I have to extract organism and host name from a NCBI .gp file but grep code is not creating something

Question

[oncelmiran6]

Hello everyone,

I have to extract accesion number and related host name from a .gp file that contains my meta data for a fasta file. I have tried this code but it shows nothing.

 grep -E 'VERSION.*/host' NCBITaxonomy_LassaVirus_\ 71720.gp -> miran.txt

accesion number starts after VERSION and host name starts after /host I couldn't figure out what is the problem I will be very happy if someone can help Thank you So much

[cpad0112]

please post few lines from input file.

[oncelmiran6]

Hello Sir Thank you for your response this is a brief summary for my input file

VERSION     QKI86563.1

                 /organism="Lassa mammarenavirus"
                 /strain="Yar-217"
                 /isolation_source="blood"
                 /host="Mastomys natalensis"
                 /db_xref="taxon:11620"
                 /country="Guinea: Yarawalia

[Joe]

This is a genbank file yes? If so the Accession and organism information will likely be in the header lines.

You also haven't told us why your grep command fails - in what way is it incorrect?

Answer 1

[JC]

The error is because grep is reading line by line and you don't have VERSION and /host in the same line, an alternative is to do 2 regex, in Perl:

$ perl -lane 'print $1 if(/VERSION\s+(.+)/ or /host="(.+)"/)' < file.gbk
QKI86563.1
Mastomys natalensis

[GenoMax]

@JC OP is using a GenPept file, which should have similar format. host entry must be specific to OP's file.

LOCUS       AAA40590                 109 aa            linear   ROD 27-APR-1993
DEFINITION  insulin [Octodon degus].
ACCESSION   AAA40590
VERSION     AAA40590.1
DBSOURCE    locus OCOINS accession M57671.1
KEYWORDS    .
SOURCE      Octodon degus (degu)
  ORGANISM  Octodon degus

Your code produces:

$ perl -lane 'print $1 if(/VERSION\s+(.+)/ or /host="(.+)"/)' < sequence.gp
AAA40590.1