levseq 1.0.0__py3-none-any.whl

levseq/barcoding/minion_barcodes.fasta

@@ -0,0 +1,386 @@
+>NB01
+CACAAAGACACCGACAACTTTCTT
+>NB02
+ACAGACGACTACAAACGGAATCGA
+>NB03
+CCTGGTAACTGGGACACAAGACTC
+>NB04
+TAGGGAAACACGATAGAATCCGAA
+>NB05
+AAGGTTACACAAACCCTGGACAAG
+>NB06
+GACTACTTTCTGCCTTTGCGAGAA
+>NB07
+AAGGATTCATTCCCACGGTAACAC
+>NB08
+ACGTAACTTGGTTTGTTCCCTGAA
+>NB09
+AACCAAGACTCGCTGTGCCTAGTT
+>NB10
+GAGAGGACAAAGGTTTCAACGCTT
+>NB11
+TCCATTCCCTCCGATAGATGAAAC
+>NB12
+TCCGATTCTGCTTCTTTCTACCTG
+>NB13
+AGAACGACTTCCATACTCGTGTGA
+>NB14
+AACGAGTCTCTTGGGACCCATAGA
+>NB15
+AGGTCTACCTCGCTAACACCACTG
+>NB16
+CGTCAACTGACAGTGGTTCGTACT
+>NB17
+ACCCTCCAGGAAAGTACCTCTGAT
+>NB18
+CCAAACCCAACAACCTAGATAGGC
+>NB19
+GTTCCTCGTGCAGTGTCAAGAGAT
+>NB20
+TTGCGTCCTGTTACGAGAACTCAT
+>NB21
+GAGCCTCTCATTGTCCGTTCTCTA
+>NB22
+ACCACTGCCATGTATCAAAGTACG
+>NB23
+CTTACTACCCAGTGAACCTCCTCG
+>NB24
+GCATAGTTCTGCATGATGGGTTAG
+>NB25
+GTAAGTTGGGTATGCAACGCAATG
+>NB26
+CATACAGCGACTACGCATTCTCAT
+>NB27
+CGACGGTTAGATTCACCTCTTACA
+>NB28
+TGAAACCTAAGAAGGCACCGTATC
+>NB29
+CTAGACACCTTGGGTTGACAGACC
+>NB30
+TCAGTGAGGATCTACTTCGACCCA
+>NB31
+TGCGTACAGCAATCAGTTACATTG
+>NB32
+CCAGTAGAAGTCCGACAACGTCAT
+>NB33
+CAGACTTGGTACGGTTGGGTAACT
+>NB34
+GGACGAAGAACTCAAGTCAAAGGC
+>NB35
+CTACTTACGAAGCTGAGGGACTGC
+>NB36
+ATGTCCCAGTTAGAGGAGGAAACA
+>NB37
+GCTTGCGATTGATGCTTAGTATCA
+>NB38
+ACCACAGGAGGACGATACAGAGAA
+>NB39
+CCACAGTGTCAACTAGAGCCTCTC
+>NB40
+TAGTTTGGATGACCAAGGATAGCC
+>NB41
+GGAGTTCGTCCAGAGAAGTACACG
+>NB42
+CTACGTGTAAGGCATACCTGCCAG
+>NB43
+CTTTCGTTGTTGACTCGACGGTAG
+>NB44
+AGTAGAAAGGGTTCCTTCCCACTC
+>NB45
+GATCCAACAGAGATGCCTTCAGTG
+>NB46
+GCTGTGTTCCACTTCATTCTCCTG
+>NB47
+GTGCAACTTTCCCACAGGTAGTTC
+>NB48
+CATCTGGAACGTGGTACACCTGTA
+>NB49
+ACTGGTGCAGCTTTGAACATCTAG
+>NB50
+ATGGACTTTGGTAACTTCCTGCGT
+>NB51
+GTTGAATGAGCCTACTGGGTCCTC
+>NB52
+TGAGAGACAAGATTGTTCGTGGAC
+>NB53
+AGATTCAGACCGTCTCATGCAAAG
+>NB54
+CAAGAGCTTTGACTAAGGAGCATG
+>NB55
+TGGAAGATGAGACCCTGATCTACG
+>NB56
+TCACTACTCAACAGGTGGCATGAA
+>NB57
+GCTAGGTCAATCTCCTTCGGAAGT
+>NB58
+CAGGTTACTCCTCCGTGAGTCTGA
+>NB59
+TCAATCAAGAAGGGAAAGCAAGGT
+>NB60
+CATGTTCAACCAAGGCTTCTATGG
+>NB61
+AGAGGGTACTATGTGCCTCAGCAC
+>NB62
+CACCCACACTTACTTCAGGACGTA
+>NB63
+TTCTGAAGTTCCTGGGTCTTGAAC
+>NB64
+GACAGACACCGTTCATCGACTTTC
+>NB65
+TTCTCAGTCTTCCTCCAGACAAGG
+>NB66
+CCGATCCTTGTGGCTTCTAACTTC
+>NB67
+GTTTGTCATACTCGTGTGCTCACC
+>NB68
+GAATCTAAGCAAACACGAAGGTGG
+>NB69
+TACAGTCCGAGCCTCATGTGATCT
+>NB70
+ACCGAGATCCTACGAATGGAGTGT
+>NB71
+CCTGGGAGCATCAGGTAGTAACAG
+>NB72
+TAGCTGACTGTCTTCCATACCGAC
+>NB73
+AAGAAACAGGATGACAGAACCCTC
+>NB74
+TACAAGCATCCCAACACTTCCACT
+>NB75
+GACCATTGTGATGAACCCTGTTGT
+>NB76
+ATGCTTGTTACATCAACCCTGGAC
+>NB77
+CGACCTGTTTCTCAGGGATACAAC
+>NB78
+AACAACCGAACCTTTGAATCAGAA
+>NB79
+TCTCGGAGATAGTTCTCACTGCTG
+>NB80
+CGGATGAACATAGGATAGCGATTC
+>NB81
+CCTCATCTTGTGAAGTTGTTTCGG
+>NB82
+ACGGTATGTCGAGTTCCAGGACTA
+>NB83
+TGGCTTGATCTAGGTAAGGTCGAA
+>NB84
+GTAGTGGACCTAGAACCTGTGCCA
+>NB85
+AACGGAGGAGTTAGTTGGATGATC
+>NB86
+AGGTGATCCCAACAAGCGTAAGTA
+>NB87
+TACATGCTCCTGTTGTTAGGGAGG
+>NB88
+TCTTCTACTACCGATCCGAAGCAG
+>NB89
+ACAGCATCAATGTTTGGCTAGTTG
+>NB90
+GATGTAGAGGGTACGGTTTGAGGC
+>NB91
+GGCTCCATAGGAACTCACGCTACT
+>NB92
+TTGTGAGTGGAAAGATACAGGACC
+>NB93
+AGTTTCCATCACTTCAGACTTGGG
+>NB94
+GATTGTCCTCAAACTGCCACCTAC
+>NB95
+CCTGTCTGGAAGAAGAATGGACTT
+>NB96
+CTGAACGGTCATAGAGTCCACCAT
+
+>RB01
+AAGAAAGTTGTCGGTGTCTTTGTG
+>RB02
+TCGATTCCGTTTGTAGTCGTCTGT
+>RB03
+GAGTCTTGTGTCCCAGTTACCAGG
+>RB04
+TTCGGATTCTATCGTGTTTCCCTA
+>RB05
+CTTGTCCAGGGTTTGTGTAACCTT
+>RB06
+TTCTCGCAAAGGCAGAAAGTAGTC
+>RB07
+GTGTTACCGTGGGAATGAATCCTT
+>RB08
+TTCAGGGAACAAACCAAGTTACGT
+>RB09
+AACTAGGCACAGCGAGTCTTGGTT
+>RB10
+AAGCGTTGAAACCTTTGTCCTCTC
+>RB11
+GTTTCATCTATCGGAGGGAATGGA
+>RB12
+CAGGTAGAAAGAAGCAGAATCGGA
+>RB13
+AGAACGACTTCCATACTCGTGTGA
+>RB14
+AACGAGTCTCTTGGGACCCATAGA
+>RB15
+AGGTCTACCTCGCTAACACCACTG
+>RB16
+CGTCAACTGACAGTGGTTCGTACT
+>RB17
+ACCCTCCAGGAAAGTACCTCTGAT
+>RB18
+CCAAACCCAACAACCTAGATAGGC
+>RB19
+GTTCCTCGTGCAGTGTCAAGAGAT
+>RB20
+TTGCGTCCTGTTACGAGAACTCAT
+>RB21
+GAGCCTCTCATTGTCCGTTCTCTA
+>RB22
+ACCACTGCCATGTATCAAAGTACG
+>RB23
+CTTACTACCCAGTGAACCTCCTCG
+>RB24
+GCATAGTTCTGCATGATGGGTTAG
+>RB25
+GTAAGTTGGGTATGCAACGCAATG
+>RB26
+ACTATGCCTTTCCGTGAAACAGTT
+>RB27
+CGACGGTTAGATTCACCTCTTACA
+>RB28
+TGAAACCTAAGAAGGCACCGTATC
+>RB29
+CTAGACACCTTGGGTTGACAGACC
+>RB30
+TCAGTGAGGATCTACTTCGACCCA
+>RB31
+TGCGTACAGCAATCAGTTACATTG
+>RB32
+CCAGTAGAAGTCCGACAACGTCAT
+>RB33
+CAGACTTGGTACGGTTGGGTAACT
+>RB34
+GGACGAAGAACTCAAGTCAAAGGC
+>RB35
+CTACTTACGAAGCTGAGGGACTGC
+>RB36
+ATGTCCCAGTTAGAGGAGGAAACA
+>RB37
+GCTTGCGATTGATGCTTAGTATCA
+>RB38
+ACCACAGGAGGACGATACAGAGAA
+>RB39
+TCTGCCACACACTCGTAAGTCCTT
+>RB40
+GTCGATACTGGACCTATCCCTTGG
+>RB41
+GGAGTTCGTCCAGAGAAGTACACG
+>RB42
+CTACGTGTAAGGCATACCTGCCAG
+>RB43
+CTTTCGTTGTTGACTCGACGGTAG
+>RB44
+AGTAGAAAGGGTTCCTTCCCACTC
+>RB45
+GATCCAACAGAGATGCCTTCAGTG
+>RB46
+GCTGTGTTCCACTTCATTCTCCTG
+>RB47
+GTGCAACTTTCCCACAGGTAGTTC
+>RB48
+GAGTCCGTGACAACTTCTGAAAGC
+>RB49
+ACTGGTGCAGCTTTGAACATCTAG
+>RB50
+ATGGACTTTGGTAACTTCCTGCGT
+>RB51
+GTTGAATGAGCCTACTGGGTCCTC
+>RB52
+TGAGAGACAAGATTGTTCGTGGAC
+>RB53
+AGATTCAGACCGTCTCATGCAAAG
+>RB54
+GGGTGCCAACTACATACCAAACCT
+>RB55
+TGGAAGATGAGACCCTGATCTACG
+>RB56
+TCACTACTCAACAGGTGGCATGAA
+>RB57
+GCTAGGTCAATCTCCTTCGGAAGT
+>RB58
+CAGGTTACTCCTCCGTGAGTCTGA
+>RB59
+TCAATCAAGAAGGGAAAGCAAGGT
+>RB60
+GAACCCTACTTTGGACAGACACCT
+>RB61
+AGAGGGTACTATGTGCCTCAGCAC
+>RB62
+CACCCACACTTACTTCAGGACGTA
+>RB63
+TTCTGAAGTTCCTGGGTCTTGAAC
+>RB64
+GACAGACACCGTTCATCGACTTTC
+>RB65
+TTCTCAGTCTTCCTCCAGACAAGG
+>RB66
+CCGATCCTTGTGGCTTCTAACTTC
+>RB67
+GTTTGTCATACTCGTGTGCTCACC
+>RB68
+GAATCTAAGCAAACACGAAGGTGG
+>RB69
+TACAGTCCGAGCCTCATGTGATCT
+>RB70
+ACCGAGATCCTACGAATGGAGTGT
+>RB71
+CCTGGGAGCATCAGGTAGTAACAG
+>RB72
+TAGCTGACTGTCTTCCATACCGAC
+>RB73
+AAGAAACAGGATGACAGAACCCTC
+>RB74
+TACAAGCATCCCAACACTTCCACT
+>RB75
+GACCATTGTGATGAACCCTGTTGT
+>RB76
+ATGCTTGTTACATCAACCCTGGAC
+>RB77
+CGACCTGTTTCTCAGGGATACAAC
+>RB78
+AACAACCGAACCTTTGAATCAGAA
+>RB79
+TCTCGGAGATAGTTCTCACTGCTG
+>RB80
+CGGATGAACATAGGATAGCGATTC
+>RB81
+CCTCATCTTGTGAAGTTGTTTCGG
+>RB82
+ACGGTATGTCGAGTTCCAGGACTA
+>RB83
+TGGCTTGATCTAGGTAAGGTCGAA
+>RB84
+GTAGTGGACCTAGAACCTGTGCCA
+>RB85
+AACGGAGGAGTTAGTTGGATGATC
+>RB86
+AGGTGATCCCAACAAGCGTAAGTA
+>RB87
+TACATGCTCCTGTTGTTAGGGAGG
+>RB88
+TCTTCTACTACCGATCCGAAGCAG
+>RB89
+ACAGCATCAATGTTTGGCTAGTTG
+>RB90
+GATGTAGAGGGTACGGTTTGAGGC
+>RB91
+GGCTCCATAGGAACTCACGCTACT
+>RB92
+TTGTGAGTGGAAAGATACAGGACC
+>RB93
+AGTTTCCATCACTTCAGACTTGGG
+>RB94
+GATTGTCCTCAAACTGCCACCTAC
+>RB95
+CCTGTCTGGAAGAAGAATGGACTT
+>RB96
+CTGAACGGTCATAGAGTCCACCAT
+

levseq/basecaller.py

@@ -0,0 +1,80 @@
+###############################################################################
+#                                                                             #
+#    This program is free software: you can redistribute it and/or modify     #
+#    it under the terms of the GNU General Public License as published by     #
+#    the Free Software Foundation, either version 3 of the License, or        #
+#    (at your option) any later version.                                      #
+#                                                                             #
+#    This program is distributed in the hope that it will be useful,          #
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of           #
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            #
+#    GNU General Public License for more details.                             #
+#                                                                             #
+#    You should have received a copy of the GNU General Public License        #
+#    along with this program. If not, see <http://www.gnu.org/licenses/>.     #
+#                                                                             #
+###############################################################################
+
+from levseq.globals import DORADO_MODELS
+import os
+import glob
+import subprocess
+
+
+class Basecaller:
+
+    def __init__(self, model, file_folder, save_folder, fastq = True):
+        self.model = model
+        self.file_folder = file_folder
+        self.save_folder = save_folder
+        self.fastq = fastq
+        self.model_path = self.check_model()
+
+    def check_model(self):
+        """Checks if the required dorado model is downloaded."""
+
+        model_path = os.path.join(os.path.dirname(__file__), "dorado_models")
+
+        # Check if model already exists
+        models = glob.glob(model_path + "/*")
+        if DORADO_MODELS[self.model] in models:
+            return os.path.join(model_path, DORADO_MODELS[self.model])
+        
+        else:
+            self.download_model()
+            model_path = os.path.join(model_path, DORADO_MODELS[self.model])
+
+        return model_path
+    
+    def download_model(self):
+        """Downloads the required dorado model."""
+        model = DORADO_MODELS[self.model]
+        
+        input = f"dorado download --model {model} --directory {self.model_path}"
+        subprocess.run(input, shell=True)
+        return "Model downloaded."
+    
+    def run_dorado(self):
+        """
+        Runs dorado basecaller.
+
+        Args: 
+            - .pod5 files
+        Returns: 
+            - .bam files
+        """
+
+        model_path = self.check_model()
+
+        if self.fastq:
+            input = f"dorado basecaller {model_path} {self.file_folder} --emit-fastq > {self.save_folder}/basecalled.fastq"
+        
+        else:
+            input = f"dorado basecaller {model_path} {self.file_folder} > {self.save_folder}/basecalled.fastq"
+
+        subprocess.run(input, shell=True)
+        
+        return "Basecalling submitted"
+
+
+

levseq/cmd.py

@@ -0,0 +1,23 @@
+###############################################################################
+#                                                                             #
+#    This program is free software: you can redistribute it and/or modify     #
+#    it under the terms of the GNU General Public License as published by     #
+#    the Free Software Foundation, either version 3 of the License, or        #
+#    (at your option) any later version.                                      #
+#                                                                             #
+#    This program is distributed in the hope that it will be useful,          #
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of           #
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            #
+#    GNU General Public License for more details.                             #
+#                                                                             #
+#    You should have received a copy of the GNU General Public License        #
+#    along with this program. If not, see <http://www.gnu.org/licenses/>.     #
+#                                                                             #
+###############################################################################
+
+from levseq.interface import execute_LevSeq
+def main():
+    execute_LevSeq()
+                
+if __name__ == "__main__":
+    main()

levseq/globals.py

@@ -0,0 +1,66 @@
+###############################################################################
+#                                                                             #
+#    This program is free software: you can redistribute it and/or modify     #
+#    it under the terms of the GNU General Public License as published by     #
+#    the Free Software Foundation, either version 3 of the License, or        #
+#    (at your option) any later version.                                      #
+#                                                                             #
+#    This program is distributed in the hope that it will be useful,          #
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of           #
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            #
+#    GNU General Public License for more details.                             #
+#                                                                             #
+#    You should have received a copy of the GNU General Public License        #
+#    along with this program. If not, see <http://www.gnu.org/licenses/>.     #
+#                                                                             #
+###############################################################################
+
+# Global parameters for minIon
+
+# Parameter for Demultiplexing
+SCORE_MATRIX = {
+    ('A', 'A'): 96, ('A', 'C'): -316, ('A', 'G'): -192, ('A', 'T'): -369, ('A', 'N'): 0,
+    ('C', 'A'): -316, ('C', 'C'): 100, ('C', 'G'): -352, ('C', 'T'): -295, ('C', 'N'): 0,
+    ('G', 'A'): -192, ('G', 'C'): -352, ('G', 'G'): 98, ('G', 'T'): -329, ('G', 'N'): 0,
+    ('T', 'A'): -369, ('T', 'C'): -295, ('T', 'G'): -329, ('T', 'T'): 100, ('T', 'N'): 0,
+    ('N', 'A'): 0, ('N', 'C'): 0, ('N', 'G'): 0, ('N', 'T'): 0, ('N', 'N'): 0,
+}  # Adapted from Guppy Barcoder
+
+SW_ALIGN_PARAMS = {
+    "start_gap1": 40,
+    "end_gap1": 40,
+    "open_gap1": 0,
+    "extend_gap1": -40,
+    "start_gap2": 40,
+    "end_gap2": 40,
+    "open_gap2": -160,
+    "extend_gap2": -160,
+    "min_score_barcode_front": 60.0,
+    "front_window_size": 150,
+    "rear_window_size": 150,
+}  # Adapted from Guppy Barcoder
+
+
+# Defaul target folder names from ONT
+DEFAULT_TARGETS = {"Not_basecalled": ["pod5"], "Basecalled": ["fastq_pass"]}
+
+
+# Codons
+CODONS = {
+    'ATA': 'I', 'ATC': 'I', 'ATT': 'I', 'ATG': 'M',
+    'ACA': 'T', 'ACC': 'T', 'ACG': 'T', 'ACT': 'T',
+    'AAC': 'N', 'AAT': 'N', 'AAA': 'K', 'AAG': 'K',
+    'AGC': 'S', 'AGT': 'S', 'AGA': 'R', 'AGG': 'R',
+    'CTA': 'L', 'CTC': 'L', 'CTG': 'L', 'CTT': 'L',
+    'CCA': 'P', 'CCC': 'P', 'CCG': 'P', 'CCT': 'P',
+    'CAC': 'H', 'CAT': 'H', 'CAA': 'Q', 'CAG': 'Q',
+    'CGA': 'R', 'CGC': 'R', 'CGG': 'R', 'CGT': 'R',
+    'GTA': 'V', 'GTC': 'V', 'GTG': 'V', 'GTT': 'V',
+    'GCA': 'A', 'GCC': 'A', 'GCG': 'A', 'GCT': 'A',
+    'GAC': 'D', 'GAT': 'D', 'GAA': 'E', 'GAG': 'E',
+    'GGA': 'G', 'GGC': 'G', 'GGG': 'G', 'GGT': 'G',
+    'TCA': 'S', 'TCC': 'S', 'TCG': 'S', 'TCT': 'S',
+    'TTC': 'F', 'TTT': 'F', 'TTA': 'L', 'TTG': 'L',
+    'TAC': 'Y', 'TAT': 'Y', 'TAA': '_', 'TAG': '_',
+    'TGC': 'C', 'TGT': 'C', 'TGA': '_', 'TGG': 'W',
+}

levseq/interface.py

@@ -0,0 +1,85 @@
+###############################################################################
+#                                                                             #
+#    This program is free software: you can redistribute it and/or modify     #
+#    it under the terms of the GNU General Public License as published by     #
+#    the Free Software Foundation, either version 3 of the License, or        #
+#    (at your option) any later version.                                      #
+#                                                                             #
+#    This program is distributed in the hope that it will be useful,          #
+#    but WITHOUT ANY WARRANTY; without even the implied warranty of           #
+#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the            #
+#    GNU General Public License for more details.                             #
+#                                                                             #
+#    You should have received a copy of the GNU General Public License        #
+#    along with this program. If not, see <http://www.gnu.org/licenses/>.     #
+#                                                                             #
+###############################################################################
+"""
+Contain argument parsers used for command line interface and web interface
+"""
+# Import packages
+import os
+import tqdm
+import argparse
+# Import local packages
+from levseq.run_levseq import run_LevSeq
+
+# Get the working directory
+CWD = os.getcwd()
+
+# Set default arguments 
+padding_start = 0
+padding_end = 0
+min_depth = 5
+threshold = 0.2
+basecall_model = 'sup'
+
+
+# Build the CLI argparser
+def build_cli_parser():
+    # Initialize
+    parser = argparse.ArgumentParser()
+
+    # Add required arguments
+    required_args_group = parser.add_argument_group("Required Arguments", "Arguments required for each run")
+    required_args_group.add_argument('name',
+            help = 'User defined name for the output folder')
+    required_args_group.add_argument("path",
+            help="Path to folder containing fastq.pass or pod5_pass files.")
+    required_args_group.add_argument("summary",
+            help="CSV file containig barcodes used, name of each plate and reference sequence in string")
+    # Add optional arguments
+    optional_args_group = parser.add_argument_group("Optional Arguments", "Aditional arguments")
+    optional_args_group.add_argument("--output",
+                                     help="Save location for run. Defaults to current working directory.",
+                                     required=False,
+                                     default=CWD)
+    optional_args_group.add_argument("--perform_basecalling",
+                                     action="store_true",
+                                     help="Skip the basecalling step, default is false")
+    optional_args_group.add_argument("--skip_demultiplexing",
+                                     action="store_true",
+                                     help="Skip the demultiplexing step, default is false")
+    optional_args_group.add_argument("--skip_variantcalling",
+                                     action="store_true",
+                                     help="Skip the variant calling step, default is false")
+    optional_args_group.add_argument("--show_msa",
+                                     default=False,
+                                     help="Skip showing msa")                                 
+    return parser
+
+
+# Execute LevSeq
+def execute_LevSeq():
+    # Build parser
+    parser = build_cli_parser()
+    # Parse the arguments
+    CL_ARGS = vars(parser.parse_args())
+    # Set up progres bar
+    tqdm_fn = tqdm.tqdm
+    # Run LevSeq
+    try:
+        run_LevSeq(CL_ARGS, tqdm_fn)
+    except Exception as e:
+        print(e)
+    print("Run Complete, add log info")