diff --git a/README.md b/README.md index c15cdc8..859684e 100644 --- a/README.md +++ b/README.md @@ -6,7 +6,7 @@ Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedto ## Requirements ``` -abyss>=2.0.0 +abyss==2.0.1 (something is happening with 2.0.2 and abyss-bloom kmers) bedtools (tested on 2.0) python3 biopython diff --git a/exfi/__init__.py b/exfi/__init__.py index 7579919..44bea25 100644 --- a/exfi/__init__.py +++ b/exfi/__init__.py @@ -3,4 +3,4 @@ filters. """ -__version__ = '1.4.11' +__version__ = '1.4.12' diff --git a/exfi/build_splice_graph_dict.py b/exfi/build_splice_graph_dict.py index a020acc..ebdf520 100644 --- a/exfi/build_splice_graph_dict.py +++ b/exfi/build_splice_graph_dict.py @@ -191,13 +191,13 @@ def build_splice_graph_dict( bed6df_dict = bed3_records_to_bed6df_dict(bed3records) # Initialize pool of workers - pool = mp.Pool(args["threads"]) + pool = mp.Pool(args["threads"], maxtasksperchild=1) # Build graphs in parallel and merge results splice_graphs = pool.map( build_splice_graph, bed6df_dict.values(), - chunksize=1000 + chunksize=1000 # Number of Transcripts to process at one ) pool.close() pool.join() diff --git a/exfi/correct.py b/exfi/correct.py index 5b92696..0506911 100644 --- a/exfi/correct.py +++ b/exfi/correct.py @@ -400,14 +400,14 @@ def correct_splice_graph_dict(splice_graph_dict: SpliceGraphDict, args: dict) -> filled_edges_by_transcript[transcript] = set() # Initialize pool of workers - pool = mp.Pool(args["threads"]) + pool = mp.Pool(args["threads"], maxtasksperchild=1) # Process each graph in parallel logging.info("\tCorrecting each splice graph") corrected_splice_graphs = pool.starmap( _sculpt_graph, zip(splice_graph_dict.values(), filled_edges_by_transcript.values()), - chunksize=1000 + chunksize=1000 # Number of splice graphs to process at once. ) pool.close() pool.join() diff --git a/exfi/polish.py b/exfi/polish.py index 4c65dbe..7aef2ac 100644 --- a/exfi/polish.py +++ b/exfi/polish.py @@ -153,7 +153,7 @@ def polish_splice_graph_dict( """ # Initialize pool of workers - pool = mp.Pool(args["threads"]) + pool = mp.Pool(args["threads"], maxtasksperchild=1) splice_graphs = (splice_graph for splice_graph in splice_graph_dict.values()) fasta_dicts = ( @@ -163,7 +163,7 @@ def polish_splice_graph_dict( results = pool.starmap( polish_splice_graph, zip(splice_graphs, fasta_dicts), - chunksize=1000 + chunksize=1000 # Number of splice_graphs to process at once ) pool.close() pool.join()