How download a sequence fasta from PDB using biopython / python?

I need download a sequence from PDB puting only the code of protein in algorithm

example: to put 1ZNI and download the sequence FASTA using python

fasta

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updated 5.7 years ago by Biostar

• written 7.8 years ago by thayana.vt •

Using REST services from PDB. Python example.

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written 7.8 years ago by GenoMax

1 answer

not python

$ echo -e "1ZNI\n1ZNJ" | while read P; do wget -q -O - "https://www.rcsb.org/pdb/download/viewFastaFiles.do?structureIdList=${P}&compressionType=uncompressed"; done
>1ZNI:A|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNI:B|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKA
>1ZNI:C|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNI:D|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKA
>1ZNJ:A|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNJ:B|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>1ZNJ:C|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNJ:D|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>1ZNJ:E|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNJ:F|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>1ZNJ:G|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNJ:H|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>1ZNJ:I|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNJ:J|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKT
>1ZNJ:K|PDBID|CHAIN|SEQUENCE
GIVEQCCTSICSLYQLENYCN
>1ZNJ:L|PDBID|CHAIN|SEQUENCE
FVNQHLCGSHLVEALYLVCGERGFFYTPKT

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written 7.8 years ago by Pierre Lindenbaum

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