Get metadatas from NCBI refseq database by refseq_metadata

A python scrip to get metadata infomation from NCBI by refseq ID.

This scrip will help your download the "all information(it shuld?)" from NCBI Refesq database.

Build date: 10-1-2015

Required enviroments(solved by mamba strongly recommanded, or just find a env which have biopython)

mamba create -n refseq_metadata
source activate refseq_metadata
mamba install biopython=1.84

Files perpared

Your Refseq ID information should be one by one in you files, such as:

GCF_003695465.1
GCF_016036915.1
GCF_003003695.1
GCF_011045685.1
GCF_014325982.1

One step to sovle the problem

python refseq.py -i YOU_LIST_FILES_NAME -o YOU_OTUPUTFILES_NAME.csv -e YOU E-MAIL ADDRESS (such as:*******@*****.com)
#The E-mail address was requested by NCBI datbase, not me

The output shuld like this

RsUid	GbUid	AssemblyAccession	LastMajorReleaseAccession	LatestAccession	.....
15833318	15786928	GCF_009866865.1	GCF_009866865.1	.....
23960828	23909188	GCF_016065415.1	GCF_016065415.1	.....
6302018	6251988	GCF_003008635.1	GCF_003008635.1	.....

In case of banning IP, the requesting time was set by 0.5s after each query.

Command line parameters including(requested and essential)

Argument	Useage
-i	your input files, you need to number them one by one
-o	your out put files, shuld name as ".csv"
-e	your E-mail address

Author

Cecli Fang @IUE.CAS

If this scrip help you, please cite: