# HG changeset patch
# User p.lucas
# Date 1644423643 0
# Node ID b5b8f3cb240c66aa3afe9382cbc31fc3af87ae17
# Parent  7b55dec91dd1ab44330e31b19f530defc59d12c5
MAJ python script by FT

diff -r 7b55dec91dd1 -r b5b8f3cb240c MEGABLAST_TAB_get_taxid_acc.py
--- a/MEGABLAST_TAB_get_taxid_acc.py	Fri Feb 04 14:11:46 2022 +0000
+++ b/MEGABLAST_TAB_get_taxid_acc.py	Wed Feb 09 16:20:43 2022 +0000
@@ -10,21 +10,14 @@
 # NOTE: to update krona tax in conda env, run:
 # ktUpdateTaxonomy.sh
 # ktUpdateTaxonomy.sh --accessions (this one NOT PROVIDED IN DOCUMENTATION)
-import argparse, os, sys, csv, re, warnings
+import argparse, os, sys, warnings
 # NEEDS to use krona conda environnement if access ktGetTaxIDFromAcc
 from os import path
-# from optparse import OptionParser
-from datetime import datetime #, timezone
-import pytz
-from natsort import natsorted
 
 # to be able to report line number in error messages
 import inspect
 frame = inspect.currentframe()
 
-# start_time = datetime.now(timezone.utc)
-start_time = datetime.now(pytz.utc)
-
 # debug
 b_test_creates_taxid_acc_f_from_megablast_res = False # ok 2022 01 21
 
@@ -106,8 +99,9 @@
 krona_taxid_acc_f = ''
 def creates_taxid_acc_f_from_megablast_res(megablast_f, tax_acc_out_f):
     acc_col_nb_in_megablast_res = str(2)
-    krona_taxdb_f = os.path.expanduser("/db/krona/") # krona['taxdb'] # "/nfs/data/db/tax_krona/"
-    if not os.path.isfile(krona_taxdb_f + "all.accession2taxid.sorted"):
+    # krona_taxdb_f = os.path.expanduser('~/miniconda3/envs/krona/opt/krona/taxonomy/') # krona['taxdb'] # "/nfs/data/db/tax_krona/"
+    krona_taxdb_f = os.path.expanduser('/db/krona/') # krona['taxdb'] # "/nfs/data/db/tax_krona/"
+    if not os.path.isfile(krona_taxdb_f + 'all.accession2taxid.sorted'):
         sys.exit(prog_tag + "[Error] missing "+krona_taxdb_f+" file, please run 'ktUpdateTaxonomy.sh --accessions' in your krona conda environment (and 'ktUpdateTaxonomy.sh' before if you have not done)")
 
     # conda: "../envs/krona.yaml"
@@ -146,9 +140,6 @@
     # creates taxid acc file from megablast result
     creates_taxid_acc_f_from_megablast_res(megablast_f, tax_acc_out_f)
 
-    stop_time = datetime.now(pytz.utc)
-    duration = stop_time - start_time
-    print("duration:",duration)
 #### MAIN END
 if __name__ == "__main__": __main__()