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* Major DROP update * removed obsolete file * changed project folder structure for initialisation * API change: separated config and sample annotation parsers * fixed missin root path * import config differently * package finding for subpackage * running pipeline * added circleci config * removed obsolete file * changed project folder structure for initialisation * API change: separated config and sample annotation parsers * fixed missin root path * import config differently * package finding for subpackage * using correct .travis.yml * removed subworkflow and running pipeline for aberrantExpression; new functions introduced for Script-Rule-Html conversions; analysis script directory renamed; pipeline code copied to different destination * removed subworkflow for AS and MAE; changed folder structure; using log for tmp snakemake objects * fixed input flags for analysis scripts * running pipeline * added circleci config * removed obsolete file * changed project folder structure for initialisation * API change: separated config and sample annotation parsers * fixed missin root path * import config differently * package finding for subpackage * API change: separated config and sample annotation parsers * fixed missin root path * import config differently * package finding for subpackage * removed subworkflow and running pipeline for aberrantExpression; new functions introduced for Script-Rule-Html conversions; analysis script directory renamed; pipeline code copied to different destination * removed subworkflow for AS and MAE; changed folder structure; using log for tmp snakemake objects * fixed input flags for analysis scripts * set submodules to master * applied branch-specific modifications * removed submodules.py and refactored path setup * fixed Readme and config copy errors * fixed copying helpers functions * using wbuild with fixed Readme.html functionality and saving wbuild config in DropConfig * moved exportCounts into separate class * parsing GENE_COUNT_FILE column in sample annotation * removed wbuild from conda recipe * using bioconda version of drop for dependencies, pip install drop, no conda building * remove bioconda wbuild * install wbuild with expl pip * remove wbuild with pip * get count info from AE class * some refactoring and saving external counts IDs in separate dictionary * removed ID renaming in merge script (naming already in counts script); fixed missing input bug in DropConfig * add external counts to count files * merge counts and coverage including external counts * file checks for config and sample annotation reimplemented * config file getters for submodules * refactored export counts * travis run export counts rule * reapplied bcftools command modification * Documentation update (#102) * README update to include Baylor counts * updated drop installation command * update install command docs to include conda-forge plus better descriptions Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Michaela Müller <mi.mueller@tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> * updated documentation to include count import * splicing export counts all columns added * resolved requested formality errors * fixed requested MAE changes * removed scanBamParam * create missing columns for MAE results * Subindex (#3) * first version of subindex implemented * including readme and dependency graph for subindexes; removed fileRegex key from config (using default of ".*\.(R|md)") * using different (wb1.8) config file * separated dependency graph computation from rest of the pipeline * using latest updated wbuild version * use conda install for wbuild Co-authored-by: mumichae <mi.mueller@tum.de> * Fix version for wbuild (#108) Co-authored-by: mumichae <mi.mueller@tum.de> * updated version number in README and drop/cli * Tests (#4) Added pytest suite to project. The main things tested are: * cli: basic drop command line functions * all config classes * pipeline runs for all submodules (including checking numbers of entries in output) and count export ## Commits * first setup of pytest, pipeline runthroughs, no output checking yet * updated version number in README and drop/cli * fixed dependencies * pip uninstall with -y * changed pytest installation and error catching * compare pipeline output and add more pipeline tests * refactored pipeline tests * fixed demo creation * refactored pipeline tests again & fixed fixture scoping * fixed minor issues in tests * added config tests * refactored getHtmlFromScript Co-authored-by: mumichae <mi.mueller@tum.de> * downloading data to temporary directory * updated version to 1.0.0 Co-authored-by: Michaela Müller <mi.mueller@tum.de> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> * updated travis to use correct R and wbuild versions * use github release badge instead of fixing it * Fix Issue #114 (#116) * refactored drop demo code s.t. config and sample annotation files are in the package * adapted pipeline to handle non-existing external counts new group in demo to distinguish count import from no count import cases some bugfixes regarding exportCounts parsing and import counts subsetting * fixed AE pipeline test * travis with latest R version 4 * revert pipeline in pytest to 2 cores * R 4.0.2 Co-authored-by: mumichae <mi.mueller@tum.de> * Refactoring (#118) * refactored Submodule classes into separate files * using MAE and AS functions from respective classes instead of Snakefile or R script header * fixed input for MAE rules * use chr with bam counts for ASEReadCounter * added test for aberrant splicing count file functions * FRASER compatibility fixes * fixed subsetGroup API change Co-authored-by: Michaela Müller <mi.mueller@tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> * using wbuild 1.8.0 for pip installation * fixed travis install error * adapt DROP to theta usage in FRASER (#129) * adapt DROP to theta usage in FRASER * use travis wait * due to new filters one donor site is deleted * Fix import counts (#122) * updated version number * version checking for drop * use defaultdict for group IDs; add testcase for removing import counts in demo input; fix count param data types * moved no import file modifications into separate fixture * fixed sample annotation ID mapping check * using groups defined in config instead of inferring from ID objects * force ignoring first column as index when reading sample annotation file * added wait to pytest command * drop update to overwrite files every time & shortened output for creating drop demo fixture * fixed deprecation message * profiling runtime for tests Co-authored-by: mumichae <mi.mueller@tum.de> * Offline addons (#137) * Update gene_name_mapping.R * add hpoFile option * fix hg38 on FRASER counting * doc hpoFile, files to download * add hpoFile option * doc hpoFile, files to download * vcf doc fixed * gene_biotype added Co-authored-by: Vicente <yepez@in.tum.de> * Offline addons (#139) * Update gene_name_mapping.R * add hpoFile option * fix hg38 on FRASER counting * doc hpoFile, files to download * add hpoFile option * doc hpoFile, files to download * vcf doc fixed * gene_biotype added * hpo term column can be blank Co-authored-by: Vicente <yepez@in.tum.de> * remove file extension in outrider module (#140) * Update splicing export (#141) * export known junction with K and N counts * add AnnotationDbi * fix type * properly load BSgenome * correctly export splice counts (use K and N) and use GTF seqlevelsStyle * speed up conda install * fix package removal * use travis python version for drop environment Co-authored-by: mumichae <51025211+mumichae@users.noreply.github.com> * Version check (#143) * include version check for R packages when calling pipeline * silence package loading when checking R installation * hide warning messages in R install Co-authored-by: mumichae <mi.mueller@tum.de> * better check for chromosome style (#148) * GitHub actions (#151) * Create python-package-conda.yml * install repo version of drop * commented out travis file * Export counts meta (#144) * refactored writing export count meta files in separate python script rather than SampleAnnotation script * include python scripts in non-module directories upon installation Co-authored-by: mumichae <mi.mueller@tum.de> * use buildins for flake8 * Install needed BSgenome on the fly (#147) * remove assembly specific packages closes #142 * fix pipeline when no import count matrix in sample annotation #114 * refactored config parsers by submodule * update to FRASER 1.2.0 @c-mertes * update aberrant splicing export @c-mertes * local loading of HPO file if present @vyepez88 * fixed buggy file extension when saving ods @jemten * Add files via upload (#146) * update OUTRIDER version and bugfixes * allow NCBI based assembly in config fixes #135 * move assembly version test to DropConf and adjust the pipeline. * add unlock if snakemake fails * use addAF to check installation * Add badge to readme Co-authored-by: mumichae <51025211+mumichae@users.noreply.github.com> Co-authored-by: Vicente Yepez <30469316+vyepez88@users.noreply.github.com> * Offline res (#160) * annotate splice results using GTF (requires FRASER 1.3.0) * added random seed for demo Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> * add bumpversion config * Bump version: 1.0.2 → 1.0.3 * rename gene_biotype->gene_type in GTF (#162) * Apply suggestions from code review Co-authored-by: Christian Mertes <mertes@in.tum.de> * FRASER version and author list Co-authored-by: Christian Mertes <mertes@in.tum.de> * Simplify MAE Pipeline (#158) * removed separate QC VCF workflow, reusing MAE workflow * Chr style (#177) * mae chr style fixed * bug in chr style of FRASER fixed * add possibility of both chr styles * ncbi fds object added * minor fixes chr subset * count matrices added Co-authored-by: Vicente <yepez@in.tum.de> * Qol changes (#179) QOL changes are made to improve the ease and user experience. This branch contains changes to allow the following: * safe overwriting of the local working directory with changes from the source drop directory. This should save some reprocessing time as only modified scripts will be rerun * allowing multiple genomic reference files. allow for user to designate multiple references or a global reference from the config file and sample annotation table * added additional checks and error messages * use changes in the sample annotation to trigger reruns of the aberrantExpression and MAE pipelines. (aberrantSplicing is still in progress) * Update warnings/errors * Update tests * Handle GENOME column * Backwards compatibility: ANNOTATION -> GENE_ANNOTATION * Docs sample anno expanded including genome option * update wildcard constraint * Refactored genome operations to separate Genome class * sampleParams file and class * remove sampleParam code from Submodule class Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: nickhsmith <smithnickh@gmail.com> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> * Qol changes real (#185) * fresh QOL branch * remove GENOME when not in SA * configure paths, and fix tests to be more specific * update pytest test_AS.py * Update 07_extract_results_FraseR.R * Update DropConfig.py * Update SampleAnnotation.py * Update test_AS.py add potential future test for ncbi_fds obj * Update test_AS.py update assert * additional checks and warnings for reading genome path * fix warning trigger * update sa-table column header. ANNOTATION -> GENE_ANNOTATION * docs sample anno expanded * check if sample has both BAM and extcount inputs * update warnings * docs updated with genome option * force r-dpylr later version install * correct typo * set r-dpylr value * update warnings * update warnings/errors * add comments, and changes based on code review discussion * update wildcard constraint, and move it from AS to main template * Refactored genome operations to separate Genome class * rename sample sa to annotationTable * fix reference mapping * save local changes * sampleParams file and class * remove sampleParam code from Submodule class * update errors and warnings for MAE Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> Co-authored-by: mumichae <51025211+mumichae@users.noreply.github.com> Co-authored-by: Michaela Müller <mi.mueller@tum.de> Co-authored-by: Vicente <yepez@in.tum.de> Co-authored-by: Christian Mertes <mertes@in.tum.de> Co-authored-by: Anders Jemt <jemten@users.noreply.github.com> Co-authored-by: Michaela Mueller <mumichae@in.tum.de> Co-authored-by: Alex Paul <github@ajpdev.com> Co-authored-by: Smith Nicholas <smith@in.tum.de> Co-authored-by: nickhsmith <smithnickh@gmail.com>
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