ix slice numbers for start and end/stop locations add ne versions of …

…GUI executables

README.md

@@ -1,4 +1,4 @@
-# bioinfo_gui_scripts [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5719342.svg)](https://doi.org/10.5281/zenodo.5719342)
+# 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)
@@ -11,13 +11,14 @@ python scripts that can be easily transformed to gui programs for wet lab scient
 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)
 10. add adapters on single-fastas GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5559117.svg)](https://doi.org/10.5281/zenodo.5559117)
-11. Trim multi-fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5565197.svg)](https://doi.org/10.5281/zenodo.5565197)
-12. Trim single-fastas GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5565299.svg)](https://doi.org/10.5281/zenodo.5565299)
+11. Trim multi-fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5725555.svg)](https://doi.org/10.5281/zenodo.5725555)
+12. Trim single-fastas GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5725465.svg)](https://doi.org/10.5281/zenodo.5725465)
 13. fasta to tab GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5699003.svg)](https://doi.org/10.5281/zenodo.5699003)
 14. tab to fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5703366.svg)](https://doi.org/10.5281/zenodo.5703366)
 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)
-19. subset pdb to fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5718967.svg)](https://doi.org/10.5281/zenodo.5718967)
+19. subset pdb to fasta GUI: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5725658.svg)](https://doi.org/10.5281/zenodo.5725658)
+
 

fasta_manipulation/trim_multifasta_gui.py

@@ -2,33 +2,47 @@
 from gooey import *
 from Bio import SeqIO
 # input parameters
-@Gooey(required_cols=3, program_name='trim multifasta', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+@Gooey(required_cols=2, program_name='trim multifasta', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
 def main():
     ap = GooeyParser()
     ap.add_argument("-in", "--input", required=True, widget='FileChooser', help="input fasta file")
     ap.add_argument("-start", "--start", required=False, default=1, type=int, help="region to start writing the fasta file")
-    ap.add_argument("-stop", "--stop", required=True, type=int, help="region to stop writing the fasta file(it can be both a positive and  a negative number)")
+    ap.add_argument("-stop", "--stop", required=False, type=int, help="region to stop writing the fasta file(it can be both a positive and  a negative number)")
+    ap.add_argument("-pro", "--program", required=False,default=1, type=int, help="program to choose 1) add both start and stop location 2) the stop location with be that of the sequence length. Default is 1")
     ap.add_argument("-out", "--output", required=True, widget='FileSaver', help="output fasta file")
     args = vars(ap.parse_args())
-    # main
+# main
     sequences = []  # setup an empty list
-    # fix the index for start parameter
-    if args['start'] > 0:
-        seq_start = args['start'] -1
-    else:
-        print("-start parameter must be a positive integer")
-        exit(1)
-    # fix the index for end parameter
-    if args['stop'] > 0:
-        seq_end = args['stop'] -1
-    else:
-        seq_end = args['stop']
-    # iterate for each record
+# create function to trim fasta records
+    def fastatrim(fastarec,fastaseq):
+        # choose program
+        if args['program'] == 1:
+            # fix the index for start parameter
+            if args['start'] > 0:
+                seq_start = args['start'] -1
+            else:
+                print("-start parameter must be a positive integer")
+                exit(1)
+            # add end parameter
+            seq_end = args['stop']
+        else:
+            # fix the index for start parameter
+            if args['start'] > 0:
+                seq_start = args['start'] -1
+            else:
+                print("-start parameter must be a positive integer")
+                exit(1)
+            # add end parameter according to program 2
+            args['stop'] = len(fastaseq)
+            seq_end = args['stop']
+        # subset each fasta record
+        return fastarec[seq_start:seq_end]
+# iterate for each record
     for record in SeqIO.parse(args['input'], "fasta"):
             # add this record to the list
-        sequences.append(record[seq_start:seq_end])
+        sequences.append(fastatrim(record,record.seq))
 
-    # export to fasta
+# export to fasta
     SeqIO.write(sequences, args['output'], "fasta")
 
 if __name__ == '__main__':

fasta_manipulation/trim_singlefastas_gui.py

@@ -3,34 +3,47 @@
 from gooey import *
 from Bio import SeqIO
 # input parameters
-@Gooey(required_cols=2, program_name='trim multiple single-fasta files', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+@Gooey(required_cols=1, program_name='trim multiple single-fasta files', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
 def main():
     ap = GooeyParser()
-    ap.add_argument("-start", "--start_fasta", required=False, default=1, type=int, help="region to start writing the fasta file")
-    ap.add_argument("-stop", "--stop", required=True, type=int, help="region to stop writing the fasta file(it can be both a positive and  a negative number)")
+    ap.add_argument("-start", "--start", required=False, default=1, type=int, help="region to start writing the fasta file")
+    ap.add_argument("-stop", "--stop", required=False, type=int, help="region to stop writing the fasta file(it can be both a positive and  a negative number)")
     ap.add_argument("-dir", "--directory", required=True, type=str, widget='DirChooser', help="directory to search for fasta files")
+    ap.add_argument("-pro", "--program", required=False,default=1, type=int, help="program to choose 1) add both start and stop location 2) the stop location with be that of the sequence length. Default is 1")
     args = vars(ap.parse_args())
 # main
-# fix the index for start parameter
-    if args['start'] > 0:
-        seq_start = args['start'] -1
-    else:
-        print("-start parameter must be a positive integer")
-        exit(1)
-# fix the index for end parameter
-    if args['stop'] > 0:
-        seq_end = args['stop'] -1
-    else:
-        seq_end = args['stop']
-# import each fasta file from a working directory of choice
+# create function to trim fasta records
+    def fastatrim(fastarec,fastaseq):
+        # choose program
+        if args['program'] == 1:
+            # fix the index for start parameter
+            if args['start'] > 0:
+                seq_start = args['start'] -1
+            else:
+                print("-start parameter must be a positive integer")
+                exit(1)
+            # add end parameter
+            seq_end = args['stop']
+        else:
+            # fix the index for start parameter
+            if args['start'] > 0:
+                seq_start = args['start'] -1
+            else:
+                print("-start parameter must be a positive integer")
+                exit(1)
+            # add end parameter according to program 2
+            args['stop'] = len(fastaseq)
+            seq_end = args['stop']
+        # subset each fasta record
+        return fastarec[seq_start:seq_end]
+# import each fasta file from the working directory
     for filename in sorted(os.listdir(os.chdir(args['directory']))):
         if filename.endswith(".fa") or filename.endswith(".fasta"):
             # read each file, trim and create SeqRecord to export
             record = SeqIO.read(filename, "fasta")
-            sequence = record[seq_start:seq_end]
+            sequence = fastatrim(record,record.seq)
             # export to fasta
             SeqIO.write(sequence, "".join([filename.split(".")[0],"_","trimmed",".fasta"]), "fasta")
 
-
 if __name__ == '__main__':
     main()

pdb_corner/subset_pdb_to_fasta_gui.py

@@ -36,21 +36,17 @@ def main():
         else:
             print("-start parameter must be a positive integer")
             exit(1)
-        # fix the index for end parameter
-        if args['end'] > 0:
-            aa_end = args['end'] -1
-        else:
-            aa_end = args['end']
+        # add end parameter
+        aa_end = args['end']
     else:
-
         # fix the index for start parameter
         if args['start'] > 0:
             aa_start = args['start'] -1
         else:
             print("-start parameter must be a positive integer")
             exit(1)
-        # fix the index for end parameter
-        args['end'] = len(aa_chain) -1
+        # add end parameter according to program 2
+        args['end'] = len(aa_chain)
         aa_end = args['end']
     # subset based on aa in chain
     sub_seq = aa_chain[aa_start:aa_end]