wrap lines in fasta file, added link to gui executable

README.md

@@ -18,3 +18,4 @@ python scripts that can be easily transformed to gui programs for wet lab scient
 15. single-fastas to tabular GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5672075.svg)](https://doi.org/10.5281/zenodo.5672075)
 16. tabular file to single-fastas GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5652249.svg)](https://doi.org/10.5281/zenodo.5652249)
 17. fasta formatter GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5703665.svg)](https://doi.org/10.5281/zenodo.5703665)
+18. chain pdb to fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5706468.svg)](https://doi.org/10.5281/zenodo.5706468)

pdb_corner/chain_pdb_to_fasta_gui.py

@@ -1,29 +1,31 @@
 # python3
 from gooey import *
 from Bio.PDB import *
-import sys
+import os
+from Bio import SeqIO
+from Bio.Seq import Seq
+from Bio.SeqRecord import SeqRecord
 # input parameters
-@Gooey(required_cols=5, program_name='pdb chain to fasta', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+@Gooey(required_cols=2, program_name='pdb chain to fasta', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
 def main():
     ap = GooeyParser(description="subsets a pdb file by selecting the model and chain and convert the output to fasta format")
     ap.add_argument("-pdb", "--pdb", required=True, widget='FileChooser', help="input pdb file")
-    ap.add_argument("-model", "--model", required=True, help="model from pdb file to select(integer)")
+    ap.add_argument("-model", "--model",default=0, required=False, help="model from pdb file to select(integer). Default is 0(1 model only)")
     ap.add_argument("-chain", "--chain", required=True, help="chain from pdb file to select")
-    ap.add_argument("-id", "--id", required=True, help="pdb id of the protein structure")
-    ap.add_argument("-fasta", "--fasta", required=True, widget='FileSaver', 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['id']+"_"+args['chain'],pp.get_sequence(), sep="\n")
-
+# main
+# select chain
     parser = PDBParser()
     s = parser.get_structure("name", args['pdb'])
     fill = s[int(args['model'])][args['chain']]
-    sys.stdout = open(args['fasta'], 'a')
-    seq_from_pdb(fill)
-    sys.stdout.close()
-
+# retrieve the pdb id of the input file
+    filename = os.path.split(args['pdb'])[1]
+    pdb_id = filename.split(".")[0]
+# export to fasta
+    ppb = PPBuilder()
+    for pp in ppb.build_peptides(fill):
+        record = SeqRecord(Seq(str(pp.get_sequence())),id="".join([str(pdb_id),"_",str(args['chain'])]),description="")
+        SeqIO.write(record, "".join([str(pdb_id),"_",str(args['chain']),".fasta"]), "fasta")
+
 if __name__ == '__main__':
     main()