From aec2228c3e63938de207af96ea1096d842eaa9f9 Mon Sep 17 00:00:00 2001 From: Tobias Andermann Date: Fri, 15 Jan 2021 03:23:01 +0100 Subject: [PATCH] complete rewrite of align_sequences, added trimal trimming --- secapr/align_sequences.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/secapr/align_sequences.py b/secapr/align_sequences.py index 0ba594a..c0914f2 100755 --- a/secapr/align_sequences.py +++ b/secapr/align_sequences.py @@ -203,7 +203,7 @@ def main(args): # align sequence collections #too_short_alignments = [] - seq_collections = glob.glob(tmp_dir+'/*.fasta')[:40] #XXXXXXXXXXXXXXXXXXX REMOVE [:20] + seq_collections = glob.glob(tmp_dir+'/*.fasta') pool_input = [[i,len(seq_collections),seq_collection,aligner,gap_opening_penalty,gap_extension_penalty,no_trim,trimal_setting,window_size,seq_proportion,conserve_alignment_percentage,min_length,outdir] for i,seq_collection in enumerate(seq_collections)]