Use esearch on python to get nucleotide sequence from the protein ses id

Question

[Chvatil]

I would like from a protein fasta file to get the corresponding NCBI nucleotide sequences in a new fasta file.

I know that esearch can do it in python but I do know how to handle it with fasta file etc.

I guess it should be something like:

from Bio import SeqIO
import Entrez
    with open Nucleotide_fasta_file as nuc_file:
       for record in SeqIO.parse("Protein_fasta_file", "fasta"):
           Entrez.esearch (db='protein',query=record.id)
           print(">",the nucleotide id,file=nuc_file)
           print(the nucleotide sequence,file=nuc_file)

Here is an exemple: If I have a fasta prom file such as:

>YP_001883411.1
MDEMPQHSHNLPSPPTDTLRPSSSHNGPRKENGDKDLQPLQPPSSTMGNQHNISVKIGMI
MDNFNDVIERTLNRMHIYVMTEKINFICMAQTQYHNLVFERELFDILCKNKYAIEHEAAD
NNPSDDSLHLANNDYPFSLIICSKEAKRSSILLSNVGLVLVKFILYLRMLYRNVARPDSP
NCFLAINTRILPFGRVCIDIDYKIPLLGEGDGDYDEFVRKSFELVAQYTTMGNIIMTRNC
YTPNTRSFHLITEQQFDATTRHIIFMRIAEGIRALNDNVKIDQVHVWMLPFGRGHVPVRK
YDRRLNEFMDLVYPYTEVDFELMMPFDVSQGMDNLYTLYSLNTDEVAVANGDDFNYDVLH
ECLGRDIMDSYYIGDTSDIAKNLQLLSRVLSSRYEFAFSSQFRQRYDANYLSRVMGNKFN
NAFIIMSNKKLQLETSWNIPKPKAKPRPSERYEIYRFIEHRLLGEMRTLEDLFKVMPSDL
VKRNVNIGNVDELQNEELAKRKLASEINVDSVYTGPVHNLALDIAENQCIDFVWDNIVED
TSSHPWPYVYIGRSQIVQTAMSHMRNVHEYYTRTIVDNVYTYEKHDGIMRCFENIQSMFD
GQLLADTMNALCQNIFCSDFQRVQSYLFTMYEFFCRVHYIDACVTRSEFEEVVEAYLLET
VRPMFDEADLKTYRERHVQMTPGPKAYAKFPSPCSPLARVWDSIRPANKILLHIIYLMIV
EHNYSSVFFHLHTITRNKDNSQILASLFLHIIDNSYMTTPEGDEDSGDDTMNVVRSYASK
EFLNFIYMMFINAGVNYECDLRGKNVVFSSVDSKDYINDMKELIVTSPLWFFLCNYQYVD
EQMSYSNRFDLFAAIFRQDNSAGGRQTSSPPSADQRTSNGPSPPKQRRGVSGGGSGGSGG
NNGAANFNTERVLNANNISDRYHADLLRIFFRYILAYMKTETGVYIYDGVRMMSLPFKEP
SNIPQLEVKDPVSFLGMYRHQYGIYNTWTMQMERNINVLNGQINISNDELGNYPHLFNPY
NDDIYRLLVNRFLKSITFTRVINYQKNLALFLAPIYDPNVENNLKVLNYNIDSIQINIHD
LASSEFNIPQEMFVDILDVGKKPKNKLYEMFKWLYCIVCHYSENYSCVITTPSTFIPKCM
LPECGEDKENIFSMVKGNGAMDDDDNNNNGYGGGDNFLQRLHSVLESKNREQKEIITDEL
QKLSQFELSTLVNLFKNAYMFEEDGEDAENGILEGIEGMDNNMEVDHDISAQSQTPGSPS
PQSSSANATTEEIFKFNLSVHRNMAGGGGGNGTDIMDFFEGDEFVENSKIKLLLNLFNRK
LSAEIKQMSPEAFKQIIEDNHSHHITRFVLLTLSWLIRTLHTHIFADTRFFRELQQYRQL
LYDDLSDLVFRHNGYFMYNNRITDVAQIFSHYCRHVELVVDPVFEMSMSVDRDLYLQHDA
ELEKRVSPEIVRDIEDACVSAIYQGQFIEDTNVDLSRLWARVTVPRNKHRISPLFTLHTA
TGKSEYLTERCRRHFNNKYFNNVLDPSSLAQTDHRGTDMARELNTNLIVCIEEFNSLTAK
FKQVCGYTSVAYKPLFADTKVSFQNNSTVILSTNNDPKCNEEAIVARLHVYPRRIQYANV
NKYLKFQRSSMLASTSLLKINNIMSVQMIMEKMPRVLAENYRGNFMMTWLLKRFFLFNII
DHVTVHTSETLQNHINNFYTMINAQEFVLQRLDMTTTSTMTLVQFRRLVNRICEENRSLF
NTKIDTYNVYKILCDRLKALINNDQQTIRISEKNDNALRQ

>YP_009345696.1
MDRYFINEMQLFERKLTFDSNNDYHHLEIISSHENQHIKKTKITLFTYNLLLDCLHYFYM
KCVDSNLFYDSGLTLVLHKEKKIFLNQLIFDVDFKSANISAIISKEKINDYNDFLNERNN
IIKNMIYIIFKYLKIDFTVENIQKYCSVTSRPLKLSFHLHIFYHVDYFTERILRFKMHNN
WKTFVTSMDTNFILDEPILHSLPFSRQHRPNKIHCQQTESEDVNAICINVDLLFLKDSLD
ISISNETWKLFSIFNIEKVLLKNISLLTKKKSDFTILIKEDYGNEINIFNGKKIGFFSFE
DINNFISTSMEIENVKNKEIGIIDEDEYNIHIPSVYINHIKRQHKIILYDIKDSIVHESI
DSVLFFDLLKYASFLSRYNKTDNFSINLSTKNYNENENIDEFYETVNLFSLKYKKDFFSI
FDDASNDEKEQNNIENSCEFDENDVYRRGEKNKEEINIICSDEKMKKFQHFSDSSFFPFT
EKQIHFLESIINKYNEDILSETDNAVCSKVLEYLESLNSLYPPLLFLLGSSFFNYSNDED
LQLISMYINNVDVNLPKIQTNKKRKLTTSKVDKNDIQRILKMDYKWIKEILNYIINCGCV
TSSVYLLSRIGVFQSLFDNIYYILSSMSLTLHAQYILSKWIQIVPEPITFFSSSFYNSDI
AYMCLILFDFNEKSREHKEKKNFLSGDNLNIKFIYSLFIKILSKFEIEYNSELEVFFITQ
ILMCRSLGYRAIYFNGHGHVISQDTSFLKDFCEKKSTLMLPKYKATDDVLNSFVYIENVG
IFNTLFNVYEFPSPSLNSLVTHKLPSVLTYCDNNINYFSHTTYPLLQNFIFELYGKMFHF
SKKCKENVVSLILFSPNVRISKKCPEILMELDILNFYDSSFIFLLEDYAKILNNHSNIEE
YWNDDFISIITTTNDKYSFFLKRLLFIFYIIFQENKILNFSNIILFIQTLFGQSKYEQLG
LRKQTFFKNINANNNKNNNNNCTTTDDASNGENKDIEMIEDDKLYHKTISYSAKHFTDKM
EDNTCFFNDIRKRINSVLYEQHELKKKIINETILTTKIIKPSLLSKCEEQNNYMNFCLSD
YYENVDDIILPFDKNDKSLFNTKIKNHFLNVLLNIDNSENNDYIELISSIDLTKQFKKNL
YFLVLLLNWFLKMGNIHAYSNTSFFKDIQKYRQEIYNLMTNHVLKSFGPLLKFSSSFHLA
NIIQKFNENTELDFDFVLEKFSHLKHPFYEKNNNKKLLNNENIKKKYFSISDRDIIADNE
MLRSKNHIYHAMAVLLMFSEFNFDTLTDVIKFMIYILYKGNMLRICLYLFGVTESLKSRF
TEILANLTQTDQTQSFNNANISRSAVQDFDSIVISGASNTFIFFDEVEKVCITRFKTIVN
SIAMSSRDIKNSEAINLKLACTPLMSSNSPFVVDNASCARLRPIRKKMQFCETFSGETFD
RFSIDSLKEYISTPNIGGIFLINRIPMWHDNSASIIGFLLIQRYLYPYFFKSYTSPISKK
MSKTMKNELRIYMSNNHPVAFFLNTVKISVDHNFISEQDFYKLIDKWWLAYKDRFKNSDF
DSKSLVKEISQYLTQYKSTLNNVKGYNIKIVLE

Answer 1

[GenoMax]

You should only need the accession number not the actual sequence to get nucleotide sequence (sequence truncated for brevity)

$ efetch -db protein -id "YP_001883411.1" -format fasta_cds_na
>lcl|NC_010671.1_cds_YP_001883411.1_1 [locus_tag=MdSGHV083] [db_xref=GeneID:6295473] [protein=hypothetical protein] [protein_id=YP_001883411.1] [location=complement(85755..91097)] [gbkey=CDS]
ATGGACGAAATGCCCCAGCACAGCCACAATCTCCCCTCGCCGCCAACGGACACACTCCGACCATCATCGT
CCCACAACGGACCGAGGAAGGAGAACGGGGACAAGGATCTGCAACCACTGCAACCGCCGTCATCAACAAT
GGGCAATCAGCATAACATCAGCGTCAAGATCGGTATGATAATGGATAATTTTAATGATGTAATCGAGCGT
ACACTGAATCGTATGCATATCTATGTAATGACCGAGAAAATAAACTTTATCTGCATGGCGCAGACACAGT
ATCACAATTTGGTCTTTGAGCGAGAACTTTTCGACATTCTGTGCAAGAACAAGTATGCCATCGAACATGA

[Chvatil]

Ok thank you I tried in python :

handle = Entrez.efetch(db="sequences", id="YP_001883411.1", rettype="fasta_cds_na", retmode="text")

[GenoMax]

So you were able to make it work? I can move my comment to an answer in that case.

[Chvatil]

yes it is done thank you :)