position in the list of base conservation dictionaries.
-    """
-
-    cons_seq = ""
-    cons_confs = []
-
-    if do_not_include is None:
-        do_not_include = []
-
-    for count_dict in cons_list:
-        max_count = 0
-        cons_dict = defaultdict(float)
-
-        if counter in do_not_include:
-            counter += 1
-            cons_seq += "N"
-            continue
-
-        for base, count in count_dict.items():
-            if base not in ("A", "T", "C", "G"):
-                continue
-
-            if max_line_count is None:
-                cons_dict[base] = count / read_count
-            else:
-                cons_dict[base] = count / max_line_count
-
-            if count > max_count:
-                max_count = count
-
-        counter += 1
-
-        try:
-            if max_line_count is None:
-                max_prop = max_count / read_count
-            else:
-                max_prop = max_count / max_line_count
-
-            cons_bases = []
-            curr_prop = 0.0
-            sorted_cons_dict = dict(
-                sorted(cons_dict.items(), key=lambda x: x[1], reverse=True)
-            )
-
-            for base, prop in sorted_cons_dict.items():
-                cons_bases.append(base)
-                curr_prop += prop
-                if curr_prop >= cons_threshold:
-                    break
-
-            cons_bases = sorted(cons_bases)
-
-            if len(cons_bases) == 1:
-                cons_seq += cons_bases[0]
-            else:
-                amb_string = ",".join(cons_bases)
-                amb_base = _AMBIGUOUS_BASES_DICT_REV[amb_string]
-                cons_seq += amb_base
-
-        except ZeroDivisionError:
-            max_prop = 0.0
-
-        cons_confs.append(max_prop)
-
-    return cons_seq, cons_confs
-
-
-def primer_regex_query_builder(primer):
-    """
-    Takes an input nucleotide sequence that can contain IUPAC ambiguous codes
-    Returns a string formatted as a regex query that considers the different
-    potential bases valid at a position with am abiguity code.
-    """
-
-    query = ""
-
-    for char in primer:
-        if char in ("A", "C", "T", "G"):
-            query += char
-        else:
-            query += str(_AMBIGUOUS_BASES_DICT[char])
-
-    query = f"(.*{query}){{e<=1}}"
-
-    return query
-
-
-def build_mcp_cons_dict_list(mcp_count_dict, mcp_len):
-    """
-    Generate list of dictionaries of base conservation for mcp output (mcp_cons_list)
-    e.g. [{'A':0.9, 'C':0.1}, {'T':1.0}, ....] for every base position
-    """
-
-    mcp_cons_list = []
-
-    for i in range(mcp_len):
-        index_base_dict = defaultdict(int)
-        for mcp in mcp_count_dict.keys():
-            if len(mcp) < mcp_len:
-                continue
-            base = mcp[i]
-            index_base_dict[base] += mcp_count_dict[mcp]
-        mcp_cons_list.append(index_base_dict)
-
-    return mcp_cons_list
-
-
-def fetch_mcp(fastq, prefix_len, start=1, rev=False, max_line_count=None):
-    """
-    Generates the most common prefix sequences along with their counts in a fastq file.
-    Outputs dictionary containing counts for each generated MCP in the fastq.
-    """
-
-    selected_lines = []
-
-    with gzip.open(fastq, "rt") as file:
-        for i, line in enumerate(file):
-            line = line.strip()
-            if i % 4 == 1:
-                if not rev:
-                    selected_lines.append(line[start - 1 : start + prefix_len - 1])
-                else:
-                    rev_line = line[::-1]
-                    selected_lines.append(rev_line[start - 1 : start + prefix_len - 1])
-            if max_line_count is not None:
-                if len(selected_lines) > max_line_count:
-                    break
-
-    sequence_counts = Counter(selected_lines)
-    mcp_count_dict = dict(
-        sorted(sequence_counts.items(), key=lambda x: x[1], reverse=True)
-    )
-
-    return mcp_count_dict

mgnify_pipelines_toolkit/analysis/amplicon/are_there_primers.py

@@ -1,164 +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
-
-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,
-)
-
-
-def parse_args(argv=None):
-    parser = argparse.ArgumentParser()
-
-    parser.add_argument(
-        "-i",
-        "--input",
-        required=True,
-        type=str,
-        help="Path to fastq file to check for primers",
-    )
-    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(argv)
-
-    path = args.input
-    sample = args.sample
-    output = args.output
-
-    return path, sample, output
-
-
-def are_there_primers_in_this_sample(path, rev=False):
-    """
-    Predict the presence of primers based on windows of base conservation.
-
-    Takes a fastq file as input. Extracts proportion of most common base for the first 100 bases.
-    Computes the a threshold (Q3 - 0.15) based on this proportion and counts the number of bases below
-    it in windows of 10 bases.
-    If at least one of the first two windows contains at most one such a base, then the presence of a primer is flagged as true.
-    A primer is also flagged as true if the combined count of bases below Q3 is at most 4.
-
-    The output of this function is a boolean flag:
-        True if a primer was identified
-        False if a primer was not identified
-    """
-
-    read_count = get_read_count(
-        path, file_type="fastq"
-    )  # Get read count for fastq file
-    mcp_len = 100  # Script will look at first 100 base mcps (for rev=True, it will look at first 100 from 3' to 5')
-
-    mcp_count_dict = fetch_mcp(
-        path, mcp_len, rev=rev
-    )  # mcp dict where key is the mcp and value is the count
-    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
-    )  # get list of max base conservations for each index
-
-    window_size = 10
-    # Counter that will reset to 0 every 10 bases
-    window_count = 0
-    # Will append the window count to this list every 10 bases
-    window_count_list = []
-    # Compute Q3-based threshold
-    max_cons = np.quantile(cons_confs, 0.75)
-    threshold = max_cons - 0.15
-
-    if max_cons < 0.75:
-        threshold = 0.75
-    # Immediately return false (no primer) if the max conservation is less than 0.6
-    if max_cons < 0.6:
-        return False
-
-    # Loop through every base
-    for i, val in enumerate(cons_confs):
-        if i % window_size == 0 and i != 0:  # After looping through a window..
-            window_count_list.append(window_count)  # ..append window count
-            window_count = 0  # ..reset window count
-
-        if (
-            val < threshold
-        ):  # If the conservation at i is less than threshold, increment count for the window
-            window_count += 1
-
-    primer_flag = False  # Initialise primer flag as false
-
-    if (
-        1 in window_count_list[:2] or 0 in window_count_list[:2]
-    ):  # If window count is at most 1 of first two windows...
-        primer_flag = True  # ..primer flag is true
-    elif (
-        sum(window_count_list[:2]) <= 4
-    ):  # If sum of window counts of the first two windows is at most 4..
-        primer_flag = True  # ..primer flag is true
-
-    return primer_flag
-
-
-def save_out(results, sample_id, output):
-    """
-    Save primer presence flags into output .txt file.
-
-    1: primer exists
-    0: primer doesn't exist
-
-    First line will be the forward strand
-    Second line will be the reverse strand
-    """
-
-    with open(f"{output}/{sample_id}_general_primer_out.txt", "w") as fw:
-        fw.write(f"{results[0]}\n")
-        fw.write(f"{results[1]}\n")
-
-
-def main(argv=None):
-    path, sample, output = parse_args(argv)
-
-    fwd_primer_flag = are_there_primers_in_this_sample(
-        path
-    )  # Check for general primers in fwd
-    rev_primer_flag = are_there_primers_in_this_sample(
-        path, rev=True
-    )  # Check for general primers in rev
-
-    fwd_status = "0"
-    rev_status = "0"
-    # Flag for primer presence: 1 for yes 0 for no
-    if fwd_primer_flag:
-        print("Forward primer detected!")
-        fwd_status = 1
-    else:
-        print("No forward primer detected")
-    if rev_primer_flag:
-        print("Reverse primer detected!")
-        rev_status = 1
-    else:
-        print("No reverse primer detected")
-
-    save_out((fwd_status, rev_status), sample, output)  # Save primer flags to .txt file
-
-
-if __name__ == "__main__":
-    main()