diff --git a/cutseq/run.py b/cutseq/run.py index 9b0e769..d87d205 100644 --- a/cutseq/run.py +++ b/cutseq/run.py @@ -33,7 +33,7 @@ ) from cutadapt.pipeline import PairedEndPipeline, SingleEndPipeline from cutadapt.predicates import Predicate, TooShort -from cutadapt.report import Statistics +from cutadapt.report import Statistics, minimal_report from cutadapt.runners import make_runner from cutadapt.steps import ( PairedEndFilter, @@ -300,6 +300,7 @@ def pipeline_single(input1, output1, short1, untrimmed1, barcode, settings): ) pipeline = SingleEndPipeline(modifiers, steps) _stats = runner.run(pipeline, Progress(), outfiles) + print(minimal_report(_stats, time=None, gc_content=None), file=sys.stderr) # _ = stats.as_json() outfiles.close() @@ -495,12 +496,13 @@ def pipeline_paired( ) pipeline = PairedEndPipeline(modifiers, steps) _stats = runner.run(pipeline, Progress(), outfiles) + print(minimal_report(_stats, time=None, gc_content=None), file=sys.stderr) # _ = stats.as_json() outfiles.close() def run_cutseq(args): - barcode_config = BarcodeConfig(args.replace(" ", "").adapter_scheme.upper()) + barcode_config = BarcodeConfig(args.adapter_scheme.replace(" ", "").upper()) settings = CutadaptConfig() settings.rname_suffix = args.with_rname_suffix settings.ensure_inline_barcode = args.ensure_inline_barcode diff --git a/pyproject.toml b/pyproject.toml index eef7e9b..6bc48a0 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,6 +1,6 @@ [tool.poetry] name = "cutseq" -version = "0.0.8" +version = "0.0.9" description = "Automatically cut adapter / barcode / UMI from NGS data" authors = ["Ye Chang "] license = "MIT"