Extracting information from a genbank file

Question

[l.souza]

Hello,

How can I export some features (like country and date) from sequences inside a genbank file?

Thank you in advance!

[cpad0112]

Did you go through this biostar question?

[dewshrs]

you can use this python program to extract different fields from gene bank file https://github.com/dewshr/NCBI-Genbank-file-parser

Answer 1

[l.souza]

I could get it using the python script in this question

[cpad0112]

Please upvote the script provider in that question

Answer 2

[lakhujanivijay]

The " LOCUS" tag typically contains the date at the end like mentioned below:

LOCUS       NM_001204686             968 bp    mRNA    linear   INV 28-MAY-2017

This could be extracted like this:

grep "LOCUS" <your_genbank_file.txt> | awk '{print $NF}'

I am not sure what do you mean by "country" information. Please elaborate or provide example.

[l.souza]

I mean from where the sequences come. Like in this exemple:

LOCUS       KT968663                8103 bp    RNA     linear   VRL 29-MAR-2016 
DEFINITION  Foot-and-mouth disease virus - type A isolate A/HY/CHA/2013,
        complete genome. 
ACCESSION   KT968663 
VERSION     KT968663.1 
KEYWORDS    . SOURCE      Foot-and-mouth disease virus - type A (FMDV-A)   
  ORGANISM  Foot-and-mouth disease virus - type A
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Picornavirales; Picornaviridae; Aphthovirus. 
REFERENCE   1  (bases 1 to 8103)   
  AUTHORS   Yang,X., Yang,J., Wang,H. and Zeng,F.   
  TITLE     Direct Submission   
  JOURNAL   Submitted (30-OCT-2015) College of Life Science, Sichuan
            University, Wangjiang Road 29#, Chengdu, Sichuan 610064, China 
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END## 
FEATURES             Location/Qualifiers
 source          1..8103
                 /organism="Foot-and-mouth disease virus - type A"
                 /mol_type="genomic RNA"
                 /serotype="A"
                 /isolate="A/HY/CHA/2013"
                 /host="Bos grunniens"
                 /db_xref="taxon:12111"
                 **/country="China"**
                 /collection_date="15-Aug-2013"
                 /note="subtype: Sea97"

[lakhujanivijay]

in a shell file, say "run.sh"

grep "^LOCUS" gb.txt | awk '{print $NF}'
grep "country" gb.txt | sed 's/ //g' | cut -d "=" -f2 | sed 's/"//g'

• gb.txt = your genbank file

run as

$sh run.sh

output

[user@desktop]$ sh run.sh
29-MAR-2016
China