From dd6f11313e4b90b27bd805b36efd9c142d1a5973 Mon Sep 17 00:00:00 2001 From: isaacvock Date: Tue, 30 Apr 2024 21:07:57 -0400 Subject: [PATCH 1/8] Add makeCB option to all dunk --- slamdunk/slamdunk.py | 1 + 1 file changed, 1 insertion(+) diff --git a/slamdunk/slamdunk.py b/slamdunk/slamdunk.py index b812d59..56a91ce 100755 --- a/slamdunk/slamdunk.py +++ b/slamdunk/slamdunk.py @@ -430,6 +430,7 @@ def run(): allparser.add_argument('-st', "--sampleTime", type=int, dest="sampleTime", required = False, default = 0, help="Use this sample time for all supplied samples") allparser.add_argument("-i", "--sample-index", type=int, required=False, default=-1, dest="sampleIndex", help="Run analysis only for sample . Use for distributing slamdunk analysis on a cluster (index is 1-based).") allparser.add_argument("-ss", "--skip-sam", action='store_true', dest="skipSAM", help="Output BAM while mapping. Slower but, uses less hard disk.") + allparser.add_argument('-cb', "--makeCB", action='store_true', dest="makeCB", help="Make cB file that can be used for mixture modeling") args = parser.parse_args() From 6b5bfc77b4676435a972398f2ecc5982674bc280 Mon Sep 17 00:00:00 2001 From: isaacvock Date: Wed, 1 May 2024 20:51:47 -0400 Subject: [PATCH 2/8] Fix T overcounting bug --- slamdunk/dunks/tcounter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slamdunk/dunks/tcounter.py b/slamdunk/dunks/tcounter.py index 73a4761..4b4cd26 100644 --- a/slamdunk/dunks/tcounter.py +++ b/slamdunk/dunks/tcounter.py @@ -261,7 +261,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC ### NEW CODE if (makeCB): - key = (testk, testN) + key = (testk, read.getTcount()) if key in cB: cB[key] += 1 From 97746a5b7136fe2dd27fbba29a7f47121ed4b32a Mon Sep 17 00:00:00 2001 From: isaacvock Date: Wed, 1 May 2024 20:55:27 -0400 Subject: [PATCH 3/8] Make cB header consistent with _tcount.tsv header --- slamdunk/dunks/tcounter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slamdunk/dunks/tcounter.py b/slamdunk/dunks/tcounter.py index 4b4cd26..97018e4 100644 --- a/slamdunk/dunks/tcounter.py +++ b/slamdunk/dunks/tcounter.py @@ -155,7 +155,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC ## Create cB output file if necessary if (makeCB): - header = ['chromosome', 'UTR_name', 'UTR_start', 'UTR_end', 'UTR_strand', 'TC', 'nT', 'n'] + header = ['Chromosome', 'Name', 'Start', 'End', 'Strand', 'TC', 'nT', 'n'] fileCB = open(outputCB, 'w') wr = csv.writer(fileCB) wr.writerow(header) From 4b9703183313c1947eccb571df93a75efaf1a73b Mon Sep 17 00:00:00 2001 From: isaacvock Date: Mon, 6 May 2024 08:54:41 -0400 Subject: [PATCH 4/8] Changes to be thrown out --- slamdunk.egg-info/PKG-INFO | 64 ++++++++++++++++++++++++++ slamdunk.egg-info/SOURCES.txt | 48 +++++++++++++++++++ slamdunk.egg-info/dependency_links.txt | 1 + slamdunk.egg-info/entry_points.txt | 4 ++ slamdunk.egg-info/requires.txt | 7 +++ slamdunk.egg-info/top_level.txt | 1 + slamdunk/dunks/tcounter.py | 23 ++++----- 7 files changed, 137 insertions(+), 11 deletions(-) create mode 100644 slamdunk.egg-info/PKG-INFO create mode 100644 slamdunk.egg-info/SOURCES.txt create mode 100644 slamdunk.egg-info/dependency_links.txt create mode 100644 slamdunk.egg-info/entry_points.txt create mode 100644 slamdunk.egg-info/requires.txt create mode 100644 slamdunk.egg-info/top_level.txt diff --git a/slamdunk.egg-info/PKG-INFO b/slamdunk.egg-info/PKG-INFO new file mode 100644 index 0000000..bc563e2 --- /dev/null +++ b/slamdunk.egg-info/PKG-INFO @@ -0,0 +1,64 @@ +Metadata-Version: 2.1 +Name: slamdunk +Version: 0.4.3 +Summary: SLAMdunk suite for analyzing SLAM-seq data +Home-page: http://t-neumann.github.io/slamdunk +Author: Tobias Neumann, Philipp Rescheneder +Author-email: tobias.neumann.at@gmail.com, philipp.rescheneder@univie.ac.at +License: GNU Affero General Public License v3 or later (AGPLv3+) +Keywords: Next-Generation-Sequencing NGS QuantSeq SLAMSeq +Classifier: Development Status :: 4 - Beta +Classifier: Intended Audience :: Science/Research +Classifier: Topic :: Scientific/Engineering :: Bio-Informatics +Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+) +Classifier: Programming Language :: Python :: 2 +Classifier: Programming Language :: Python :: 2.6 +Classifier: Programming Language :: Python :: 2.7 +Classifier: Programming Language :: Python :: 3 +Classifier: Programming Language :: Python :: 3.3 +Classifier: Programming Language :: Python :: 3.4 +Classifier: Programming Language :: Python :: 3.5 +Classifier: Programming Language :: C++ +Classifier: Programming Language :: Java +License-File: LICENSE +Requires-Dist: joblib>=0.9.4 +Requires-Dist: pybedtools>=0.6.4 +Requires-Dist: intervaltree>=2.1.0 +Requires-Dist: pandas>=0.13.1 +Requires-Dist: biopython>=1.63 +Requires-Dist: pysam>=0.8.3 +Requires-Dist: Cython>=0.20.1 + + + +### Streamlining SLAM-Seq analysis with ultra-high sensitivity. + +[![GitHub release](https://img.shields.io/github/release/t-neumann/slamdunk.svg)](https://github.com/t-neumann/slamdunk/releases/latest) +[![Travis CI](https://img.shields.io/travis/t-neumann/slamdunk.svg)](https://travis-ci.org/t-neumann/slamdunk) + +[![Docker Pulls](https://img.shields.io/docker/pulls/tobneu/slamdunk.svg)](https://hub.docker.com/r/tobneu/slamdunk) +[![Docker Automated build](https://img.shields.io/docker/automated/tobneu/slamdunk.svg)](https://hub.docker.com/r/tobneu/slamdunk/builds/) + +[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/slamdunk/README.html) +[![Anaconda build](https://anaconda.org/bioconda/slamdunk/badges/version.svg +)](https://anaconda.org/bioconda/slamdunk) +[![Anaconda downloads](https://anaconda.org/bioconda/slamdunk/badges/downloads.svg +)](https://anaconda.org/bioconda/slamdunk) + +[![PyPI release](https://img.shields.io/pypi/v/slamdunk.svg)](https://pypi.python.org/pypi/slamdunk) +![Github Stars](https://img.shields.io/github/stars/t-neumann/slamdunk.svg?style=social&label=Star) + +----- + +### Slamdunk documentation + +http://t-neumann.github.io/slamdunk + +### nf-core slamseq workflow + +[![nfcore/slamseq](https://github.com/nf-core/slamseq/raw/master/docs/images/nf-core-slamseq_logo.png)](https://nf-co.re/slamseq) + +### Please cite + +Neumann, T., Herzog, V. A., Muhar, M., Haeseler, von, A., Zuber, J., Ameres, S. L., & Rescheneder, P. (2019). [Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2849-7). BMC Bioinformatics, 20(1), 258. http://doi.org/10.1186/s12859-019-2849-7 + diff --git a/slamdunk.egg-info/SOURCES.txt b/slamdunk.egg-info/SOURCES.txt new file mode 100644 index 0000000..78456ab --- /dev/null +++ b/slamdunk.egg-info/SOURCES.txt @@ -0,0 +1,48 @@ +LICENSE +MANIFEST.in +README.md +setup.py +slamdunk/__init__.py +slamdunk/alleyoop.py +slamdunk/slamdunk.py +slamdunk/splash.py +slamdunk/version.py +slamdunk.egg-info/PKG-INFO +slamdunk.egg-info/SOURCES.txt +slamdunk.egg-info/dependency_links.txt +slamdunk.egg-info/entry_points.txt +slamdunk.egg-info/requires.txt +slamdunk.egg-info/top_level.txt +slamdunk/dunks/__init__.py +slamdunk/dunks/deduplicator.py +slamdunk/dunks/dump.py +slamdunk/dunks/filter.py +slamdunk/dunks/mapper.py +slamdunk/dunks/simulator.py +slamdunk/dunks/snps.py +slamdunk/dunks/stats.py +slamdunk/dunks/tcounter.py +slamdunk/plot/PCAPlotter.R +slamdunk/plot/SNPeval.R +slamdunk/plot/__init__.py +slamdunk/plot/checkLibraries.R +slamdunk/plot/compute_context_TC_rates.R +slamdunk/plot/compute_conversion_rate_mle.R +slamdunk/plot/compute_halflifes.R +slamdunk/plot/compute_overall_rates.R +slamdunk/plot/compute_sample_comparison_statistics.R +slamdunk/plot/conversion_per_read_position.R +slamdunk/plot/eval_conversion_rate_plots.R +slamdunk/plot/eval_halflife_per_gene_plots.R +slamdunk/plot/eval_halflifes_error_plot.R +slamdunk/plot/globalRatePlotter.R +slamdunk/plot/merge_rate_files.R +slamdunk/plot/splash_eval_count_files.R +slamdunk/slamseq/SlamSeqFile.py +slamdunk/slamseq/__init__.py +slamdunk/test/__init__.py +slamdunk/test/test_sample.py +slamdunk/utils/BedReader.py +slamdunk/utils/SNPtools.py +slamdunk/utils/__init__.py +slamdunk/utils/misc.py \ No newline at end of file diff --git a/slamdunk.egg-info/dependency_links.txt b/slamdunk.egg-info/dependency_links.txt new file mode 100644 index 0000000..8b13789 --- /dev/null +++ b/slamdunk.egg-info/dependency_links.txt @@ -0,0 +1 @@ + diff --git a/slamdunk.egg-info/entry_points.txt b/slamdunk.egg-info/entry_points.txt new file mode 100644 index 0000000..7881900 --- /dev/null +++ b/slamdunk.egg-info/entry_points.txt @@ -0,0 +1,4 @@ +[console_scripts] +alleyoop = slamdunk.alleyoop:run +slamdunk = slamdunk.slamdunk:run +splash = slamdunk.splash:run diff --git a/slamdunk.egg-info/requires.txt b/slamdunk.egg-info/requires.txt new file mode 100644 index 0000000..b73a689 --- /dev/null +++ b/slamdunk.egg-info/requires.txt @@ -0,0 +1,7 @@ +joblib>=0.9.4 +pybedtools>=0.6.4 +intervaltree>=2.1.0 +pandas>=0.13.1 +biopython>=1.63 +pysam>=0.8.3 +Cython>=0.20.1 diff --git a/slamdunk.egg-info/top_level.txt b/slamdunk.egg-info/top_level.txt new file mode 100644 index 0000000..3d939ae --- /dev/null +++ b/slamdunk.egg-info/top_level.txt @@ -0,0 +1 @@ +slamdunk diff --git a/slamdunk/dunks/tcounter.py b/slamdunk/dunks/tcounter.py index 97018e4..221f449 100644 --- a/slamdunk/dunks/tcounter.py +++ b/slamdunk/dunks/tcounter.py @@ -225,6 +225,18 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC for read in readIterator: + ### NEW CODE + # Create cB before mutations get overwritten + if (makeCB): + + key = (read.tcCount, read.getTcount()) + + if key in cB: + cB[key] += 1 + + else: + cB[key] = 1 + # Overwrite any conversions for non-TC reads (reads with < 2 TC conversions) if (not read.isTcRead) : read.tcCount = 0 @@ -258,17 +270,6 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC if(mismatch.isTCMismatch(read.direction == ReadDirection.Reverse)): testk += 1 - ### NEW CODE - if (makeCB): - - key = (testk, read.getTcount()) - - if key in cB: - cB[key] += 1 - - else: - cB[key] = 1 - #print(utr.name, read.name, read.direction, testN, testk, read.sequence, sep="\t") tInReads.append(testN) tcInRead.append(testk) From 27dc665ce4280feef683ff799a52d41a6c4095cc Mon Sep 17 00:00:00 2001 From: isaacvock Date: Mon, 6 May 2024 09:37:30 -0400 Subject: [PATCH 5/8] Count total number of ref Ts and TC mutations --- slamdunk/dunks/tcounter.py | 29 +++++++++++++++++++---------- 1 file changed, 19 insertions(+), 10 deletions(-) diff --git a/slamdunk/dunks/tcounter.py b/slamdunk/dunks/tcounter.py index 221f449..dd51c73 100644 --- a/slamdunk/dunks/tcounter.py +++ b/slamdunk/dunks/tcounter.py @@ -225,17 +225,11 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC for read in readIterator: - ### NEW CODE - # Create cB before mutations get overwritten - if (makeCB): + # Total number of T-to-C mutations in the read + totalTCcnt = read.tcCount - key = (read.tcCount, read.getTcount()) - - if key in cB: - cB[key] += 1 - - else: - cB[key] = 1 + # Total number of reference Ts overlapped (minus those mutated to something other than C) + totalTcnt = read.getTcount() + totalTCcnt # Overwrite any conversions for non-TC reads (reads with < 2 TC conversions) if (not read.isTcRead) : @@ -267,8 +261,23 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC if(mismatch.referencePosition >= 0 and mismatch.referencePosition < utr.getLength()): if(mismatch.isT(read.direction == ReadDirection.Reverse)): testN += 1 + totalTcnt += 1 if(mismatch.isTCMismatch(read.direction == ReadDirection.Reverse)): testk += 1 + else: + if(mismatch.isT(read.direction == ReadDirection.Reverse)): + totalTcnt += 1 + + # Increment TC and nT counts for cB + if (makeCB): + + key = (totalTCcnt, totalTcnt) + + if key in cB: + cB[key] += 1 + + else: + cB[key] = 1 #print(utr.name, read.name, read.direction, testN, testk, read.sequence, sep="\t") tInReads.append(testN) From d648cb3244082edb86efb049c9189b6b39087e55 Mon Sep 17 00:00:00 2001 From: isaacvock Date: Mon, 6 May 2024 09:49:26 -0400 Subject: [PATCH 6/8] Don't double count TC mismatches in nT --- slamdunk/dunks/tcounter.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/slamdunk/dunks/tcounter.py b/slamdunk/dunks/tcounter.py index dd51c73..ae2d48a 100644 --- a/slamdunk/dunks/tcounter.py +++ b/slamdunk/dunks/tcounter.py @@ -229,7 +229,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC totalTCcnt = read.tcCount # Total number of reference Ts overlapped (minus those mutated to something other than C) - totalTcnt = read.getTcount() + totalTCcnt + totalTcnt = read.getTcount() # Overwrite any conversions for non-TC reads (reads with < 2 TC conversions) if (not read.isTcRead) : From 51d369ad3f1eaa6ba63f6aedf1a692af70640a13 Mon Sep 17 00:00:00 2001 From: isaacvock Date: Mon, 6 May 2024 09:53:54 -0400 Subject: [PATCH 7/8] Remove unnecessary files from local install --- slamdunk.egg-info/PKG-INFO | 64 -------------------------- slamdunk.egg-info/SOURCES.txt | 48 ------------------- slamdunk.egg-info/dependency_links.txt | 1 - slamdunk.egg-info/entry_points.txt | 4 -- slamdunk.egg-info/requires.txt | 7 --- slamdunk.egg-info/top_level.txt | 1 - 6 files changed, 125 deletions(-) delete mode 100644 slamdunk.egg-info/PKG-INFO delete mode 100644 slamdunk.egg-info/SOURCES.txt delete mode 100644 slamdunk.egg-info/dependency_links.txt delete mode 100644 slamdunk.egg-info/entry_points.txt delete mode 100644 slamdunk.egg-info/requires.txt delete mode 100644 slamdunk.egg-info/top_level.txt diff --git a/slamdunk.egg-info/PKG-INFO b/slamdunk.egg-info/PKG-INFO deleted file mode 100644 index bc563e2..0000000 --- a/slamdunk.egg-info/PKG-INFO +++ /dev/null @@ -1,64 +0,0 @@ -Metadata-Version: 2.1 -Name: slamdunk -Version: 0.4.3 -Summary: SLAMdunk suite for analyzing SLAM-seq data -Home-page: http://t-neumann.github.io/slamdunk -Author: Tobias Neumann, Philipp Rescheneder -Author-email: tobias.neumann.at@gmail.com, philipp.rescheneder@univie.ac.at -License: GNU Affero General Public License v3 or later (AGPLv3+) -Keywords: Next-Generation-Sequencing NGS QuantSeq SLAMSeq -Classifier: Development Status :: 4 - Beta -Classifier: Intended Audience :: Science/Research -Classifier: Topic :: Scientific/Engineering :: Bio-Informatics -Classifier: License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+) -Classifier: Programming Language :: Python :: 2 -Classifier: Programming Language :: Python :: 2.6 -Classifier: Programming Language :: Python :: 2.7 -Classifier: Programming Language :: Python :: 3 -Classifier: Programming Language :: Python :: 3.3 -Classifier: Programming Language :: Python :: 3.4 -Classifier: Programming Language :: Python :: 3.5 -Classifier: Programming Language :: C++ -Classifier: Programming Language :: Java -License-File: LICENSE -Requires-Dist: joblib>=0.9.4 -Requires-Dist: pybedtools>=0.6.4 -Requires-Dist: intervaltree>=2.1.0 -Requires-Dist: pandas>=0.13.1 -Requires-Dist: biopython>=1.63 -Requires-Dist: pysam>=0.8.3 -Requires-Dist: Cython>=0.20.1 - - - -### Streamlining SLAM-Seq analysis with ultra-high sensitivity. - -[![GitHub release](https://img.shields.io/github/release/t-neumann/slamdunk.svg)](https://github.com/t-neumann/slamdunk/releases/latest) -[![Travis CI](https://img.shields.io/travis/t-neumann/slamdunk.svg)](https://travis-ci.org/t-neumann/slamdunk) - -[![Docker Pulls](https://img.shields.io/docker/pulls/tobneu/slamdunk.svg)](https://hub.docker.com/r/tobneu/slamdunk) -[![Docker Automated build](https://img.shields.io/docker/automated/tobneu/slamdunk.svg)](https://hub.docker.com/r/tobneu/slamdunk/builds/) - -[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat-square)](http://bioconda.github.io/recipes/slamdunk/README.html) -[![Anaconda build](https://anaconda.org/bioconda/slamdunk/badges/version.svg -)](https://anaconda.org/bioconda/slamdunk) -[![Anaconda downloads](https://anaconda.org/bioconda/slamdunk/badges/downloads.svg -)](https://anaconda.org/bioconda/slamdunk) - -[![PyPI release](https://img.shields.io/pypi/v/slamdunk.svg)](https://pypi.python.org/pypi/slamdunk) -![Github Stars](https://img.shields.io/github/stars/t-neumann/slamdunk.svg?style=social&label=Star) - ------ - -### Slamdunk documentation - -http://t-neumann.github.io/slamdunk - -### nf-core slamseq workflow - -[![nfcore/slamseq](https://github.com/nf-core/slamseq/raw/master/docs/images/nf-core-slamseq_logo.png)](https://nf-co.re/slamseq) - -### Please cite - -Neumann, T., Herzog, V. A., Muhar, M., Haeseler, von, A., Zuber, J., Ameres, S. L., & Rescheneder, P. (2019). [Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2849-7). BMC Bioinformatics, 20(1), 258. http://doi.org/10.1186/s12859-019-2849-7 - diff --git a/slamdunk.egg-info/SOURCES.txt b/slamdunk.egg-info/SOURCES.txt deleted file mode 100644 index 78456ab..0000000 --- a/slamdunk.egg-info/SOURCES.txt +++ /dev/null @@ -1,48 +0,0 @@ -LICENSE -MANIFEST.in -README.md -setup.py -slamdunk/__init__.py -slamdunk/alleyoop.py -slamdunk/slamdunk.py -slamdunk/splash.py -slamdunk/version.py -slamdunk.egg-info/PKG-INFO -slamdunk.egg-info/SOURCES.txt -slamdunk.egg-info/dependency_links.txt -slamdunk.egg-info/entry_points.txt -slamdunk.egg-info/requires.txt -slamdunk.egg-info/top_level.txt -slamdunk/dunks/__init__.py -slamdunk/dunks/deduplicator.py -slamdunk/dunks/dump.py -slamdunk/dunks/filter.py -slamdunk/dunks/mapper.py -slamdunk/dunks/simulator.py -slamdunk/dunks/snps.py -slamdunk/dunks/stats.py -slamdunk/dunks/tcounter.py -slamdunk/plot/PCAPlotter.R -slamdunk/plot/SNPeval.R -slamdunk/plot/__init__.py -slamdunk/plot/checkLibraries.R -slamdunk/plot/compute_context_TC_rates.R -slamdunk/plot/compute_conversion_rate_mle.R -slamdunk/plot/compute_halflifes.R -slamdunk/plot/compute_overall_rates.R -slamdunk/plot/compute_sample_comparison_statistics.R -slamdunk/plot/conversion_per_read_position.R -slamdunk/plot/eval_conversion_rate_plots.R -slamdunk/plot/eval_halflife_per_gene_plots.R -slamdunk/plot/eval_halflifes_error_plot.R -slamdunk/plot/globalRatePlotter.R -slamdunk/plot/merge_rate_files.R -slamdunk/plot/splash_eval_count_files.R -slamdunk/slamseq/SlamSeqFile.py -slamdunk/slamseq/__init__.py -slamdunk/test/__init__.py -slamdunk/test/test_sample.py -slamdunk/utils/BedReader.py -slamdunk/utils/SNPtools.py -slamdunk/utils/__init__.py -slamdunk/utils/misc.py \ No newline at end of file diff --git a/slamdunk.egg-info/dependency_links.txt b/slamdunk.egg-info/dependency_links.txt deleted file mode 100644 index 8b13789..0000000 --- a/slamdunk.egg-info/dependency_links.txt +++ /dev/null @@ -1 +0,0 @@ - diff --git a/slamdunk.egg-info/entry_points.txt b/slamdunk.egg-info/entry_points.txt deleted file mode 100644 index 7881900..0000000 --- a/slamdunk.egg-info/entry_points.txt +++ /dev/null @@ -1,4 +0,0 @@ -[console_scripts] -alleyoop = slamdunk.alleyoop:run -slamdunk = slamdunk.slamdunk:run -splash = slamdunk.splash:run diff --git a/slamdunk.egg-info/requires.txt b/slamdunk.egg-info/requires.txt deleted file mode 100644 index b73a689..0000000 --- a/slamdunk.egg-info/requires.txt +++ /dev/null @@ -1,7 +0,0 @@ -joblib>=0.9.4 -pybedtools>=0.6.4 -intervaltree>=2.1.0 -pandas>=0.13.1 -biopython>=1.63 -pysam>=0.8.3 -Cython>=0.20.1 diff --git a/slamdunk.egg-info/top_level.txt b/slamdunk.egg-info/top_level.txt deleted file mode 100644 index 3d939ae..0000000 --- a/slamdunk.egg-info/top_level.txt +++ /dev/null @@ -1 +0,0 @@ -slamdunk From e529e776d796233a7b7efcdda4c4dca26b0bd5a9 Mon Sep 17 00:00:00 2001 From: isaacvock Date: Fri, 10 May 2024 20:54:41 -0400 Subject: [PATCH 8/8] Update comments --- slamdunk/dunks/tcounter.py | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/slamdunk/dunks/tcounter.py b/slamdunk/dunks/tcounter.py index ae2d48a..9ccbe0e 100644 --- a/slamdunk/dunks/tcounter.py +++ b/slamdunk/dunks/tcounter.py @@ -24,7 +24,6 @@ import os import re -### NEW CODE import csv from os.path import basename @@ -151,7 +150,6 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC print("#annotation:", os.path.basename(bed), bedMD5, sep="\t", file=fileCSV) print(SlamSeqInterval.Header, file=fileCSV) - ### NEW CODE ## Create cB output file if necessary if (makeCB): @@ -216,7 +214,6 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC multiMapFwd = 0 multiMapRev = 0 - ### NEW CODE ## Dictionary to track number of unique combos ## of T-to-C counts and T counts if (makeCB): @@ -288,7 +285,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC if(i >= 0 and i < utr.getLength()): coverageUtr[i] += 1 - ### NEW CODE + # Write to cB file if (makeCB): for (tc, nt), count in cB.items(): @@ -375,7 +372,7 @@ def computeTconversions(ref, bed, snpsFile, bam, maxReadLength, minQual, outputC fileBedgraphPlus.close() fileBedgraphMinus.close() - ### NEW CODE + # Close cB file connection if (makeCB): fileCB.close()