From 6d7681c76c8962a9229770dbed4be4726d3c8c03 Mon Sep 17 00:00:00 2001 From: aljpetri Date: Thu, 21 Sep 2023 10:26:54 +0300 Subject: [PATCH] Added contact information to README, improved argument explanations --- README.md | 4 ++++ main.py | 13 +++++++------ 2 files changed, 11 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index 53ccc78..8083a1c 100644 --- a/README.md +++ b/README.md @@ -65,6 +65,10 @@ the isON-pipeline (isONclust, isONcorrect, isONform) can be run via: (Note that this requires pychopper, isONclust and isONcorrect to be installed) +## Contact +If you encounter any problems, please raise an issue on the issues page, you can also contact the developer of this repository via: +alexander.petri[at]math.su.se + ## Credits diff --git a/main.py b/main.py index 68ceeb0..f47b9d7 100644 --- a/main.py +++ b/main.py @@ -339,6 +339,7 @@ def find_most_supported_span(r_id, m1, p1, m1_curr_spans, minimizer_combinations def main(args): + #Todo: add timestamp print("ARGS",args) all_batch_reads_dict={} # start = time() @@ -527,7 +528,7 @@ def main(args): #profiler = Profiler() #profiler.start() #generate the graph from the intervals - + #TODO: add timestamp DG, reads_for_isoforms = GraphGeneration.generateGraphfromIntervals( all_intervals_for_graph, k_size, delta_len, read_len_dict,new_all_reads) #profiler.stop() @@ -593,7 +594,7 @@ def main(args): parser.add_argument('--xmin', type=int, default=18, help='Upper interval length') parser.add_argument('--xmax', type=int, default=80, help='Lower interval length') parser.add_argument('--T', type=float, default=0.1, help='Minimum fraction keeping substitution') - parser.add_argument('--exact', action="store_true", help='Get exact solution for WIS for evary read (recalculating weights for each read (much slower but slightly more accuracy,\ + parser.add_argument('--exact', action="store_true", help='Get exact solution for WIS for every read (recalculating weights for each read (much slower but slightly more accuracy,\ not to be used for clusters with over ~500 reads)') parser.add_argument('--disable_numpy', action="store_true", help='Do not require numpy to be installed, but this version is about 1.5x slower than with numpy.') @@ -607,17 +608,17 @@ def main(args): help='Set w = k + max(2*k, floor(cluster_size/1000)).') parser.add_argument('--verbose', action="store_true", help='Print various developer stats.') - parser.add_argument('--compression', action="store_true", help='Use homopolymenr compressed reads. (Deprecated, because we will have fewer \ + parser.add_argument('--compression', action="store_true", help='Use homopolymer compressed reads. (Deprecated, because we will have fewer \ minmimizer combinations to span regions in homopolymenr dense regions. Solution \ - could be to adjust upper interval legnth dynamically to guarantee a certain number of spanning intervals.') + could be to adjust upper interval length dynamically to guarantee a certain number of spanning intervals.') parser.add_argument('--outfolder', type=str, default=None, - help='A fasta file with transcripts that are shared between samples and have perfect illumina support.') + help='The outfolder of isONform, into which the algorithm will write the results.') parser.add_argument('--iso_abundance', type=int,default=5, help='Cutoff parameter: abundance of reads that have to support an isoform to show in results') parser.add_argument('--delta_iso_len_3', type=int, default=30, help='Cutoff parameter: maximum length difference at 3prime end, for which subisoforms are still merged into longer isoforms') parser.add_argument('--delta_iso_len_5', type=int, default=50, help='Cutoff parameter: maximum length difference at 5prime end, for which subisoforms are still merged into longer isoforms') - parser.add_argument('--parallel',type=bool,default=False,help='indicates whether we run the parallelization wrapper script') + parser.add_argument('--parallel',type=bool,default=False,help='Indicates whether we run the parallelization wrapper script') parser.add_argument('--slow',action="store_true", help='EXPERIMENTAL PARAMETER: has high repercussions on run time use the slow mode for the simplification of the graph (bubble popping), slow mode: every bubble gets popped.') args = parser.parse_args()