I am trying to download information from NCBI Entrez databases (nucleotide), using Biopython package.
I don't need molecular data at all. I just want to check the textual information about certain records, to see references, authors, journals, and information about voucher specimens from which the genome sample was extracted.
My query returns a lot of records, and I need to check if they are related or not to my institution staff (if so, then I extract relevant information about authors, journal, acc number and voucher specimen).
This is my code:
from Bio import Entrez
Entrez.email = "Your.Name.Here@example.org"
# first I try to find the records I am interested in. Example:
query = "Helianthus[Organism]"
handle = Entrez.esearch(db="nuccore", retmax=1000, term=query, idtype="acc")
records = Entrez.read(handle)
idsList = record["IdList"]
handle.close()
# now I want to retrieve information about each record (but NOT sequences):
handle = Entrez.efetch(db="nuccore", id=idsList, rettype="gb", retmode="text")
# and then I would parse this handle to check the info I am interest in
No problem doing this. But I found that some records include very long sequences (full genome I guess). So the downloaded file will be huge.
Is there any way to avoid genome information to be included in the download?
Or perhaps there is a way to get info about each accession size in my Entrez.esearch query, so I can remove those records from my idsList above?
For example, given this record, this is the only information I want to read.
I am particularly interested in the /specimen_voucher="SF193" line near the end of this text:
LOCUS MNCJ02000332 195042445 bp DNA linear PLN 13-JUL-2020
DEFINITION Helianthus annuus cultivar XRQ/B chromosome 17, whole genome
shotgun sequence.
ACCESSION MNCJ02000332 MNCJ02000000
VERSION MNCJ02000332.1
DBLINK BioProject: PRJNA345532
BioSample: SAMN05868438
KEYWORDS WGS.
SOURCE Helianthus annuus (common sunflower)
ORGANISM Helianthus annuus
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae;
Pentapetalae; asterids; campanulids; Asterales; Asteraceae;
Asteroideae; Heliantheae alliance; Heliantheae; Helianthus.
REFERENCE 1 (bases 1 to 195042445)
AUTHORS Badouin,H., Gouzy,J., Grassa,C.J., Murat,F., Staton,S.E.,
Cottret,L., Lelandais-Briere,C., Owens,G.L., Carrere,S.,
Mayjonade,B., Legrand,L., Gill,N., Kane,N.C., Bowers,J.E.,
Hubner,S., Bellec,A., Berard,A., Berges,H., Blanchet,N.,
Boniface,M.C., Brunel,D., Catrice,O., Chaidir,N., Claudel,C.,
Donnadieu,C., Faraut,T., Fievet,G., Helmstetter,N., King,M.,
Knapp,S.J., Lai,Z., Le Paslier,M.C., Lippi,Y., Lorenzon,L.,
Mandel,J.R., Marage,G., Marchand,G., Marquand,E., Bret-Mestries,E.,
Morien,E., Nambeesan,S., Nguyen,T., Pegot-Espagnet,P., Pouilly,N.,
Raftis,F., Sallet,E., Schiex,T., Thomas,J., Vandecasteele,C.,
Vares,D., Vear,F., Vautrin,S., Crespi,M., Mangin,B., Burke,J.M.,
Salse,J., Munos,S., Vincourt,P., Rieseberg,L.H. and Langlade,N.B.
TITLE The sunflower genome provides insights into oil metabolism,
flowering and Asterid evolution
JOURNAL Nature 546 (7656), 148-152 (2017)
PUBMED 28538728
REFERENCE 2 (bases 1 to 195042445)
AUTHORS Gouzy,J., Langlade,N. and Munos,S.
TITLE Helianthus annuus Genome sequencing and assembly Release 2
JOURNAL Unpublished
REFERENCE 3 (bases 1 to 195042445)
AUTHORS Langlade,N. and Munos,S.
TITLE Direct Submission
JOURNAL Submitted (27-FEB-2017) Laboratoire des Interactions Plantes
Micro-organismes, INRA/CNRS, Chemin de Borderouge, Castanet-Tolosan
31200, France
REFERENCE 4 (bases 1 to 195042445)
AUTHORS Gouzy,J., Langlade,N. and Munos,S.
TITLE Direct Submission
JOURNAL Submitted (08-JUN-2020) Laboratoire des Interactions Plantes
Micro-organismes, INRAE/CNRS, Chemin de Borderouge,
Castanet-Tolosan 31320, France
COMMENT ##Genome-Assembly-Data-START##
Assembly Date :: 17-AUG-2018
Assembly Method :: CANU v. 1.3; CANU v. 1.4; FALCON v. 0.7;
Bionano-Solve v. 3.2.1_04122018
Assembly Name :: HanXRQr2.0-SUNRISE
Genome Representation :: Full
Expected Final Version :: No
Genome Coverage :: 100.0x
Sequencing Technology :: PacBio RSII
##Genome-Assembly-Data-END##
FEATURES Location/Qualifiers
source 1..195042445
/organism="Helianthus annuus"
/mol_type="genomic DNA"
/submitter_seqid="HanXRQChr17"
/cultivar="XRQ/B"
/specimen_voucher="SF193"
/db_xref="taxon:4232"
/chromosome="17"
/tissue_type="leaves"
/dev_stage="4 leaves"
/country="France"
/collected_by="INRA, LIPM"
Below that, there is a lot of more info (gene, mRNA, CDS ...) up to 11 MB which I do NOT need.
Are there any chances that I can avoid all that stuff to be downloaded?
Or at least, is there a way to skip records bigger than a given size?