Differences

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--- taxonomy_recovery [2021/09/21 13:33] – 134.190.232.139
+++ taxonomy_recovery [2024/06/11 10:31] (current) – 129.173.94.151
@@ Line 10: / Line 10: @@
 don't forget to make sure that your input file contains only the accession numbers without their version, see the example file given above.
--_- E.g., MBI4782295.1 shall be MBI4782295, otherwise the bugs will occur:
+:-( E.g., MBI4782295.1 shall be MBI4782295, otherwise the bugs will occur:
 <code>
@@ Line 17: / Line 17: @@
 </code>
-'^_^' Trim the version ".1" behind the accession MBI4782295.1
+:-D Trim the version ".1" behind the accession MBI4782295.1
 <code>
-> sed 's/\(.*\)\..*/\1/g' file >out_file
+> cat file | cut -d '.' -f1 > out_file
 </code>
-Note: It still could acquire a lot of unknown even the NCBI taxonomy database is the latest. Any ideas?
+Note:
+. You can get the accession list from Blast/Plast result (output.txt) directly using the command below:
+<code>
+> cat output.txt | cut  -f2 | cut -d '.' -f1 > out_file
+</code>
+. If there are "|" in the accession numbers (i.e., gb|KAA8922376.1|)
+<code>
+> cat output.txt | cut -d "|" -f2 | cut -d '.' -f1 > out_file
+</code>
+. It can still acquire a list of unknown like below even the NCBI taxonomy database is updated to the latest.
+<code>
 Couldn't find: [MBR3349819]
 Couldn't find: [HBS54143]
 Couldn't find: [MYJ28876]
+</code>
+This might due to these protein IDs(MBR3349819,HBS54143) from the species cannot put into the taxonomy like NP_051083. i.e., Lineage is not in (full) status.
+<code>
+NP_051083	cellular organisms,Eukaryota,Viridiplantae,Streptophyta,Streptophytina,Embryophyta,Tracheophyta,Euphyllophyta,Spermatophyta,Magnoliopsida,Mesangiospermae,eudicotyledons,Gunneridae,Pentapetalae,rosids,malvids,Brassicales,Brassicaceae,Camelineae,Arabidopsis,Arabidopsis thaliana
+</code>
 ==========================
-acc2tax database:\\
+acc2tax database Location:\\
-/scratch3/rogerlab_databases/other_dbs/Acc2Tax_Feb122021		(Up to date Feb 23, 2021)
+/db1/extra-data-sets/Acc2tax/
+/db1/extra-data-sets/Acc2tax/Acc2Tax_04_01_2024		(Up to date Jan 04, 2024)
-/misc/db1/extra-data-sets/Acc2tax/Acc2tax_092021		(Up to date Sep 20, 2021)
 \\
+<Last updated by Dandan Zhao on Jun 11, 2024>