how to find family information from species name using entrez efetch
1
0
Entering edit mode
2.2 years ago
Priya ▴ 20

i have a fasta file with following information-

>mgm4958441.3|SRR16124173.15913997_1_130_+|RefSeq|002074a53cc252b220bf90d1e2737f50 accession=[NP_049991.1]  function=[immunity region]  organism=[Streptococcus phage Sfi21]
AGCAAAGCGATTGATAAAGCTAGTTCGTCCATTGATGCTGATTATAGTAAGTCGTCTTCTGAAAAAGCTAGTAAAGAAG

>mgm4958441.3|SRR16124173.29100137_1_150_+|RefSeq|002074a53cc252b220bf90d1e2737f50 accession=[NP_049991.1]  function=[immunity region]  organism=[Streptococcus phage Sfi21]
AAAAACAAAAAAGTGCTTGCTATTGTCGGAACTTGTTTATCTATAGCTTCAATCATCATTGTTCTTGTGACTCAAACAAT    
>mgm4958441.3|SRR16124173.10240675_1_150_-|RefSeq|0036f809e785ecade55b2f0a227ac0c3 accession=[YP_003347665.1]   function=[putative DNA primase] organism=[Klebsiella phage KP34]
CGCATACAGTTACAGGAAGAGCCGAGGGTGCAGCCCTCTGCACCTGCAGATGCAATTTGCATTAGCCAAGCGCATG

i need to find a way to retrieve family name using species name here in this fasta file. i don't know how to use e-utelities to do it, any link or direction would be helpful. thanks!

e-utelities • 959 views
ADD COMMENT
0
Entering edit mode

. i don't know how to use e-utelities to do it

https://www.ncbi.nlm.nih.gov/books/NBK25501/ "Entrez Programming Utilities Help"

ADD REPLY
0
Entering edit mode
2.2 years ago
GenoMax 142k

Using EntrezDirect (linked by @Pierre above):

$ esearch -db taxonomy -query "Klebsiella phage KP34" | efetch -format native -mode xml | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -tab "\n" -element Rank,ScientificName
superkingdom    Viruses
clade   Duplodnaviria
kingdom Heunggongvirae
phylum  Uroviricota
class   Caudoviricetes
order   Caudovirales
family  Autographiviridae
subfamily   Slopekvirinae
genus   Drulisvirus
species Klebsiella virus KP34

If you just need family

$ esearch -db taxonomy -query "Streptococcus phage Sfi21" | efetch -format native -mode xml | xtract -pattern Taxon -block "*/Taxon" -unless Rank -equals "no rank" -tab "\n" -element Rank,ScientificName | grep family
family  Siphoviridae
ADD COMMENT
0
Entering edit mode

I to get the family information of multiple viruses using the species information using this command?

ADD REPLY

Login before adding your answer.

Traffic: 1738 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6