Mercurial > repos > artbio > repenrich2

diff RepEnrich2.py @ 8:567549a49eb2 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich2 commit b3b166a8e991f49227e4888b8065b57cec0ba949
author artbio
date Thu, 25 Apr 2024 09:06:48 +0000
parents 61e0404f0d76
children 2b61c6407efb
line wrap: on
line diff
--- a/RepEnrich2.py	Tue Apr 23 21:44:44 2024 +0000
+++ b/RepEnrich2.py	Thu Apr 25 09:06:48 2024 +0000
@@ -110,7 +110,7 @@
     write to files to save memory
     '''
     metagenome, fastqfile = args
-    b_opt = "-k 1 -p 1 --quiet --no-hd"
+    b_opt = "-k 1 -p 1 --quiet --no-hd --no-unal"
     command = shlex.split(f"bowtie2 {b_opt} -x {metagenome} {fastqfile}")
     bowtie_align = subprocess.run(command, check=True,
                                   capture_output=True, text=True).stdout
@@ -148,6 +148,7 @@
         repeats_by_reads[read].append(repname)
 for repname in repeats_by_reads:
     repeats_by_reads[repname] = list(set(repeats_by_reads[repname]))
+    # this repeats_by_reads dictionary is far too big
 
 # 3 dictionnaries and 1 pointer variable to be populated
 fractionalcounts = defaultdict(float)