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pdb_corner/chain_pdb_to_fasta.py

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+# python3
+import argparse
+from Bio.PDB import *
+import sys
+# input parameters
+ap = argparse.ArgumentParser()
+ap.add_argument("-pdb", "--input_pdb", required=True, help="input pdb file")
+ap.add_argument("-model", "--pdb_model", required=True, help="model from pdb file to select(integer)")
+ap.add_argument("-chain", "--pdb_chain", required=True, help="chain from pdb file to select")
+ap.add_argument("-id", "--pdb_id", required=True, help="pdb id of the protein structure")
+ap.add_argument("-fasta", "--fasta_file", required=True, help="output fasta file")
+args = vars(ap.parse_args())
+#main
+def seq_from_pdb(structure):
+    ppb = PPBuilder()
+    for pp in ppb.build_peptides(structure):
+        print(">"+args['pdb_id']+"_"+args['pdb_chain'],pp.get_sequence(), sep="\n")
+
+parser = PDBParser()
+s = parser.get_structure("name", args['input_pdb'])
+fill = s[int(args['pdb_model'])][args['pdb_chain']]
+sys.stdout = open(args['fasta_file'], 'a')
+seq_from_pdb(fill)
+sys.stdout.close()