celescope 2.3.0.dev0__tar.gz → 2.3.0.dev2__tar.gz

{celescope-2.3.0.dev0/celescope.egg-info → celescope-2.3.0.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: celescope
-Version: 2.3.0.dev0
+Version: 2.3.0.dev2
 Summary: Single Cell Analysis Pipelines
 Home-page: https://github.com/singleron-RD/CeleScope
 Author: zhouyiqi

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope/__init__.py

@@ -1,6 +1,6 @@
 import os
 
-__VERSION__ = "2.3.0dev"
+__VERSION__ = "2.3.0dev2"
 __version__ = __VERSION__
 
 ASSAY_LIST = [

celescope-2.3.0.dev2/celescope/bulk_rna/starsolo.py

@@ -0,0 +1,286 @@
+import subprocess
+import sys
+
+import numpy as np
+import pandas as pd
+
+from celescope.__init__ import HELP_DICT
+from celescope.tools.__init__ import COUNTS_FILE_NAME
+from celescope.chemistry_dict import chemistry_dict
+from celescope.tools.emptydrop_cr import get_plot_elements
+from celescope.tools.starsolo import (
+    Demultiplexing,
+    Mapping,
+    create_solo_args,
+)
+from celescope.tools.starsolo import (
+    Starsolo as tools_Starsolo,
+)
+from celescope.tools.matrix import CountMatrix
+from celescope.tools import utils
+from celescope.tools.step import Step, s_common
+
+SAM_attributes = "NH HI nM AS CR UR CB UB GX GN "
+
+
+def get_well_barcode(
+    bc_file: str,
+) -> dict[int, str]:
+    barcodes = utils.one_col_to_list(bc_file)
+    return {i: x for i, x in enumerate(barcodes, start=1)}
+
+
+def get_barcode_sample(
+    bc_file: str,
+    well_sample_file: str,
+) -> dict[str, str]:
+    well_barcode = get_well_barcode(bc_file)
+    well_sample = utils.two_col_to_dict(well_sample_file)
+    barcode_sample = {
+        well_barcode[well]: sample for well, sample in well_sample.items()
+    }
+    return barcode_sample
+
+
+class Starsolo(tools_Starsolo):
+    def __init__(self, args, display_title=None):
+        super().__init__(args, display_title=display_title)
+        self.well_barcode = get_well_barcode(self.bc[0])
+        self.barcode_sample = get_barcode_sample(self.bc[0], args.well_sample)
+
+        self.tsv_matrix_file = f"{self.out_prefix}_matrix.tsv.gz"
+        self.outs.append(self.tsv_matrix_file)
+
+    def run_starsolo(self):
+        cmd = create_solo_args(
+            pattern_args=self.pattern_args,
+            whitelist_args=self.whitelist_args,
+            outFileNamePrefix=self.out_prefix + "_",
+            fq1=self.args.fq1,
+            fq2=self.args.fq2,
+            genomeDir=self.args.genomeDir,
+            soloCellFilter=self.args.soloCellFilter,
+            runThreadN=self.args.thread,
+            clip3pAdapterSeq=self.args.adapter_3p,
+            outFilterMatchNmin=self.args.outFilterMatchNmin,
+            soloFeatures=self.args.soloFeatures,
+            outSAMattributes=self.outSAMattributes,
+            soloCBmatchWLtype=self.args.soloCBmatchWLtype,
+            extra_starsolo_args=self.extra_starsolo_args,
+        )
+        if self.chemistry == "bulk_rna-bulk_vdj_match":
+            cmd += "--soloStrand Reverse \\\n"
+        sys.stderr.write(cmd)
+        subprocess.check_call(cmd, shell=True)
+        cmd = f"chmod -R 755 {self.solo_out_dir}"
+        sys.stderr.write(cmd)
+        subprocess.check_call(cmd, shell=True)
+
+    @utils.add_log
+    def keep_barcodes(self):
+        """take in raw matrix, only keep barcodes in the input file, and convert barcodes to sample names"""
+        matrix = CountMatrix.from_matrix_dir(self.raw_matrix)
+
+        for barcode in self.barcode_sample:
+            if barcode not in matrix.get_barcodes():
+                sys.stderr.write(
+                    f"WARNING: barcode:{barcode} {self.barcode_sample[barcode]} not found in raw matrix!\n"
+                )
+                self.barcode_sample.pop(barcode)
+        filtered = matrix.slice_matrix_bc(self.barcode_sample.keys())
+        filtered.to_matrix_dir(self.filtered_matrix)
+        samples = [self.barcode_sample[bc] for bc in filtered.get_barcodes()]
+        converted = CountMatrix(filtered.get_features(), samples, filtered.get_matrix())
+        df = converted.to_df()
+        df.to_csv(self.tsv_matrix_file, sep="\t")
+        return filtered
+
+    def run(self):
+        self.run_starsolo()
+        filtered = self.keep_barcodes()
+        self.gzip_matrix()
+        q30_cb, q30_umi = self.get_Q30_cb_UMI()
+        return q30_cb, q30_umi, filtered, self.barcode_sample, self.well_barcode
+
+
+class Cells(Step):
+    def __init__(self, args, display_title=None):
+        super().__init__(args, display_title=display_title)
+        solo_dir = f"{self.outdir}/{self.sample}_Solo.out/GeneFull_Ex50pAS"
+        self.summary_file = f"{solo_dir}/Summary.csv"
+        self.counts_file = f"{self.outs_dir}/{COUNTS_FILE_NAME}"
+
+    @utils.add_log
+    def parse_summary(self):
+        df = pd.read_csv(self.summary_file, index_col=0, header=None)
+        s = df.iloc[:, 0]
+        saturation = float(s["Sequencing Saturation"])
+        n_reads = int(s["Number of Reads"])
+        q30_RNA = float(s["Q30 Bases in RNA read"])
+
+        return n_reads, q30_RNA, saturation
+
+    def run(self, filtered: CountMatrix, barcode_sample: dict, well_barcode: dict):
+        df_counts = pd.read_csv(self.counts_file, index_col=0, header=0, sep="\t")
+        reads_total = df_counts["countedU"].sum()
+        bcs = filtered.get_barcodes()
+        n_cells = len(bcs)
+        reads_cell = df_counts.loc[bcs, "countedU"].sum()
+        fraction_reads_in_cells = float(reads_cell / reads_total)
+        mean_used_reads_per_cell = int(reads_cell // len(bcs))
+        median_umi_per_cell = int(df_counts.loc[bcs, "UMI"].median())
+
+        bc_geneNum, total_genes = filtered.get_bc_geneNum()
+        median_genes_per_cell = int(np.median(list(bc_geneNum.values())))
+
+        df_counts.loc[:, "mark"] = "UB"
+        df_counts.loc[bcs, "mark"] = "CB"
+        df_counts.to_csv(self.counts_file, sep="\t", index=True)
+
+        self.add_metric(
+            "Number of Wells",
+            n_cells,
+            help_info="number of barcodes with at least one UMI",
+        )
+        self.add_metric(
+            "Fraction of Reads in Wells",
+            fraction_reads_in_cells,
+            value_type="fraction",
+            help_info="Fraction of reads which were mapped to a barcode",
+        )
+        self.add_metric(
+            "Mean Reads per Well",
+            mean_used_reads_per_cell,
+            help_info="Mean number of reads per barcode",
+        )
+        self.add_metric(
+            "Median UMI per Well",
+            median_umi_per_cell,
+            help_info="Median UMI count per barcode",
+        )
+        self.add_metric(
+            "Median Genes per Well",
+            median_genes_per_cell,
+            help_info="Median number of genes per barcode",
+        )
+        self.add_data(chart=get_plot_elements.plot_barcode_rank(self.counts_file))
+
+        n_reads, q30_RNA, saturation = self.parse_summary()
+        self.add_metric(
+            "Saturation",
+            saturation,
+            value_type="fraction",
+            help_info="the fraction of read originating from an already-observed UMI.",
+        )
+
+        # table
+        df_cells = df_counts[df_counts["mark"] == "CB"]
+        df_cells["Sample"] = df_cells.index.map(lambda x: barcode_sample[x])
+        df_cells["Genes"] = df_cells.index.map(lambda x: bc_geneNum[x])
+        df_cells["Barcode"] = df_cells.index
+        barcode_well = {v: k for k, v in well_barcode.items()}
+        df_cells["Well"] = df_cells["Barcode"].map(lambda x: barcode_well[x])
+        df_cells = df_cells.loc[:, ["Well", "Sample", "Barcode", "UMI", "Genes"]]
+
+        table_dict = self.get_table_dict(
+            title="Metrics for a Single Well",
+            table_id=self.assay,
+            df_table=df_cells,
+        )
+        self.add_data(table_dict=table_dict)
+
+        return n_reads, q30_RNA
+
+
+def starsolo(args):
+    with Starsolo(args) as runner:
+        q30_cb, q30_umi, filtered, barcode_sample, well_barcode = runner.run()
+
+    with Mapping(args) as runner:
+        valid_reads, corrected = runner.run()
+
+    with Cells(args, display_title="Wells") as runner:
+        n_reads, q30_RNA = runner.run(filtered, barcode_sample, well_barcode)
+
+    with Demultiplexing(args) as runner:
+        runner.run(valid_reads, n_reads, corrected, q30_cb, q30_umi, q30_RNA)
+
+
+def get_opts_starsolo(parser, sub_program=True):
+    parser.add_argument(
+        "--chemistry",
+        help=HELP_DICT["chemistry"],
+        choices=list(chemistry_dict.keys()),
+        default="auto",
+    )
+    parser.add_argument(
+        "--pattern",
+        help="""The pattern of R1 reads, e.g. `C8L16C8L16C8L1U12T18`. The number after the letter represents the number 
+        of bases.  
+        - `C`: cell barcode  
+        - `L`: linker(common sequences)  
+        - `U`: UMI    
+        - `T`: poly T""",
+    )
+    parser.add_argument(
+        "--whitelist",
+        help="whitelist file path.",
+    )
+    parser.add_argument(
+        "--adapter_3p",
+        help="Adapter sequence to clip from 3 prime. Multiple sequences are seperated by space",
+        default="AAAAAAAAAAAA",
+    )
+    parser.add_argument(
+        "--genomeDir",
+        help=HELP_DICT["genomeDir"],
+    )
+    parser.add_argument(
+        "--outFilterMatchNmin",
+        help="""Alignment will be output only if the number of matched bases 
+is higher than or equal to this value.""",
+        default=50,
+    )
+    parser.add_argument(
+        "--soloCellFilter",
+        help="The same as the argument in STARsolo",
+        default="None",
+    )
+    parser.add_argument(
+        "--starMem", help="Maximum memory that STAR can use.", default=32
+    )
+    parser.add_argument("--STAR_param", help=HELP_DICT["additional_param"], default="")
+    parser.add_argument(
+        "--SAM_attributes",
+        help=f"Additional attributes(other than {SAM_attributes}) to be added to SAM file",
+        default="",
+    )
+    parser.add_argument(
+        "--soloFeatures",
+        help="The same as the argument in STARsolo",
+        default="GeneFull_Ex50pAS Gene",
+    )
+    parser.add_argument(
+        "--soloCBmatchWLtype",
+        help="The same as the argument in STARsolo. Please note `EditDist 2` only works with `--soloType CB UMI Complex`. ",
+        default="1MM",
+    )
+    parser.add_argument(
+        "--well_sample",
+        help="tsv file of well numbers and sample names. The first column is well numbers and the second column is sample names.",
+        required=True,
+    )
+    if sub_program:
+        parser.add_argument(
+            "--fq1",
+            help="R1 fastq file. Multiple files are separated by comma.",
+            required=True,
+        )
+        parser.add_argument(
+            "--fq2",
+            help="R2 fastq file. Multiple files are separated by comma.",
+            required=True,
+        )
+        parser = s_common(parser)
+
+    return parser

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope/chemistry_dict.py

@@ -7,7 +7,10 @@ chemistry_dict = {
     "customized": {
         "pattern": ""  # user defined
     },
-    "GEXSCOPE-MicroBead": {"pattern": "C12U8"},
+    "GEXSCOPE-MicroBead": {
+        "pattern": "C12U8",
+        "bc": [],
+    },
     "GEXSCOPE-V1": {
         "pattern": "C8L16C8L16C8L1U12",
         "bc": ["bc.txt", "bc.txt", "bc.txt"],

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope/templates/html/bulk_rna/base.html

@@ -12,7 +12,7 @@
 
     {% if cells_summary is defined%}
     {% set step_summary = cells_summary %}
-    {% include "html/rna/count.html" %}
+    {% include "html/bulk_rna/cells.html" %}
     {% endif %}
 
 

celescope-2.3.0.dev2/celescope/templates/html/bulk_rna/cells.html

@@ -0,0 +1,18 @@
+<div class="abc" style="float: left; margin-left: 15%; margin-right:15%; width: 70%" >
+    <h2>{{ step_summary.display_title}}    <i class="icon-help-circled" onClick="toggle1(this.parentNode.parentNode)" style="cursor:pointer;"></i></h2>
+    <div class="box">
+      {% include "html/utils/help_info.html" %}
+      {% include "html/utils/col1_metrics.html" %}
+  
+      <div id="myDivUMI" style="float: left; margin-left: 3%; margin-top: 1%;margin-right:0%; width: 47%">
+        {{ step_summary.chart|safe }}
+      </div>
+  
+      <div class="clear" ></div>
+    </div>
+  </div>
+
+<div class="abc" style="float: left; margin-left: 15%; margin-right:15%; width: 70%" >
+    {% include "html/utils/table_dict.html" %}
+    <div class="clear" ></div>
+</div>

celescope-2.3.0.dev2/celescope/templates/html/utils/table_script/bulk_rna.html

@@ -0,0 +1,10 @@
+<script>
+    $(document).ready(function () {
+        var table_id = {{ step_summary.table_dict['id']|safe }};
+        var table = $(table_id).DataTable({
+            dom: 'Bfrtip',
+            buttons: ['excel']
+        });
+        table.columns(0).order('asc').draw();
+    });
+</script>

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope/tools/matrix.py

@@ -234,9 +234,11 @@ class CountMatrix:
         gene_index, bc_index = self.__matrix.nonzero()
         total_genes = len(set(gene_index))
         bc_gene = defaultdict(set)
-        for gene, bc in zip(gene_index, bc_index):
-            bc_gene[bc].add(gene)
-        return {bc: len(bc_gene[bc]) for bc in bc_gene}, total_genes
+        for gene, bc_i in zip(gene_index, bc_index):
+            bc_gene[bc_i].add(gene)
+        return {
+            self.__barcodes[bc_i]: len(bc_gene[bc_i]) for bc_i in bc_gene
+        }, total_genes
 
     def get_barcodes(self):
         return self.__barcodes
@@ -271,3 +273,13 @@ class CountMatrix:
             matrix[barcode_indices[barcode], feature_indices[feature]] = count
 
         return matrix.tocsr()
+
+    def to_df(self, gene_id=True):
+        """
+        Returns:
+            df: pd.DataFrame
+        """
+        index = self.__features.gene_id if gene_id else self.__features.gene_name
+        return pd.DataFrame.sparse.from_spmatrix(
+            self.__matrix, index=index, columns=self.__barcodes
+        )

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope/tools/split_fastq.py

@@ -6,6 +6,7 @@ import celescope.tools.parse_chemistry as parse_chemistry
 import pysam
 from celescope.chemistry_dict import chemistry_dict
 from celescope.__init__ import HELP_DICT
+from celescope.bulk_rna.starsolo import get_barcode_sample
 
 
 UMI_SEPARATOR = ":"
@@ -17,7 +18,6 @@ class Split_fastq(Step):
 
         self.fq1_list = args.fq1.split(",")
         self.fq2_list = args.fq2.split(",")
-        self.barcodes = set(utils.one_col_to_list(args.barcodes))
 
         chemistry = parse_chemistry.get_chemistry(
             self.assay, args.chemistry, self.fq1_list
@@ -29,12 +29,14 @@ class Split_fastq(Step):
             parse_chemistry.create_mismatch_origin_dicts_from_whitelists(bc, 1)
         )
 
+        self.barcode_sample = get_barcode_sample(bc[0], args.well_sample)
+
     @utils.add_log
     def split(self):
         self.fh_dict = {}
-        for barcode in self.barcodes:
+        for barcode, sample in self.barcode_sample.items():
             self.fh_dict[barcode] = utils.generic_open(
-                f"{self.out_prefix}_{barcode}.fq.gz", "wt"
+                f"{self.outdir}/{sample}.fq.gz", "wt"
             )
 
         for fq1, fq2 in zip(self.fq1_list, self.fq2_list):
@@ -45,7 +47,7 @@ class Split_fastq(Step):
                 valid, corrected, corrected_bc = parse_chemistry.check_seq_mismatch(
                     bc_list, self.raw_list, self.mismatch_list
                 )
-                if valid and corrected_bc in self.barcodes:
+                if valid and corrected_bc in self.barcode_sample:
                     umi = e1.sequence[self.pattern_dict["U"][0]]
                     name = e1.name + UMI_SEPARATOR + umi
                     self.fh_dict[corrected_bc].write(
@@ -81,6 +83,11 @@ def get_opts_split_fastq(parser, sub_program):
         "--whitelist",
         help="Cell barcode whitelist file path, one cell barcode per line.",
     )
+    parser.add_argument(
+        "--well_sample",
+        help="tsv file of well numbers and sample names. The first column is well numbers and the second column is sample names.",
+        required=True,
+    )
     if sub_program:
         parser.add_argument(
             "--fq1",

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope/tools/utils.py

@@ -1,27 +1,27 @@
 import glob
 import gzip
 import importlib
+import json
 import logging
 import os
 import re
 import subprocess
+import sys
 import time
 import unittest
-import json
-import sys
-from collections import Counter, defaultdict
+from collections import Counter, OrderedDict, defaultdict
 from datetime import timedelta
 from functools import wraps
 
 import pandas as pd
 import pysam
 
+from celescope.__init__ import ROOT_PATH
 from celescope.tools.__init__ import (
-    FILTERED_MATRIX_DIR_SUFFIX,
     BARCODE_FILE_NAME,
+    FILTERED_MATRIX_DIR_SUFFIX,
     OUTS_DIR,
 )
-from celescope.__init__ import ROOT_PATH
 
 
 def add_log(func):
@@ -160,6 +160,16 @@ def one_col_to_list(file) -> list:
     return [item.strip() for item in col1]
 
 
+def two_col_to_dict(file):
+    """
+    Read file with two columns.
+    Returns dict
+    """
+    df = pd.read_csv(file, header=None, sep="\t")
+    df = df.dropna()
+    return OrderedDict(zip(df[0], df[1]))
+
+
 def get_bed_file_path(panel):
     bed_file_path = f"{ROOT_PATH}/data/snp/panel/{panel}.bed"
     if not os.path.exists(bed_file_path):

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2/celescope.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: celescope
-Version: 2.3.0.dev0
+Version: 2.3.0.dev2
 Summary: Single Cell Analysis Pipelines
 Home-page: https://github.com/singleron-RD/CeleScope
 Author: zhouyiqi

{celescope-2.3.0.dev0 → celescope-2.3.0.dev2}/celescope.egg-info/SOURCES.txt

@@ -149,6 +149,7 @@ celescope/templates/css/fontello-323401c3/font/fontello.ttf
 celescope/templates/css/fontello-323401c3/font/fontello.woff
 celescope/templates/css/fontello-323401c3/font/fontello.woff2
 celescope/templates/html/bulk_rna/base.html
+celescope/templates/html/bulk_rna/cells.html
 celescope/templates/html/bulk_vdj/base.html
 celescope/templates/html/bulk_vdj/count_vdj.html
 celescope/templates/html/capture_rna/base.html

celescope-2.3.0.dev0/celescope/bulk_rna/starsolo.py

@@ -1,135 +0,0 @@
-import subprocess
-import sys
-from celescope.tools.starsolo import (
-    Starsolo as tools_Starsolo,
-    create_solo_args,
-    Mapping,
-    Cells,
-    Demultiplexing,
-)
-from celescope.tools.step import s_common
-from celescope.__init__ import HELP_DICT
-from celescope.chemistry_dict import chemistry_dict
-
-SAM_attributes = "NH HI nM AS CR UR CB UB GX GN "
-
-
-class Starsolo(tools_Starsolo):
-    def __init__(self, args, display_title=None):
-        super().__init__(args, display_title=display_title)
-
-    def run_starsolo(self):
-        cmd = create_solo_args(
-            pattern_args=self.pattern_args,
-            whitelist_args=self.whitelist_args,
-            outFileNamePrefix=self.out_prefix + "_",
-            fq1=self.args.fq1,
-            fq2=self.args.fq2,
-            genomeDir=self.args.genomeDir,
-            soloCellFilter=self.args.soloCellFilter,
-            runThreadN=self.args.thread,
-            clip3pAdapterSeq=self.args.adapter_3p,
-            outFilterMatchNmin=self.args.outFilterMatchNmin,
-            soloFeatures=self.args.soloFeatures,
-            outSAMattributes=self.outSAMattributes,
-            soloCBmatchWLtype=self.args.soloCBmatchWLtype,
-            extra_starsolo_args=self.extra_starsolo_args,
-        )
-        if self.chemistry == "bulk_rna-bulk_vdj_match":
-            cmd += "--soloStrand Reverse \\\n"
-        sys.stderr.write(cmd)
-        subprocess.check_call(cmd, shell=True)
-        cmd = f"chmod -R 755 {self.solo_out_dir}"
-        sys.stderr.write(cmd)
-        subprocess.check_call(cmd, shell=True)
-
-
-def starsolo(args):
-    with Starsolo(args) as runner:
-        q30_cb, q30_umi, chemistry = runner.run()
-
-    with Mapping(args) as runner:
-        valid_reads, corrected = runner.run()
-
-    with Cells(args) as runner:
-        n_reads, q30_RNA = runner.run(chemistry, valid_reads)
-
-    with Demultiplexing(args) as runner:
-        runner.run(valid_reads, n_reads, corrected, q30_cb, q30_umi, q30_RNA)
-
-
-def get_opts_starsolo(parser, sub_program=True):
-    parser.add_argument(
-        "--chemistry",
-        help=HELP_DICT["chemistry"],
-        choices=list(chemistry_dict.keys()),
-        default="auto",
-    )
-    parser.add_argument(
-        "--pattern",
-        help="""The pattern of R1 reads, e.g. `C8L16C8L16C8L1U12T18`. The number after the letter represents the number 
-        of bases.  
-        - `C`: cell barcode  
-        - `L`: linker(common sequences)  
-        - `U`: UMI    
-        - `T`: poly T""",
-    )
-    parser.add_argument(
-        "--whitelist",
-        help="Cell barcode whitelist file path, one cell barcode per line. Multiple whitelist files are seperated by space.",
-    )
-    parser.add_argument(
-        "--adapter_3p",
-        help="Adapter sequence to clip from 3 prime. Multiple sequences are seperated by space",
-        default="AAAAAAAAAAAA",
-    )
-    parser.add_argument(
-        "--genomeDir",
-        help=HELP_DICT["genomeDir"],
-    )
-    parser.add_argument(
-        "--outFilterMatchNmin",
-        help="""Alignment will be output only if the number of matched bases 
-is higher than or equal to this value.""",
-        default=50,
-    )
-    # 96 wells
-    parser.add_argument(
-        "--soloCellFilter",
-        help="The same as the argument in STARsolo",
-        default="CellRanger2.2 384 0.99 10",
-    )
-    parser.add_argument(
-        "--starMem", help="Maximum memory that STAR can use.", default=32
-    )
-    parser.add_argument("--STAR_param", help=HELP_DICT["additional_param"], default="")
-    parser.add_argument(
-        "--SAM_attributes",
-        help=f"Additional attributes(other than {SAM_attributes}) to be added to SAM file",
-        default="",
-    )
-    parser.add_argument(
-        "--soloFeatures",
-        help="The same as the argument in STARsolo",
-        default="GeneFull_Ex50pAS Gene",
-    )
-    parser.add_argument(
-        "--soloCBmatchWLtype",
-        help="The same as the argument in STARsolo. Please note `EditDist 2` only works with `--soloType CB UMI Complex`. ",
-        default="1MM",
-    )
-
-    if sub_program:
-        parser.add_argument(
-            "--fq1",
-            help="R1 fastq file. Multiple files are separated by comma.",
-            required=True,
-        )
-        parser.add_argument(
-            "--fq2",
-            help="R2 fastq file. Multiple files are separated by comma.",
-            required=True,
-        )
-        parser = s_common(parser)
-
-    return parser

celescope-2.3.0.dev0/celescope/templates/html/utils/table_script/bulk_rna.html

@@ -1,32 +0,0 @@
-<script>
-
-    $(document).ready(function () {
-            var table = $('#bulk_rna').DataTable({
-                dom: 'Bfrtip',
-                buttons: ['excel'],
-                "aaSorting": []
-            });
-            var indexOfMyCol = 0 ;
-            var collator = new Intl.Collator(undefined, {numeric: true, sensitivity: 'base'});
-    $("#bulk_rna  thead th").each( function ( i ) {
-        if (i==indexOfMyCol){
-
-          var select = $('<select><option value=""></option></select>')
-            .appendTo( $(this).empty() )
-            .on( 'change', function () {
-                var pattern = ""
-                if ($(this).val()!="") {
-                    pattern= pattern="^"+$(this).val() +"$"
-                }
-                table.column( i )
-                .search(input=pattern, regex=true, smart=false)
-                .draw();
-            } );
- 
-        table.column( i).data().unique().sort(collator.compare).each( function ( d, j ) {
-            select.append( '<option value="'+d+'">'+d+'</option>' )
-        } );
-    }
-    } );
-    });
-</script>