cgeb2001's DokuWiki!

This part, basically, we are trying to figure out how to acquire the taxa for the genes in MMETSP and NCBI database. First, we display the acc2tax software usage here:

1. Usage of Acc2tax

#acc2tax https://github.com/richardmleggett/acc2tax 
# Given a file of accessions or Genbank IDs (one per line), this program will return a taxonomy string for each.
# http://129.173.88.134:81/dokuwiki/doku.php?id=taxonomy_recovery 

#Input file
CDH53707
XP_011133305
KMU79707
XP_002963095

#Outputfile
CDH53707	cellular organisms,Eukaryota,Opisthokonta,Fungi,Fungi incertae sedis,Mucoromycota,Mucoromycotina,Mucoromycetes,Mucorales,Lichtheimiaceae,Lichtheimia,Lichtheimia corymbifera,Lichtheimia corymbifera JMRC:FSU:9682
XP_011133305	cellular organisms,Eukaryota,Alveolata,Apicomplexa,Conoidasida,Gregarinasina,Eugregarinorida,Gregarinidae,Gregarina,Gregarina niphandrodes
KMU79707	cellular organisms,Eukaryota,Opisthokonta,Fungi,Dikarya,Ascomycota,saccharomyceta,Pezizomycotina,leotiomyceta,Eurotiomycetes,Eurotiomycetidae,Onygenales,Onygenales incertae sedis,Coccidioides,Coccidioides immitis,Coccidioides immitis RMSCC 3703

   acc2tax -i /db1/extra-data-sets/Acc2tax/acc2taxIN_example -p -d /db1/extra-data-sets/Acc2tax/Acc2Tax_071119 -o taxonomy.out

Note: 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:

Couldn't find: [MBI4782295.1]

Trim the version “.1” behind the accession MBI4782295.1

> sed 's/\(.*\)\..*/\1/g' file >out_file

Note: It can still acquire a list of unknown like below even the NCBI taxonomy database is updated to the latest.

Couldn't find: [MBR3349819]
Couldn't find: [HBS54143]
Couldn't find: [MYJ28876]

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.

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

# acc2tax database directory:
/misc/db1/extra-data-sets/Acc2tax/Acc2tax_092021

2. MMETSP hierarchical taxonomic info

#New MMETSP database was used containing the taxonomy information.
dir: >/db1/extra-data-sets/MMETSP/MMETSP_db/MMETSP_DB_clean.v2018.fa
fasta: >MMETSP0484-20121128|722 Rhodomonas_lens_Strain_RHODO 
HHYGDSHFBSJBSCJSJKCHSFBSMCNSBCMBSM

# VS
dir: >/scratch3/sibbald/DATABASES/CAM_P_0001000.pep.renamed_nr_db_temp.fas
fasta: >Symbiodinium_sp@CP_0181467638_Eukaryota_Alveolata_Dinophyceae_Suessiales_Symbiodiniaceae_Symbiodinium_zzz_CP_0181467638_174948_Symbiodinium_sp_CCMP421
SDFHSJFBSNVMSNVMSBHVDBCDMSNCSKFNB

Reducing the redundancy of MMETSP and NCBI-nr. CD-HIT

> cd-hit-est -i out_AT5G15450.1_hits.fa -o AT5G15450.1_clp -c 0.8 -n 10

#CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses.

#sequence identity threshold, default 0.9
 this is the default cd-hit's "global sequence identity" calculated as:
 number of identical amino acids in alignment
 divided by the full length of the shorter sequence
#nword_length, default 10, see user's guide for choosing it

3. Trivia

# acquire the taxon info. 
>grep 'AT5G53350.1' /Users/####/Desktop/MMETSP/CAM_MMETSP/BLASTP_CAM_MMETSP_tair10_5.tsv |awk '{print $2}'|sed 's/_/\t/g'|awk '{print $3}'|sort -V|uniq >1.txt

#acquire the length of fasta file.
awk '/^>/{if (l!="") print l; print; l=0; next}{l+=length($0)}END{print l}' /Users/####/Desktop/Athaliana_Project_2021/Athaliana_24_aa.fasta |paste - - |cut -f 1 > col3.txt

# MMETSP DATASET
CP_0198131824_1486917_Craspedostauros_australis_CCMP3328

CP_0198725784__Unidentified_sp_CCMP1999

CP_0202964930__Pseudokeronopsis_sp_Brazil

CP_0174260800_1078864_Stereomyxa_ramosa_Chinc5 (0)

# If for some reason the source organism cannot be mapped to the taxonomy 
 	 database, the column will contain 0.

Links

https://github.com/richardmleggett/acc2tax 
https://ftp.ncbi.nih.gov/pub/taxonomy/

	https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/
	names.dmp, node.dmp
	
# JGI Taxonomy Guide

https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/taxonomy-guide/ 
	wget ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdmp.zip 
	gi_taxid_nucl.dmp   gi_taxid_prot.dmp

Directories

	
/misc/scratch2/xizhang/arabidopsis/Taxonomy
/misc/db1/extra-data-sets/Acc2tax/Acc2tax_092021
/scratch3/rogerlab_databases/other_dbs/Acc2Tax_Feb122021

nohup zcat dead_nucl.accession2taxid.gz dead_wgs.accession2taxid.gz nucl_gb.accession2taxid.gz nucl_wgs.accession2taxid.gz |sort > nucl_all.txt
nohup zcat dead_prot.accession2taxid.gz prot.accession2taxid.gz | sort > prot_all.txt

What is the difference of the GenPept format and the GenPept (full)?

Full
Accession.version	taxid
0308206A	8058
0308221A	9606
0308230A	1049

accession	accession.version	taxid	gi
A0A009IHW8	A0A009IHW8.1	1310613	1835922267
A0A023FBW4	A0A023FBW4.1	34607	1939884164
A0A023FBW7	A0A023FBW7.1	34607	1939884197

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