Linux command line downloads NCBI data using Entrez Direct

First, the installation of software

1. Software Download:

Curl Ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/edirect.zip-O (familiar with Curl download file method, see http://www.cnblogs.com/duhuo/p /5695256.html)

2. Unzip

Unzip Edirect.zip

3. Add Environment variables

Echo ' Export path=/home/lmt/desktop/edirect/: $PATH ' >> ~/.ZSHRC (depending on your profile selection, it may make ~/.BASHRC)

Ii.. Entrez Direct functions

1.esearch search based on the given indexed fields

2.efilter filter results found before the search

3.efetch Download the required data according to the specified format

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Iii. Examples of usage

Download nucleic acid or protein sequence (fasta format)

Esearch-db nucleotide-query ' chn-js-2014 ' | Efetch-format fasta > 11.fasta #下载的为全基因组碱基序列

>kp757892. 1 Porcine DeltaCoronavirus isolate chn-js-completegenome Acatggggactaaagataaaaattatagcattagtctataattttatctccctagcttcgctagttctctaccgacaccaatccaggtgcgtctgccaccaagttggctaccctttctagg GGCGCTTTCGCGCTTGCTCACCATTAGATTACCTGGAAACCAGCCATTCAGGTTGGAGTTTCCCCAGGCTCTTTTGTGTGGGCATTAGC

Esearch-db necleotide-query ' chn-js-2014 ' | Efetch-format gene_fasta > 22.fasta #下载的为各个区段的基因的碱基序列, such as s/e/m, separate

>lcl| Kp757892.1_gene_3 [gene=e] [LOCUS_TAG=PDCOV-CHN-JS-2014_GP3] [location=22797..23048]atggtagtcgacgactgggccgttaccatccctggacaatatattattgctatactagttgtcatctgcattggtgtggcactactttttattaacacttgcttagcttgtgttaa Attattttacaagtgctacctaggggcagcataccttgttaggcctattatagtgtactactccaagccgaaccccgtacctgaggatgagtttgtaaaagtacaccaatttcctagaaac Actcactatgtctga>lcl| Kp757892.1_gene_4[Gene=m][LOCUS_TAG=PDCOV-CHN-JS-2014_GP4] [location=23041..23694]atgtctgacgcagaagagtggcaaattattgttttcattgcgatcatatgggcgcttggcgtcatcctccaaggaggctatgccacgcgtaatcgtgtgatctatgttattaaact Tattctgctttggctgctccaacccttcaccctagtggtgaccatttggaccgcagttgacagatcatctaagaaggacgcagttttcattgtgtccataatttttgccgtactgaccttc Atatcctgggccaagtactggtatgactcaattcgcttattaatgaaaaccagatctgcatgggcactctcacctgagagtagactccttgcagggattatggatccaatgggtacatgga GGTGCATTCCCATCGACCACATGGCTCCAATTCTCACACCAGTCGTTAAGCATGGCAAGCTC

Esearch-db necleotide-query ' chn-js-2014 ' | Efetch-format fasta_cds_aa > 33.fasta #下载的为各个区段的基因的蛋白序列, Separate (search in the nucleic acid library, try to use the protein library, found an error)

>lcl| Kp757892.1_prot_akc54443.1_3 [Gene=e][LOCUS_TAG=PDCOV-CHN-JS-2014_GP3] [Protein=envelope protein] [protein_id=akc54443.1] [location=22797..23048] [gbkey=CDS] Mvvddwavtipgqyiiailvvicigvallfintclacvklfykcylgaaylvrpiivyyskpnpvpedefvkvhqfprnthyv>lcl| Kp757892.1_prot_akc54444.1_4[Gene=m][LOCUS_TAG=PDCOV-CHN-JS-2014_GP4] [Protein=membrane protein] [protein_id=akc54444.1] [location=23041..23694] [gbkey=CDS] Msdaeewqiivfiaiiwalgvilqggyatrnrviyviklillwllqpftlvvtiwtavdrsskkdavfivsiifavltfiswakywydsirllmktrsawalspesrllagimdpmgtwrc Ipidhmapiltpvvkhgklklhgqelangisvrnppqdmvivspsdtfhytfkkpvesnndpefavliyqgdrasnaglhtittskagdarlykym

Esearch-db necleotide-query ' chn-js-2014 ' | Efetch-format fasta_cds_na > 44.fasta #下载的为各个区段基因的碱基序列, such as s/e/m, separate, and 22.fasta results, just more information

Download sequence (non-fasta format)

>lcl| Kp757892.1_cds_akc54443.1_3[Gene=e][LOCUS_TAG=PDCOV-CHN-JS-2014_GP3] [Protein=envelope protein] [protein_id=akc54443.1] [location=22797..23048] [gbkey=CDS] Atggtagtcgacgactgggccgttaccatccctggacaatatattattgctatactagttgtcatctgcattggtgtggcactactttttattaacacttgcttagcttgtgttaaattat Tttacaagtgctacctaggggcagcataccttgttaggcctattatagtgtactactccaagccgaaccccgtacctgaggatgagtttgtaaaagtacaccaatttcctagaaacactca Ctatgtctga>lcl| Kp757892.1_cds_akc54444.1_4[Gene=m][LOCUS_TAG=PDCOV-CHN-JS-2014_GP4] [Protein=membrane protein] [protein_id=akc54444.1] [location=23041..23694] [gbkey=CDS] Atgtctgacgcagaagagtggcaaattattgttttcattgcgatcatatgggcgcttggcgtcatcctccaaggaggctatgccacgcgtaatcgtgtgatctatgttattaaacttattc Tgctttggctgctccaacccttcaccctagtggtgaccatttggaccgcagttgacagatcatctaagaaggacgcagttttcattgtgtccataatttttgccgtactgaccttcatatc Ctgggccaagtactggtatgactcaattcgcttattaatgaaaaccagatctgcatgggcactctcacctgagagtagactccttgcagggattatggatccaatgggtacatggaggtgc ATTCCCATCGACCACATGGCTCCAATTCTCACACCAGTCGTTAAGCATGGCAAGCTC

Esearch-db necleotide-query ' chn-js-2014 ' | Efetch-format GB > 55.fasta #下载的格式和在NCBI里的界面结果显示一样.

LOCUS KP75789225420bp Ss-rna Linear VRL --dec- -DEFINITION porcine DeltaCoronavirus isolate CHN-js- the, complete genome. Accession kp757892version KP757892.1KEYWORDS. SOURCE Porcine DeltaCoronavirus organism porcine DeltaCoronavirus Viruses; ssRNA viruses; ssRNA Positive-strand viruses, no DNA stage; Nidovirales; Coronaviridae; Coronavirinae.reference1(Bases1To25420) AUTHORS dong,n., fang,l., Zeng,s., Sun,q., Chen,h. and Xiao,s. TITLE Porcine DeltaCoronavirusinchMainland China JOURNAL emerging infect. Dis. +( A),2254-2255( -) PUBMED26584185REFERENCE2(Bases1To25420) AUTHORS dong,n., fang,l., Zeng,s., Sun,q. and Xiao,s. TITLE Direct Submission JOURNAL submitted ( .-feb- -) State Key Laboratory of agricultural Microbiology, Huazhong agricultural University,1Shizishan Street, Wuhan, Hubei430070, Chinacomment # #Assembly-data-start## sequencing technology:: Sanger dideoxy sequencing # #Assembly-data-end# #FEATURES Location/Qualifiers ..... 
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。。。。 Gene22797..23048/gene="E"/locus_tag="PDCOV-CHN-JS-2014_GP3"CDS22797..23048/gene="E"/locus_tag="PDCOV-CHN-JS-2014_GP3"/codon_start=1/product="Envelope protein"/protein_id="AKC54443.1"/translation="MVVDDWAVTIPGQYIIAILVVICIGVALLFINTCLACVKLFYKCYlgaaylvrpiivyyskpnpvpedefvkvhqfprnthyv"Gene23041..23694/gene="M"
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Linux command line downloads NCBI data using Entrez Direct