IH 19DEC2022 version to v1.0.3-dev

CHANGES.txt

@@ -21,3 +21,11 @@ Release Summary:
 
 1.0.2-dev, December 9, 2022
 	Fixed variant calling bug that caused di-nt MNPs to be called as two SNPs when the di-nt MNP was downstream of a single SNP or another di-nt MNP
+
+1.0.3-dev, December 19, 2022
+	Added back run_design_conversion.py to scripts directory
+
+	Added __init__.py to prototype directory. Now in package.
+
+	Fixed URL links in setup.cfg and in satmut_utils_manual.md to point to ijhoskins repo
+

docs/satmut_utils_manual.md

@@ -53,7 +53,7 @@ Currently, only Linux and MacOSX operating systems are supported. To get started
 
 2. Clone the satmut\_utils repository:
 ```
-git clone https://github.com/CenikLab/satmut_utils.git
+git clone https://github.com/ijhoskins/satmut_utils.git
 SATMUT_ROOT="$PWD/satmut_utils"
 ```
 
@@ -62,7 +62,7 @@ SATMUT_ROOT="$PWD/satmut_utils"
 REF_DIR="$HOME/satmut_utils_refs"
 $SATMUT_ROOT/install_satmut_utils.sh -h
 $SATMUT_ROOT/install_satmut_utils.sh -t -g -r "$REF_DIR" "$SATMUT_ROOT"
-conda activate satmut_utils
+conda activate satmut_utils_dev
 ```
 
 You are now ready to call the command-line executable ```satmut_utils```

setup.cfg

@@ -1,14 +1,14 @@
 [metadata]
 name = satmut_utils
-version = 1.0.2-dev
+version = 1.0.3-dev
 author = Ian Hoskins
 author_email = [email protected]
 description = Tools for variant simulation and variant calling in paired end, targeted sequencing saturation mutagenesis experiments
 long_description = file: README.md
 long_description_content_type = text/markdown
-url = https://github.com/CenikLab/satmut_utils
+url = https://github.com/ijhoskins/satmut_utils
 project_urls =
-    Bug Tracker = https://github.com/CenikLab/satmut_utils/issues
+    Bug Tracker = https://github.com/ijhoskins/satmut_utils/issues
 classifiers =
     Development Status :: 4 - Beta
     License :: OSI Approved :: GNU General Public License v3 (GPLv3)

src/prototype/run_design_conversion.py

@@ -0,0 +1,109 @@
+#!/usr/bin/env python3
+"""Preprocesses amplicon/tile alignments to meet dms_tools2 and Enrich2 input requirements."""
+
+import argparse
+import logging
+import os
+import sys
+
+from core_utils.file_utils import replace_extension
+from satmut_utils.definitions import LOG_FORMATTER
+from prototype.design_conversion import DesignConverter
+
+__author__ = "Ian_Hoskins"
+__credits__ = ["Ian Hoskins"]
+__license__ = "GPLv3"
+__maintainer__ = "Ian Hoskins"
+__email__ = "[email protected]"
+__status__ = "Development"
+
+LOGFILE = replace_extension(os.path.basename(__file__), "log")
+logger = logging.getLogger(__name__)
+console_handler = logging.StreamHandler()
+console_handler.setFormatter(LOG_FORMATTER)
+logger.addHandler(console_handler)
+
+
+def parse_commandline_params(args):
+    """Parses command line parameters.
+
+    :param list args: command line arguments, no script name
+    :return argparse.Namespace: namespace object with dict-like access
+    """
+
+    parser = argparse.ArgumentParser(description="%s arguments" % __name__)
+
+    # Add new arguments for command line passing of files, options, etc; see argparse docs
+    parser.add_argument("-b", "--in_bam", type=str, required=True,
+                        help='BAM file of reads in a single tile to convert. Intersect any alignments with a single '
+                             'target tile using bedtools -f (if alignments consist of multiple PCR tiles).')
+
+    parser.add_argument("-r", "--reference", type=str, required=True, help='Corresponding reference FASTA.')
+
+    parser.add_argument("-p", "--pos_range", type=str, required=True,
+                        help='Comma-delimited 1-based start and end positions of the amplicon/tile. '
+                             'Reads will be made flush with these coordinates.')
+
+    parser.add_argument("-o", "--output_dir", type=str, default=DesignConverter.DEFAULT_OUTDIR,
+                        help='Optional output directory for FASTQs and globally re-aligned BAM. '
+                             'Default current working directory.')
+
+    parser.add_argument("-l", "--umi_length", type=int, default=DesignConverter.DEFAULT_UMI_LEN,
+                        help='UMI/barcode length, for addition to 5\' end of each read in dms_tools2 conversion.')
+
+    parser.add_argument("-n", "--no_umis", action="store_true",
+                        help='Do not append UMIs to the 5\' end of reads. Use for conversion to Enrich2 format.')
+
+    parser.add_argument("-j", "--nthreads", type=int, default=DesignConverter.DEFAULT_NTHREADS,
+                        help='Number of threads to use for BAM sorting operations. Default %i, autodetect.'
+                             % DesignConverter.DEFAULT_NTHREADS)
+
+    parsed_args = vars(parser.parse_args(args))
+    return parsed_args
+
+
+def workflow(in_bam, ref, pos_range, umi_len=DesignConverter.DEFAULT_UMI_LEN, no_umis=DesignConverter.DEFAULT_NO_UMI,
+             outdir=DesignConverter.DEFAULT_OUTDIR, nthreads=DesignConverter.DEFAULT_NTHREADS):
+    """Runs the dms_tools2/Enrich2 conversion workflow.
+
+    :param str in_bam: input alignments for a single tile
+    :param str ref: reference FASTA
+    :param str pos_range: 1-based positions flush with codons spanning the target
+    :param int umi_len: length of randomer UMI. Default 8.
+    :param bool no_umis: do not add UMIs, only make reads flush with the pos_range. Default False
+    :param str outdir: output directory. Default current directory.
+    :param int nthreads: Number of threads to use for BAM operations. Default 0 (autodetect).
+    """
+
+    zipped_r1_fastq, zipped_r2_fastq = DesignConverter(
+        in_bam=in_bam, ref=ref, pos_range=pos_range, umi_len=umi_len, no_umis=no_umis,
+        outdir=outdir, nthreads=nthreads).workflow()
+
+    return zipped_r1_fastq, zipped_r2_fastq
+
+
+def main():
+    """Runs the workflow when called from command line."""
+
+    parsed_args = parse_commandline_params(sys.argv[1:])
+
+    outdir = parsed_args["output_dir"]
+    if not os.path.exists(outdir):
+        os.mkdir(outdir)
+
+    log_handler = logging.FileHandler(os.path.join(outdir, LOGFILE))
+    log_handler.setFormatter(LOG_FORMATTER)
+    logger.addHandler(log_handler)
+
+    logger.info("Started %s" % sys.argv[0])
+
+    workflow(in_bam=parsed_args["in_bam"], ref=parsed_args["reference"], pos_range=parsed_args["pos_range"],
+             umi_len=parsed_args["umi_length"], no_umis=parsed_args["no_umis"],
+             outdir=parsed_args["output_dir"], nthreads=parsed_args["nthreads"])
+
+    logger.info("Completed %s" % sys.argv[0])
+
+
+if __name__ == "__main__":
+    main()
+

src/satmut_utils/satmut_utils.py

@@ -23,7 +23,7 @@
 __author__ = "Ian Hoskins"
 __credits__ = ["Ian Hoskins"]
 __license__ = "GPLv3"
-__version__ = "1.0.2-dev"
+__version__ = "1.0.3-dev"
 __maintainer__ = "Ian Hoskins"
 __email__ = "[email protected]"
 __status__ = "Development"