refactor!: remove pybedtools as a dependency. This slightly changes the interpretation of BED files. From now on, the end position of each region will not be included.

.readthedocs_conda_env.yml

@@ -9,7 +9,6 @@ dependencies:
   - pytest
   - pytest-cov
   - numpy
-  - pybedtools
   - matplotlib-base
   - pysam
   - scipy

Dockerfile

@@ -16,7 +16,7 @@ RUN apt-get update && DEBIAN_FRONTEND="noninteractive" apt-get install -qqy \
     unzip \
     zlib1g-dev
 
-RUN pip3 install pybedtools pyvcf scipy numpy statsmodels
+RUN pip3 install pyvcf scipy numpy statsmodels
 
 # Install samtools (needed to index reference fasta files)
 RUN wget -O samtools-1.9.tar.bz2 https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2

README.rst

@@ -72,8 +72,6 @@ checkout the branch you're interested in, and run the following command from the
         pip install --upgrade pip
         pip install -e .
 
-Note: required package :code:`pybedtools` requires zlib. If you receive an error about a missing file :code:`zlib.h`, you can install on Ubuntu using :code:`sudo apt-get install zlib1g-dev` or CentOS using :code:`sudo yum install zlib-devel`.
-
 Note: make sure TRTools is not installed in the environment via a different method before installing from source. :code:`which dumpSTR` should return nothing
 
 Tools

pyproject.toml

@@ -24,7 +24,6 @@ dependencies = [
     "matplotlib",
     "numpy",
     "pandas",
-    "pybedtools",
     "pysam",
     "scikit-learn",
     "scipy",

trtools/dumpSTR/filters.py

@@ -6,7 +6,7 @@
 import os
 
 import numpy as np
-from pybedtools import BedTool
+from pysam import TabixFile, asBed
 
 import trtools.utils.common as common
 import trtools.utils.tr_harmonizer as trh
@@ -263,7 +263,7 @@ def LoadRegions(self, filename):
                 common.WARNING("Could not find tabix index %s.tbi"%filename)
                 self.pass_checks = False
                 return
-            self.regions = BedTool(filename)
+            self.regions = TabixFile(filename, parser=asBed())
         def __call__(self, record: trh.TRRecord):
             interval = "%s:%s-%s"%(record.chrom, record.pos,
                                    record.pos + record.ref_allele_length)
@@ -272,10 +272,24 @@ def __call__(self, record: trh.TRRecord):
                 interval2 = interval.replace("chr","")
             else: interval2 = "chr"+interval
             # Try with and without chr
-            tb1 = self.regions.tabix_intervals(interval)
-            if tb1.count() > 0: return self.name
-            tb2 = self.regions.tabix_intervals(interval2)
-            if tb2.count() > 0: return self.name
+            # A ValueError or StopIteration indicates that there weren't any matching
+            # regions within the given interval
+            try:
+                next(self.regions.fetch(region=interval, multiple_iterators=True))
+            except ValueError:
+                pass
+            except StopIteration:
+                pass
+            else:
+                return self.name
+            try:
+                next(self.regions.fetch(region=interval2, multiple_iterators=True))
+            except ValueError:
+                pass
+            except StopIteration:
+                pass
+            else:
+                return self.name
             return None
         def filter_name(self):
             return self.name

trtools/dumpSTR/tests/test_dumpSTR.py

@@ -653,7 +653,7 @@ def test_beagle_disallowed_call_filters(tmpdir, vcfdir):
 
 """
 These tests run dumpSTR and compare its output
-to output that has been generated by a pervious version of 
+to output that has been generated by a previous version of 
 dumpSTR and saved in the repo. The results are expected
 to be identical.
 

trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.loclog.tab

@@ -5,4 +5,4 @@ FILTER:CALLRATE0.5	473
 FILTER:HWE0.5	213
 FILTER:HETLOW0.05	8005
 FILTER:HETHIGH0.45	584
-FILTER:foo_region	341
+FILTER:foo_region	342

trtools/testsupport/sample_vcfs/dumpSTR_vcfs/locus_filters.vcf

@@ -439,7 +439,7 @@ chr21	14383027	GANGSTR_437028	TTTTGTTGTTGTTGTTG	TGTTGTTGTTGTTGTTG	.	HETLOW0.05;f
 chr21	14384512	GANGSTR_437029	CACTCCACTC	CACTCCATTC	.	foo_region	INFRAME_PGEOM=0.95;INFRAME_UP=0.01;INFRAME_DOWN=0.01;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=14384512;END=14384521;PERIOD=5;NSKIP=0;NFILT=0;BPDIFFS=0;DP=244;DSNP=0;DSTUTTER=0;DFLANKINDEL=5;AN=6;REFAC=4;AC=2;HRUN=2;HET=0.444444;HWEP=0.588477	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	0|1:0|0:1:0.5:81:0:0:4:53.04|27.96:0|0:69.99:-2.47:74:-0.35:0|57:0|53:PASS	0|0:0|0:1:1:81:0:0:1:40.50|40.50:0|0:22.26:0:.:0:0|62:0|62:PASS	0|1:0|0:1:0.5:82:0:0:0:60.16|21.84:0|0:51.35:-5.14:75:-0.23:0|54:0|54:PASS
 chr21	14390199	GANGSTR_437030	TGGTGAGTGTGTGTGTGTGT	TAGTGAGTGTGTGTGTGTGT	.	HETLOW0.05;foo_region	INFRAME_PGEOM=0.95;INFRAME_UP=0.01;INFRAME_DOWN=0.01;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0.01;OUTFRAME_DOWN=0.01;START=14390205;END=14390218;PERIOD=2;NSKIP=0;NFILT=0;BPDIFFS=0;DP=222;DSNP=0;DSTUTTER=2;DFLANKINDEL=7;AN=6;REFAC=3;AC=3;HRUN=2;HET=0;HWEP=1	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	0|1:0|0:1:0.5:77:0:1:2:48.14|28.86:0|0:66.66:-1.65:63:-0.96:-2|1;0|57:0|53:PASS	0|1:0|0:1:0.5:67:0:1:4:54.58|12.42:0|0:5.56:-8.49:54:-0.65:-2|1;0|50:0|42:PASS	0|1:0|0:1:0.5:78:0:0:1:54.02|23.98:0|0:44.75:-3.64:64:-0.4:0|55:0|53:PASS
 chr21	14394189	GANGSTR_437031	ACAAAAACAAACAAACAAAC	AAAACAAACAAACAAAC	.	CALLRATE0.5;foo_region;NO_CALLS_REMAINING	INFRAME_PGEOM=0.59;INFRAME_UP=0.02;INFRAME_DOWN=0;OUTFRAME_PGEOM=0.69;OUTFRAME_UP=0;OUTFRAME_DOWN=0.01;START=14394193;END=14394208;PERIOD=4;NSKIP=0;NFILT=3;BPDIFFS=-3;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0;AN=0;REFAC=0;AC=0;HRUN=5;HET=-1;HWEP=-1	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL	.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL	.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL
-chr21	14405799	GANGSTR_437032	ACCCACCCACCC	ACCCGCCCACCC	.	HWE0.5;HETHIGH0.45	INFRAME_PGEOM=0.95;INFRAME_UP=0;INFRAME_DOWN=0;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0;OUTFRAME_DOWN=0;START=14405799;END=14405810;PERIOD=4;NSKIP=0;NFILT=0;BPDIFFS=0;DP=342;DSNP=0;DSTUTTER=0;DFLANKINDEL=1;AN=6;REFAC=3;AC=3;HRUN=3;HET=0.5;HWEP=0.25	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	0|1:0|0:1:0.5:115:0:0:1:59.46|55.54:0|0:179.46:-0.11:104:-0.16:0|87:0|86:PASS	0|1:0|0:1:0.5:109:0:0:0:53.35|55.65:0|0:152.82:-0.04:98:-0.53:0|83:0|81:PASS	0|1:0|0:1:0.5:118:0:0:0:74.97|43.03:0|0:123.77:-2.66:104:0:0|82:0|78:PASS
+chr21	14405799	GANGSTR_437032	ACCCACCCACCC	ACCCGCCCACCC	.	HWE0.5;HETHIGH0.45;foo_region	INFRAME_PGEOM=0.95;INFRAME_UP=0;INFRAME_DOWN=0;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0;OUTFRAME_DOWN=0;START=14405799;END=14405810;PERIOD=4;NSKIP=0;NFILT=0;BPDIFFS=0;DP=342;DSNP=0;DSTUTTER=0;DFLANKINDEL=1;AN=6;REFAC=3;AC=3;HRUN=3;HET=0.5;HWEP=0.25	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	0|1:0|0:1:0.5:115:0:0:1:59.46|55.54:0|0:179.46:-0.11:104:-0.16:0|87:0|86:PASS	0|1:0|0:1:0.5:109:0:0:0:53.35|55.65:0|0:152.82:-0.04:98:-0.53:0|83:0|81:PASS	0|1:0|0:1:0.5:118:0:0:0:74.97|43.03:0|0:123.77:-2.66:104:0:0|82:0|78:PASS
 chr21	14407537	GANGSTR_437033	AACAACAACAACAAC	.	.	HETLOW0.05	INFRAME_PGEOM=1;INFRAME_UP=0;INFRAME_DOWN=0.01;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0;OUTFRAME_DOWN=0;START=14407537;END=14407551;PERIOD=3;NSKIP=0;NFILT=0;DP=384;DSNP=0;DSTUTTER=1;DFLANKINDEL=0;AN=6;REFAC=6;HRUN=2;HET=0;HWEP=1;AC=0	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	0|0:0|0:1:1:120:0:0:0:60.00|60.00:0|0:.:0:.:0:0|80:0|78:PASS	0|0:0|0:1:1:134:0:1:0:67.00|67.00:0|0:.:0:.:0:-3|1;0|101:-3|1;0|98:PASS	0|0:0|0:1:1:130:0:0:0:65.00|65.00:0|0:.:0:.:0:0|93:0|90:PASS
 chr21	14410775	GANGSTR_437034	AGGAGGAGGAGGAGG	.	.	HETLOW0.05	INFRAME_PGEOM=0.95;INFRAME_UP=0;INFRAME_DOWN=0;OUTFRAME_PGEOM=0.95;OUTFRAME_UP=0;OUTFRAME_DOWN=0;START=14410775;END=14410789;PERIOD=3;NSKIP=0;NFILT=0;DP=291;DSNP=0;DSTUTTER=0;DFLANKINDEL=1;AN=6;REFAC=6;HRUN=2;HET=0;HWEP=1;AC=0	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	0|0:0|0:1:1:89:0:0:0:44.50|44.50:0|0:.:0:.:0:-2|1;0|60:0|59:PASS	0|0:0|0:1:1:104:0:0:0:52.00|52.00:0|0:.:0:.:0:0|80:0|76:PASS	0|0:0|0:1:1:98:0:0:1:49.00|49.00:0|0:.:0:.:0:0|66:0|61:PASS
 chr21	14411793	GANGSTR_437035	AATAAATAAATAAATAAATAAATAAATA	AAATAAATAAATAAATAAATAAATAAATA,AAATAAATAAATAAATAAATAAATAAATAAATAAATA	.	CALLRATE0.5;NO_CALLS_REMAINING	INFRAME_PGEOM=0.58;INFRAME_UP=0.05;INFRAME_DOWN=0.01;OUTFRAME_PGEOM=0.27;OUTFRAME_UP=0.04;OUTFRAME_DOWN=0.03;START=14411793;END=14411820;PERIOD=4;NSKIP=0;NFILT=3;BPDIFFS=1,9;DP=0;DSNP=0;DSTUTTER=0;DFLANKINDEL=0;AN=0;REFAC=0;AC=0,0;HRUN=3;HET=-1;HWEP=-1	GT:GB:Q:PQ:DP:DSNP:DSTUTTER:DFLANKINDEL:PDP:PSNP:GLDIFF:AB:DAB:FS:ALLREADS:MALLREADS:FILTER	.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL	.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL	.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:.:NOCALL