pdbs secondary structure statistics GUI added

README.md

@@ -1,4 +1,4 @@
-# bioinfo_gui_scripts [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5277595.svg)](https://doi.org/10.5281/zenodo.5277595)
+# bioinfo_gui_scripts 
 python scripts that can be easily transformed to gui programs for wet lab scientists to use(see the wiki page for documentation and depedences)
 ## GUI stadalone programs(.exe)
 1. DSSP statistics GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4838997.svg)](https://doi.org/10.5281/zenodo.4838997)
@@ -8,4 +8,5 @@ python scripts that can be easily transformed to gui programs for wet lab scient
 5. Extract or remove sequences from fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5213003.svg)](https://doi.org/10.5281/zenodo.5213003)
 6. FASTA subset by length GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5218645.svg)](https://doi.org/10.5281/zenodo.5218645)
 7. select header or fasta by aa GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5218741.svg)](https://doi.org/10.5281/zenodo.5218741)
-8. amino acids content multifasta calculator GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5275827.svg)](https://doi.org/10.5281/zenodo.5275827)
+8. amino acids content multifasta calculator GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5275827.svg)](https://doi.org/10.5281/zenodo.5275827)
+9. pdbs secondary structure statistics GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5348006.svg)](https://doi.org/10.5281/zenodo.5348006)

pdb_corner/pdbs_secondary_structure_statistics_gui.py

@@ -0,0 +1,51 @@
+#python3
+from gooey import *
+import os
+from Bio.PDB import *
+import pandas as pd
+# input parameters
+@Gooey(required_cols=2, program_name='pdbs secondary structure statistics', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+def main():
+    ap = GooeyParser(description="search for pdb files in a user selected directory, run DSSP, calculate the percentage of secondary structures for each pdb and export a txt file with the file names as rows and the secondary structure as columns")
+    ap.add_argument("-dir", "--directory", required=True, type=str, widget='DirChooser', help="directory to search for pdb files")
+    ap.add_argument("-out", "--output", required=True, widget='FileSaver', help="output txt file")
+    args = vars(ap.parse_args())
+# retrieve fasta file names
+    file_list = []
+    for filename in sorted(os.listdir(os.chdir(args['directory']))):
+        if filename.endswith(".pdb"):
+            file_list.append(filename.split(".pdb")[0])
+# main
+    df_list = []  # setup empty list
+# retrieves each pdb file on the current directory and calculates the secondary structure percentage
+    for filename in sorted(os.listdir(os.chdir(args['directory']))):
+        if filename.endswith(".pdb"):
+            parser = PDBParser()
+            s = parser.get_structure("name", filename)
+            fill = s[0]
+            dssp = DSSP(fill, filename, dssp='mkdssp')
+            df = pd.DataFrame(dssp)
+            df = df.loc[:, 2]
+            struct_list = df.values.tolist()
+            df1 = pd.DataFrame()
+            df1['struct_list'] = struct_list
+            df1 = df1['struct_list'].value_counts()
+            df1 = round((df1 / df1.sum(axis=0)) * 100, 2)
+            df_list.append(df1)
+            del df
+            struct_list.clear()
+            del df1
+# concatenate all dataframes into 1
+    stats = pd.concat(df_list,axis=1)
+    stats.columns = file_list
+    stats = stats.fillna(stats)
+# convert rows to columns
+    stats_t = stats.T
+# export
+    with open(args['output'], 'a') as f:
+        f.write(
+            stats_t.to_csv(header = True, index = True, sep= "\t", doublequote= False, line_terminator= '\n')
+        )
+
+if __name__ == '__main__':
+    main()