initial commit

lusSTR/cli/__init__.py

@@ -8,20 +8,16 @@
 from lusSTR.cli import snps
 from lusSTR.cli import gui
 
-mains = {
-    "config": config.main,
-    "strs": strs.main,
-    "snps": snps.main,
-    "gui": gui.main
-}
+mains = {"config": config.main, "strs": strs.main, "snps": snps.main, "gui": gui.main}
 
 subparser_funcs = {
     "config": config.subparser,
     "strs": strs.subparser,
     "snps": snps.subparser,
-    "gui": gui.subparser
+    "gui": gui.subparser,
 }
 
+
 def main(args=None):
     if args is None:
         args = get_parser().parse_args()
@@ -36,6 +32,7 @@ def main(args=None):
         result = mainmethod(args)
         return result
 
+
 def get_parser():
     parser = argparse.ArgumentParser()
     parser.add_argument(
@@ -47,5 +44,6 @@ def get_parser():
         func(subparsers)
     return parser
 
+
 if __name__ == "__main__":
     main()

lusSTR/cli/config.py

@@ -101,83 +101,102 @@ def edit_str_config(config, args):
 def subparser(subparsers):
     p = subparsers.add_parser("config", description="Create config file for running STR pipeline")
     p.add_argument(
-        "-w", "--workdir", metavar="W", default=".",
-        help="directory to add config file; default is current working directory")
+        "-w",
+        "--workdir",
+        metavar="W",
+        default=".",
+        help="directory to add config file; default is current working directory",
+    )
     p.add_argument(
-        "-a", "--analysis-software", choices=["uas", "straitrazor", "genemarker"], default="uas",
-        dest="asoftware", help="Analysis software program used prior to lusSTR. Choices are uas, "
-        "straitrazor or genemarker. Default is uas."
+        "-a",
+        "--analysis-software",
+        choices=["uas", "straitrazor", "genemarker"],
+        default="uas",
+        dest="asoftware",
+        help="Analysis software program used prior to lusSTR. Choices are uas, "
+        "straitrazor or genemarker. Default is uas.",
     )
     p.add_argument("--input", help="Input file or directory")
     p.add_argument("--out", "-o", help="Output file/directory name")
     p.add_argument(
-        "--powerseq", action="store_true",
-        help="Use to indicate sequences were created using the PowerSeq Kit."
+        "--powerseq",
+        action="store_true",
+        help="Use to indicate sequences were created using the PowerSeq Kit.",
     )
     p.add_argument(
-        "--sex", action="store_true",
+        "--sex",
+        action="store_true",
         help="Use if including the X and Y STR markers. Separate reports for these markers "
         "will be created.",
     )
     p.add_argument(
-        "--nocombine", action="store_true",
+        "--nocombine",
+        action="store_true",
         help="Do not combine read counts for duplicate sequences within the UAS region "
         "during the 'convert' step. By default, read counts are combined for sequences "
         "not run through the UAS.",
     )
     p.add_argument(
-        "--reference", action="store_true", 
-        help="Use for creating Reference profiles for STR workflow"
+        "--reference",
+        action="store_true",
+        help="Use for creating Reference profiles for STR workflow",
     )
     p.add_argument(
-        "--software", choices=["efm", "mpsproto", "strmix"], default="strmix",
+        "--software",
+        choices=["efm", "mpsproto", "strmix"],
+        default="strmix",
         help="Specify the probabilistic genotyping software package of choice. The final output"
-        " files will be in the correct format for direct use. Default is strmix."
+        " files will be in the correct format for direct use. Default is strmix.",
     )
     p.add_argument(
-        "--str-type", choices=["ce", "ngs", "lusplus"], default="ngs",
-        dest="datatype", help="Data type for STRs. Options are: CE allele ('ce'), sequence "
+        "--str-type",
+        choices=["ce", "ngs", "lusplus"],
+        default="ngs",
+        dest="datatype",
+        help="Data type for STRs. Options are: CE allele ('ce'), sequence "
         "or bracketed sequence form('ngs'), or LUS+ allele ('lusplus'). Default is 'ngs'.",
     )
     p.add_argument(
-        "--noinfo", action="store_true", 
-        help="Use to not create the Sequence Information File in the 'filter' step"
+        "--noinfo",
+        action="store_true",
+        help="Use to not create the Sequence Information File in the 'filter' step",
     )
     p.add_argument(
-        "--separate", action="store_true", 
+        "--separate",
+        action="store_true",
         help="Use to separate EFM profiles in the 'filter' step. If specifying for SNPs, "
-        "each sample will also be separated into 10 different bins for mixture deconvolution."
+        "each sample will also be separated into 10 different bins for mixture deconvolution.",
     )
     p.add_argument(
-        "--nofiltering", action="store_true", 
+        "--nofiltering",
+        action="store_true",
         help="For STRs, use to perform no filtering during the 'filter' step. For SNPs, "
-        "only alleles specified as 'Typed' by the UAS will be included at the 'format' step."
+        "only alleles specified as 'Typed' by the UAS will be included at the 'format' step.",
     )
     p.add_argument(
-        "--snps", action="store_true",
-        help="Use to create a config file for the SNP workflow"
+        "--snps", action="store_true", help="Use to create a config file for the SNP workflow"
     )
     p.add_argument(
-        "--snp-type", default="all", dest="snptype",
+        "--snp-type",
+        default="all",
+        dest="snptype",
         help="Specify the type of SNPs to include in the final report. 'p' will include only the "
         "Phenotype SNPs; 'a' will include only the Ancestry SNPs; 'i' will include only the "
         "Identity SNPs; and 'all' will include all SNPs. More than one type can be specified (e.g. "
-        " 'p, a'). Default is all."
+        " 'p, a'). Default is all.",
     )
     p.add_argument(
-        "--kintelligence", action="store_true",
-        help="Use if processing Kintelligence SNPs within a Kintellience Report(s)"
+        "--kintelligence",
+        action="store_true",
+        help="Use if processing Kintelligence SNPs within a Kintellience Report(s)",
     )
     p.add_argument(
-        "--snp-reference", dest="ref",
-        help="Specify any references for SNP data for use in EFM."
+        "--snp-reference", dest="ref", help="Specify any references for SNP data for use in EFM."
     )
     p.add_argument(
-        "--strand", choices=["uas", "forward"],
+        "--strand",
+        choices=["uas", "forward"],
         help="Specify the strand orientation for the final output files. UAS orientation is "
-        "default for STRs; forward strand is default for SNPs."
-    )
-    p.add_argument(
-        "--custom", action="store_true",
-        help="Specifying custom sequence ranges."
+        "default for STRs; forward strand is default for SNPs.",
     )
+    p.add_argument("--custom", action="store_true", help="Specifying custom sequence ranges.")

lusSTR/cli/snps.py

@@ -22,15 +22,15 @@ def main(args):
         lusSTR.snakefile(workflow="snps"), targets=[pretarget], workdir=workdir, verbose=True
     )
     if result is not True:
-        raise SystemError('Snakemake failed')
+        raise SystemError("Snakemake failed")
+
 
 def subparser(subparsers):
-    p = subparsers.add_parser(
-        "snps", description="Running the SNP pipeline"
-    )
+    p = subparsers.add_parser("snps", description="Running the SNP pipeline")
     p.add_argument(
-        "target", choices=["format", "all"], 
+        "target",
+        choices=["format", "all"],
         help="Steps to run. Specifying 'format' will run only 'format'. Specifying "
-        "'all' will run all steps of the SNP workflow ('format' and 'convert')."
+        "'all' will run all steps of the SNP workflow ('format' and 'convert').",
     )
-    p.add_argument("-w", "--workdir", metavar="W", default=".", help="working directory")
+    p.add_argument("-w", "--workdir", metavar="W", default=".", help="working directory")

lusSTR/cli/strs.py

@@ -18,20 +18,18 @@
 def main(args):
     pretarget = args.target if args.target != "all" else "filter"
     workdir = args.workdir
-    result = snakemake(
-        lusSTR.snakefile(workflow="strs"), targets=[pretarget], workdir=workdir
-    )
+    result = snakemake(lusSTR.snakefile(workflow="strs"), targets=[pretarget], workdir=workdir)
     if result is not True:
-        raise SystemError('Snakemake failed')
+        raise SystemError("Snakemake failed")
+
 
 def subparser(subparsers):
-    p = subparsers.add_parser(
-        "strs", description="Running the STR pipeline"
-    )
+    p = subparsers.add_parser("strs", description="Running the STR pipeline")
     p.add_argument(
-        "target", choices=["format", "convert", "all"], 
+        "target",
+        choices=["format", "convert", "all"],
         help="Steps to run. Specifying 'format' will run only 'format'. Specifying "
         "'convert' will run both 'format' and 'convert'. Specifying 'all' will run "
-        "all steps of the STR workflow ('format', 'convert' and 'filter')."
+        "all steps of the STR workflow ('format', 'convert' and 'filter').",
     )
     p.add_argument("-w", "--workdir", metavar="W", default=".", help="working directory")

lusSTR/wrappers/filter.py

@@ -19,11 +19,13 @@
 import math
 from matplotlib.backends.backend_pdf import PdfPages
 import matplotlib.pyplot as plt
+import mpld3
 import numpy as np
 import os
 import pandas as pd
 from pathlib import Path
 import re
+import streamlit.components.v1 as components
 import sys
 
 
@@ -425,6 +427,8 @@ def make_plot(df, sample_id, sameyaxis=False, filters=False, at=True):
     else:
         title = "Marker Plots for All Alleles With Custom Y-Axis Scale"
     plt.text(0.4, 0.95, title, transform=fig.transFigure, size=24)
+    fig_html = mpld3.fig_to_html(fig)
+    components.html(fig_html, height=600)
 
 
 def get_at(df, locus):