fix: Added utilization of logging class to karyogram and simgenotype

haptools/__main__.py

@@ -58,16 +58,28 @@ def main():
     required=False,
     help="Optional color dictionary. Format is e.g. 'YRI:blue,CEU:green'",
 )
-def karyogram(bp, sample, out, title, centromeres, colors):
+@click.option(
+    "-v",
+    "--verbosity",
+    type=click.Choice(["CRITICAL", "INFO", "WARNING", "INFO", "DEBUG", "NOTSET"]),
+    default="INFO",
+    show_default="only errors",
+    help="The level of verbosity desired",
+)
+def karyogram(bp, sample, out, title, centromeres, colors, verbosity):
     """
     Visualize a karyogram of local ancestry tracks
     """
     from .karyogram import PlotKaryogram
+    from .logging import getLogger
+
+    log = getLogger(name="karyogram", level=verbosity)
 
     if colors is not None:
         colors = dict([item.split(":") for item in colors.split(",")])
+    log.info("Generating Karyogram...")
     PlotKaryogram(
-        bp, sample, out, centromeres_file=centromeres, title=title, colors=colors
+        bp, sample, out, log, centromeres_file=centromeres, title=title, colors=colors
     )
 
 
@@ -151,14 +163,12 @@ def karyogram(bp, sample, out, title, centromeres, colors):
     ),
 )
 @click.option(
-    "--verbose",
-    hidden=True,
-    is_flag=True,
-    required=False,
-    help=(
-        "Output time metrics for each section, breakpoint simulation, vcf creation, "
-        "and total exection."
-    ),
+    "-v",
+    "--verbosity",
+    type=click.Choice(["CRITICAL", "INFO", "WARNING", "INFO", "DEBUG", "NOTSET"]),
+    default="INFO",
+    show_default="only errors",
+    help="The level of verbosity desired",
 )
 def simgenotype(
     invcf,
@@ -171,7 +181,7 @@ def simgenotype(
     chroms,
     region,
     only_breakpoint,
-    verbose,
+    verbosity,
 ):
     """
     Simulate admixed genomes under a pre-defined model.
@@ -184,7 +194,9 @@ def simgenotype(
         validate_params,
         write_breakpoints,
     )
+    from .logging import getLogger
 
+    log = getLogger(name="simgenotype", level=verbosity)
     start = time.time()
 
     # parse region and chroms parameters
@@ -215,21 +227,21 @@ def simgenotype(
     popsize = validate_params(
         model, mapdir, chroms, popsize, invcf, sample_info, region, only_breakpoint
     )
-    samples, breakpoints = simulate_gt(model, mapdir, chroms, region, popsize, seed)
-    breakpoints = write_breakpoints(samples, breakpoints, out)
+    samples, breakpoints = simulate_gt(
+        model, mapdir, chroms, region, popsize, log, seed
+    )
+    breakpoints = write_breakpoints(samples, breakpoints, out, log)
     bp_end = time.time()
 
     # simulate vcfs
     vcf_start = time.time()
     if not only_breakpoint:
-        # TODO add region functionality
-        output_vcf(breakpoints, chroms, model, invcf, sample_info, region, out)
+        output_vcf(breakpoints, chroms, model, invcf, sample_info, region, out, log)
     end = time.time()
 
-    if verbose:
-        print(f"Time elapsed for breakpoint simulation: {bp_end - start}")
-        print(f"Time elapse for creating vcf: {end - vcf_start}")
-        print(f"Time elapsed for simgenotype execution: {end - start}")
+    log.debug(f"Time elapsed for breakpoint simulation: {bp_end - start}")
+    log.debug(f"Time elapse for creating vcf: {end - vcf_start}")
+    log.debug(f"Time elapsed for simgenotype execution: {end - start}")
 
 
 @main.command()

haptools/karyogram.py

@@ -199,7 +199,7 @@ def GetChromOrder(sample_blocks):
     chroms.sort()
     return chroms
 
-def PlotKaryogram(bp_file, sample_name, out_file,
+def PlotKaryogram(bp_file, sample_name, out_file, log,
         centromeres_file=None, title=None, colors=None):
     """
     Plot a karyogram based on breakpoints output by haptools simgenotypes
@@ -212,6 +212,8 @@ def PlotKaryogram(bp_file, sample_name, out_file,
        Sample ID to plot
     out_file : str
        Name of output file
+    log: log object
+        Outputs messages to the appropriate channel.
     centromeres_file : str, optional
        Path to file with centromere coordinates.
        Format: chrom, chromstart_cm, centromere_cm, chromend_cm
@@ -225,6 +227,7 @@ def PlotKaryogram(bp_file, sample_name, out_file,
     """
     # Parse haplotype blocks from the bp file for the 
     # specified sample
+    log.info("Collecting Haplotype Blocks...")
     sample_blocks = GetHaplotypeBlocks(bp_file, sample_name, centromeres_file)
     if len(sample_blocks) == 0:
         sys.stderr.write("ERROR: no haplotype blocks identified for %s. "%sample_name)
@@ -251,13 +254,15 @@ def PlotKaryogram(bp_file, sample_name, out_file,
 
     # Set up colors
     if colors is None:
+        log.info("Colors not given. Setting up colors...")
         num_pops = len(pop_list)
         cmap = plt.cm.get_cmap('rainbow', num_pops)
         colors = dict(zip(pop_list, cmap(list(range(num_pops)))))
 
     # Optionally, plot centromeres/telomeres
     clipmask_perchrom = None
     if centromeres_file is not None:
+        log.info("Centromeres present, adding into figure...")
         clipmask_perchrom = GetCentromereClipMask(centromeres_file, chrom_order)
 
     # Plot the actual haplotype blocks
@@ -279,6 +284,7 @@ def PlotKaryogram(bp_file, sample_name, out_file,
     ax.set_ylim(len(chrom_order)+3, -3)
 
     fig.savefig(out_file)
+    log.info(f"Karyogram Complete! Saved to {out_file}")
 
 def GetCentromereClipMask(centromeres_file, chrom_order):
     """

haptools/sim_genotype.py

@@ -4,7 +4,6 @@
 import re
 import sys
 import glob
-import time
 import numpy as np
 from cyvcf2 import VCF
 from pysam import VariantFile
@@ -13,7 +12,7 @@
 from .data import GenotypesRefAlt, GenotypesPLINK
 
 
-def output_vcf(breakpoints, chroms, model_file, vcf_file, sampleinfo_file, region, out):
+def output_vcf(breakpoints, chroms, model_file, vcf_file, sampleinfo_file, region, out, log):
     """
     Takes in simulated breakpoints and uses reference files, vcf and sampleinfo, 
     to create simulated variants output in file: out + .vcf
@@ -48,9 +47,11 @@ def output_vcf(breakpoints, chroms, model_file, vcf_file, sampleinfo_file, regio
         within that region.
     out: str
         output prefix
+    log: log object
+        Outputs messages to the appropriate channel.
     """
 
-    print(f"Outputting VCF file {out}.vcf")
+    log.info(f"Outputting VCF file {out}.vcf.gz")
 
     # details to know
     # vcf file: how to handle samples and which sample is which haplotype block randomly choose out of current population types
@@ -104,10 +105,10 @@ def output_vcf(breakpoints, chroms, model_file, vcf_file, sampleinfo_file, regio
     # Note: comment out the code below to enable (very experimental!) PGEN support
     # curr_bkps = current_bkps.copy()
     # _write_pgen(breakpoints, chroms, region, hapblock_samples, curr_bkps, output_samples, vcf_file, out+".pgen")
-    _write_vcf(breakpoints, chroms, region, hapblock_samples, vcf.samples, current_bkps, output_samples, vcf, out+".vcf.gz")
+    _write_vcf(breakpoints, chroms, region, hapblock_samples, vcf.samples, current_bkps, output_samples, vcf, out+".vcf.gz", log)
     return
 
-def _write_vcf(breakpoints, chroms, region, hapblock_samples, vcf_samples, current_bkps, out_samples, in_vcf, out_vcf):
+def _write_vcf(breakpoints, chroms, region, hapblock_samples, vcf_samples, current_bkps, out_samples, in_vcf, out_vcf, log):
     """
     in_vcf = cyvcf2 variants we are reading in
     out_vcf = output vcf file we output too
@@ -127,10 +128,9 @@ def _write_vcf(breakpoints, chroms, region, hapblock_samples, vcf_samples, curre
     try:
         write_vcf.header.add_samples(out_samples)
     except AttributeError:
-        print(
+        log.warning(
             "Upgrade to pysam >=0.19.1 to reduce the time required to create "
-            "VCFs. See https://github.com/pysam-developers/pysam/issues/1104",
-            file = sys.stderr,
+            "VCFs. See https://github.com/pysam-developers/pysam/issues/1104"
         )
         for sample in out_samples:
             write_vcf.header.add_sample(sample)
@@ -282,7 +282,7 @@ def _write_pgen(breakpoints, chroms, region, hapblock_samples, current_bkps, out
 
     gts.write()
 
-def simulate_gt(model_file, coords_dir, chroms, region, popsize, seed=None):
+def simulate_gt(model_file, coords_dir, chroms, region, popsize, log, seed=None):
     """
     Simulate admixed genotypes based on the parameters of model_file.
 
@@ -313,6 +313,8 @@ def simulate_gt(model_file, coords_dir, chroms, region, popsize, seed=None):
         within that region.
     popsize: int
         Size of population created for each generation. 
+    log: log object
+        Outputs messages to the appropriate channel.
     seed: int
         Seed used for randomization.
 
@@ -328,7 +330,7 @@ def simulate_gt(model_file, coords_dir, chroms, region, popsize, seed=None):
     # initialize seed used for breakpoints
     if seed:
         np.random.seed(seed)
-        print(f"Using seed {seed}")
+        log.info(f"Using seed {seed}")
 
     # load population samples and labels to be simulated 
     mfile = open(model_file, 'r')
@@ -426,13 +428,13 @@ def numeric_alpha(x):
         sim_gens = cur_gen - prev_gen
 
         # sim generation
-        print(f"Simulating generation {prev_gen+1}")
+        log.info(f"Simulating generation {prev_gen+1}")
         next_gen_samples = _simulate(popsize, pops, pop_fracs, prev_gen, chroms,
                                      coords, end_coords, recomb_probs, next_gen_samples)
 
         # simulate remaining generations
         for i in range(1, sim_gens):
-            print(f"Simulating generation {prev_gen+i+1}")
+            log.info(f"Simulating generation {prev_gen+i+1}")
 
             # update pop_fracs to have 100% admixture since this generation has not been specified in model file
             pop_fracs = [0]*len(pops)
@@ -447,7 +449,7 @@ def numeric_alpha(x):
     mfile.close()
     return num_samples, next_gen_samples
 
-def write_breakpoints(samples, breakpoints, out):
+def write_breakpoints(samples, breakpoints, out, log):
     """
     Write out a subsample of breakpoints to out determined by samples.
 
@@ -461,14 +463,16 @@ def write_breakpoints(samples, breakpoints, out):
         of ancestors for this person.
     out: str
         output prefix used to output the breakpoint file
+    log: log object
+        Outputs messages to the appropriate channel.
 
     Returns
     -------
     breakpoints: list[list[HaplotypeSegment]]
         subsampled breakpoints only containing number of samples
     """
     breakpt_file = out + '.bp'
-    print(f"Outputting breakpoint file {breakpt_file}")
+    log.info(f"Outputting breakpoint file {breakpt_file}")
 
     # randomly sample breakpoints to get the correct amount of samples to output
     breakpoints = np.array(breakpoints, dtype=object)

tests/test_outputvcf.py

@@ -3,19 +3,21 @@
 import numpy as np
 from cyvcf2 import VCF
 from pathlib import Path
+from haptools.logging import getLogger
 from haptools.sim_genotype import output_vcf, validate_params, simulate_gt
 from haptools.admix_storage import HaplotypeSegment
 
 DATADIR = Path(__file__).parent.joinpath("data")
 
 
 def _get_files():
+    log = getLogger(name="test", level="INFO")
     bkp_file = DATADIR.joinpath("outvcf_test.bp")
     model_file = DATADIR.joinpath("outvcf_gen.dat")
     vcf_file = DATADIR.joinpath("outvcf_test.vcf")
     sampleinfo_file = DATADIR.joinpath("outvcf_info.tab")
     out_prefix = DATADIR.joinpath("outvcf_out")
-    return bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix
+    return bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix, log
 
 
 def _get_breakpoints(bkp_file):
@@ -49,15 +51,15 @@ def _get_breakpoints(bkp_file):
 def test_alt_chrom_name():
     # Test when the ref VCF has chr{X|\d+} form
     # read in all files and breakpoints
-    bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix = _get_files()
+    bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix, log = _get_files()
     bkp_file = DATADIR.joinpath("outvcf_test_chr.bp")
     vcf_file = DATADIR.joinpath("outvcf_test_chr.vcf")
     chroms = ["1", "2", "X"]
     bkps = _get_breakpoints(bkp_file)
 
     # generate output vcf file
     output_vcf(
-        bkps, chroms, model_file, vcf_file, sampleinfo_file, None, str(out_prefix)
+        bkps, chroms, model_file, vcf_file, sampleinfo_file, None, str(out_prefix), log
     )
 
     # read in vcf file
@@ -97,13 +99,13 @@ def test_alt_chrom_name():
 
 def test_vcf_output():
     # read in all files and breakpoints
-    bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix = _get_files()
+    bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix, log = _get_files()
     chroms = ["1", "2"]
     bkps = _get_breakpoints(bkp_file)
 
     # generate output vcf file
     output_vcf(
-        bkps, chroms, model_file, vcf_file, sampleinfo_file, None, str(out_prefix)
+        bkps, chroms, model_file, vcf_file, sampleinfo_file, None, str(out_prefix), log
     )
 
     # Expected output for each variant (note these are phased so order matters)
@@ -147,8 +149,9 @@ def test_region_bkp():
     coords_dir = DATADIR.joinpath("map")
     chroms = ["22"]
     seed = 100
+    log = getLogger(name="test", level="INFO")
     num_samples, all_samples = simulate_gt(
-        modelfile, coords_dir, chroms, region, popsize, seed
+        modelfile, coords_dir, chroms, region, popsize, log, seed
     )
 
     # Make sure lowest bkp listed is 16111 and greatest is 18674
@@ -160,11 +163,18 @@ def test_region_bkp():
 
 def test_region_vcf():
     region = {"chr": "2", "start": 1, "end": 10122}
-    bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix = _get_files()
+    bkp_file, model_file, vcf_file, sampleinfo_file, out_prefix, log = _get_files()
     bkps = _get_breakpoints(bkp_file)
     chroms = ["2"]
     output_vcf(
-        bkps, chroms, model_file, vcf_file, sampleinfo_file, region, str(out_prefix)
+        bkps,
+        chroms,
+        model_file,
+        vcf_file,
+        sampleinfo_file,
+        region,
+        str(out_prefix),
+        log,
     )
 
     vcf = VCF(str(out_prefix) + ".vcf.gz")