From 229b2854f95d50691ce5777324937d517bdcb4e8 Mon Sep 17 00:00:00 2001 From: mlamkin7 Date: Wed, 29 Jun 2022 16:39:29 -0700 Subject: [PATCH 1/5] Added 1000genomes sampleinfo file for input. --- example-files/1000genomes_sampleinfo.tsv | 2709 ++++++++++++++++++++++ 1 file changed, 2709 insertions(+) create mode 100644 example-files/1000genomes_sampleinfo.tsv diff --git a/example-files/1000genomes_sampleinfo.tsv b/example-files/1000genomes_sampleinfo.tsv new file mode 100644 index 00000000..ff21d3af --- /dev/null +++ b/example-files/1000genomes_sampleinfo.tsv @@ -0,0 +1,2709 @@ +HG00271 FIN +HG00276 FIN +HG00288 FIN +HG00290 FIN +HG00303 FIN +HG00308 FIN +HG00310 FIN +HG00315 FIN +HG00327 FIN +HG00334 FIN +HG00339 FIN +HG00341 FIN +HG00346 FIN +HG00353 FIN +HG00358 FIN +HG00360 FIN +HG00365 FIN +HG00372 FIN +HG00132 GBR +HG00137 GBR +HG00144 GBR +HG00149 GBR +HG00151 GBR +HG00156 GBR +HG00182 FIN +HG00187 FIN +HG00136 GBR +HG00233 GBR +HG00143 GBR +HG00238 GBR +HG00148 GBR +HG00240 GBR 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CEU +HG04302 GBR +NA06986 CEU +HG04162 BEB +HG04174 BEB +HG04186 BEB +HG04198 ITU +HG04206 ITU +HG04225 ITU +NA19023 LWK +NA19028 LWK +NA19030 LWK +NA19035 LWK +NA19042 LWK +NA19054 JPT +NA19059 JPT +NA19066 JPT +NA19078 JPT +NA19080 JPT +NA19085 JPT +NA19092 YRI +NA19472 LWK +NA19648 MXL +NA19655 MXL +NA19679 MXL +NA19681 MXL +NA19701 ASW +NA19371 LWK +NA19376 LWK +NA19383 LWK +NA19390 LWK +NA19395 LWK +NA19403 LWK +NA19434 LWK +NA19439 LWK +NA19446 LWK +NA19453 LWK +NA18948 JPT +NA18950 JPT +NA18955 JPT +NA18962 JPT +NA18967 JPT +NA18974 JPT +NA18979 JPT +NA18981 JPT +NA18986 JPT +NA18993 JPT +NA18998 JPT +NA19004 JPT +NA19009 JPT +NA19011 JPT +NA19213 YRI +NA19225 YRI +NA19256 YRI +NA19307 LWK +NA19314 LWK +NA19319 LWK +NA19321 LWK +NA19338 LWK +NA19713 ASW +NA19720 MXL +NA19725 MXL +NA19732 MXL +NA19737 MXL +NA19749 MXL +NA19756 MXL +NA19143 YRI +NA19150 YRI +NA19198 YRI +NA19201 YRI +NA19206 YRI +NA18873 YRI +NA18878 YRI +NA18912 YRI +NA18917 YRI +NA18924 YRI +NA18943 JPT +NA19117 YRI +NA19129 YRI +NA19131 YRI +NA20359 ASW +NA20361 ASW +NA20412 ASW +NA20506 TSI +NA20513 TSI +NA20518 TSI +NA20520 TSI +NA20525 TSI +NA20532 TSI +NA20537 TSI +NA20544 TSI +NA20582 TSI +NA20587 TSI +NA20753 TSI +NA20758 TSI +NA20760 TSI +NA20765 TSI +NA20772 TSI +NA20796 TSI +NA20804 TSI +NA20809 TSI +NA20811 TSI +NA20816 TSI +NA19770 MXL +NA19782 MXL +NA19794 MXL +NA19819 ASW +NA19908 ASW +NA19922 ASW +NA19984 ASW +NA20126 ASW +NA20289 ASW +NA20291 ASW +NA20296 ASW +NA20828 TSI +NA20847 GIH +NA20854 GIH +NA20859 GIH +NA20861 GIH +NA20866 GIH +NA20342 ASW +NA20892 GIH +NA20897 GIH +NA20900 GIH +NA20905 GIH +NA21092 GIH +NA21097 GIH +NA21100 GIH +NA21105 GIH +NA20873 GIH +NA20878 GIH +NA20885 GIH +NA21143 GIH +NA21112 GIH +NA21117 GIH +NA21124 GIH +NA21129 GIH From e4aa6e2d4eb770e20a7747d96e7ec1e33beef36c Mon Sep 17 00:00:00 2001 From: mlamkin7 Date: Wed, 29 Jun 2022 16:46:39 -0700 Subject: [PATCH 2/5] Validation of map files' fields during execution. --- haptools/sim_genotype.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/haptools/sim_genotype.py b/haptools/sim_genotype.py index ca90a50f..befac3e1 100644 --- a/haptools/sim_genotype.py +++ b/haptools/sim_genotype.py @@ -58,10 +58,6 @@ def output_vcf(breakpoints, model_file, vcf_file, sampleinfo_file, out): for ind, sample in enumerate(vcf.samples): sample_dict[sample] = ind - # TODO read all chroms in vcf - - # TODO read all chroms in breakpoints and ensure that they each have the same ones - # create index array to store for every sample which haplotype # block we are currently processing and choose what samples # will be used for each haplotype block @@ -234,6 +230,9 @@ def numeric_alpha(x): for line in cfile: # create marker from each line and append to coords data = line.strip().split() + if len(data) != 4: + raise Exception(f"Map file contains an incorrect amount of fields {len(data)}. It should contain 4.") + if data[0] == 'X': chrom = 23 else: From 49998d8ce6a8c583598cace43240e9e741871c38 Mon Sep 17 00:00:00 2001 From: mlamkin7 Date: Wed, 29 Jun 2022 16:56:52 -0700 Subject: [PATCH 3/5] Updated with Arya's recommendations on pull request --- haptools/__main__.py | 7 ++++--- haptools/sim_genotype.py | 5 +++-- 2 files changed, 7 insertions(+), 5 deletions(-) diff --git a/haptools/__main__.py b/haptools/__main__.py index e9432303..f776b715 100644 --- a/haptools/__main__.py +++ b/haptools/__main__.py @@ -53,7 +53,7 @@ def karyogram(bp, sample, out, title, centromeres, colors): @click.option('--model', help="Admixture model in .dat format. See docs for info.", \ type=str, required=True) @click.option('--mapdir', help="Directory containing files with chr\{1-22,X\} and ending in .map in the file name with genetic map coords.", \ - type=str, required=True) + type=str, required=True, type=click.Path(exists=True, file_okay=False, dir_okay=True, readable=True)) @click.option('--out', help="Prefix to name output files.", \ type=str, required=True) @click.option('--chroms', help='Sorted and comma delimited list of chromosomes to simulate. ex: 1,2,3,5,6,21,X', \ @@ -62,8 +62,9 @@ def karyogram(bp, sample, out, title, centromeres, colors): type=int, required=False, default=None) @click.option('--popsize', help="Number of samples to simulate each generation", \ type=int, required=False, default=10000, hidden=True) -@click.option('--invcf') -@click.option('--sample_info') +@click.option('--invcf', help="VCF file used as reference for creation of simulated samples respective genotypes.", required=True) +@click.option('--sample_info', help="File that maps samples from the reference VCF (--invcf) to population codes " \ + "describing the populations in the header of the model file.", required=True) def simgenotype(invcf, sample_info, model, mapdir, out, popsize, seed, chroms): """ Simulate admixed genomes under a pre-defined model diff --git a/haptools/sim_genotype.py b/haptools/sim_genotype.py index befac3e1..b8ff3c85 100644 --- a/haptools/sim_genotype.py +++ b/haptools/sim_genotype.py @@ -7,6 +7,7 @@ from pysam import VariantFile from collections import defaultdict from .admix_storage import GeneticMarker, HaplotypeSegment +from __future__ import annotations def output_vcf(breakpoints, model_file, vcf_file, sampleinfo_file, out): """ @@ -375,7 +376,7 @@ def _simulate(samples, pops, pop_fracs, pop_gen, chroms, coords, end_coords, rec Holds probabilities for each marker for whether a recombination event will occur. prob of event = 1-np.exp(-dist/100) where dist is in cM and is calculated via the current and prior genetic markers - prev_gen_samples: list(list(HaplotypeSegment)) + prev_gen_samples: list[list[HaplotypeSegment]], optional Prior generation of samples used to choose parents and swap markers when recombination events occur. Each list is a person's haplotype of segments having a distinct population label. Returns @@ -697,4 +698,4 @@ def validate_params(model, mapdir, chroms, popsize, invcf, sample_info): if info_pop not in pops: raise Exception("Population {info_pop} in sampleinfo file is not present in the model file.") - return \ No newline at end of file + return From 8a931f9ddd18bab4a3b522481f906554689cf308 Mon Sep 17 00:00:00 2001 From: mlamkin7 Date: Wed, 29 Jun 2022 16:59:16 -0700 Subject: [PATCH 4/5] Updated docs to include simgenotypes --- docs/api/haptools.rst | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/api/haptools.rst b/docs/api/haptools.rst index d37b5ab7..66d0bab8 100644 --- a/docs/api/haptools.rst +++ b/docs/api/haptools.rst @@ -51,3 +51,11 @@ haptools.data.haplotypes module :members: :undoc-members: :show-inheritance: + +haptools.sim_genotype module +~~~~~~~~~~~~~~~~~~~~~~~~ + +.. automodule:: haptools.sim_genotype + :members: + :undoc-members: + :show-inheritance: From a760af324f086fce6d734f21957c74c3ba50687f Mon Sep 17 00:00:00 2001 From: mlamkin7 Date: Thu, 30 Jun 2022 08:57:53 -0700 Subject: [PATCH 5/5] Fixed bug with isfile instead of isdir --- haptools/sim_genotype.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/haptools/sim_genotype.py b/haptools/sim_genotype.py index b8ff3c85..3dc4cece 100644 --- a/haptools/sim_genotype.py +++ b/haptools/sim_genotype.py @@ -655,7 +655,7 @@ def validate_params(model, mapdir, chroms, popsize, invcf, sample_info): prev_gen = cur_gen # Validate mapdir ensuring it contains proper files. - if not os.path.isfile(mapdir): + if not os.path.isdir(mapdir): raise Exception("Map directory given is not a valid path.") try: