fasta formatter script and executable

README.md

@@ -17,3 +17,4 @@ python scripts that can be easily transformed to gui programs for wet lab scient
 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)

fasta_manipulation/fasta_formatter_gui.py

@@ -0,0 +1,24 @@
+# python3
+from gooey import *
+from Bio import SeqIO
+import sys
+# input parameters
+@Gooey(required_cols=2, program_name= 'fasta formatter', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC')
+def main():
+	ap = GooeyParser(description="changes the width of sequences line in a FASTA file")
+	ap.add_argument("-in", "--input", required=True, widget="FileChooser", help="input fasta file")
+	ap.add_argument("-out", "--output", required=True, widget="FileSaver", help="output fasta file")
+	ap.add_argument("-width", "--width", required=False, type=int, default=80, help="number of characters per line. Default 80")
+	args = vars(ap.parse_args())
+	# main
+	# create function to split the input sequence based on a specific number of characters
+	def split_every_width(s): return [s[i:i+args['width']] for i in range(0,len(s),args['width'])]
+	# export to a new fasta file
+	sys.stdout = open(args['output'], 'a')
+	for record in SeqIO.parse(args['input'],'fasta'):
+		print(">"+record.id)
+		print('\n'.join(split_every_width(str(record.seq)))) # add characters in new line after the number of characters surpasses the input width 
+	sys.stdout.close()
+
+if __name__ == '__main__':
+    main()