debug 0

McTavishLab · Jun 19, 2020 · 66d45fe · 66d45fe
1 parent 1474832
commit 66d45fe
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Showing 2 changed files with 2 additions and 8 deletions.
diff --git a/bin/physcraper_run.py b/bin/physcraper_run.py
@@ -204,13 +204,7 @@
     to_be_blasted = [otu.label for otu in scraper.data.aln if (scraper.data.otu_dict[otu.label]['^physcraper:ingroup'] == True and scraper.data.otu_dict[otu.label]['^physcraper:last_blasted']==None)]
     while len(to_be_blasted) >= 1:
         run += 1
-        prev_workdir = scraper.workdir()
-        new_workdir = "{}/run{}".format(workdir, run)
-        os.mkdir(new_workdir)
-        data_obj = generate_ATT_from_run(prev_workdir, configfile=conf)
-        data_obj.workdir = new_workdir
-        scraper = physcraper.PhyscraperScrape(data_obj, ids)
-        sys.stdout.write("Reloaded {} taxa in alignment and tree\n".format(len(scraper.data.aln)))
+        scraper.run_blast_wrapper()
         scraper.calculate_final_tree(boot_reps = boot_reps)
         to_be_blasted = [otu.label for otu in scraper.data.aln if (scraper.data.otu_dict[otu.label]['^physcraper:ingroup'] == True and scraper.data.otu_dict[otu.label]['^physcraper:last_blasted']==None)]
 elif not args.no_estimate_tree:

diff --git a/physcraper/scrape.py b/physcraper/scrape.py
@@ -26,7 +26,7 @@
 from physcraper import AWSWWW
 
 _VERBOSE = 1
-_DEBUG = 1
+_DEBUG = 0
 def debug(msg):
     """short debugging command
     """