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merge single-fasta and multi-fasta scripts and executables to 1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,63 @@ | ||
| # python3 | ||
| import os | ||
| from gooey import * | ||
| from Bio import SeqIO | ||
| # input parameters | ||
| @Gooey(required_cols=0, program_name='trim a multi-fasta file or multiple single-fasta files', header_bg_color= '#DCDCDC', terminal_font_color= '#DCDCDC', terminal_panel_color= '#DCDCDC') | ||
| def main(): | ||
| ap = GooeyParser() | ||
| ap.add_argument("-in", "--input", required=False ,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(default 1)") | ||
| 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=False, 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 will be that of the sequence length. Default is 1") | ||
| ap.add_argument("-type", "--type", required=False,default=1, type=int, help="type of fasta to import 1) 1 multi-fasta file 2) many single-fasta files. Default is 1") | ||
| ap.add_argument("-out", "--output", required=False, widget='FileSaver', help="output fasta file") | ||
| args = vars(ap.parse_args()) | ||
| # main | ||
| # 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] | ||
| # choose fasta type to import | ||
| if args['type'] == 1: | ||
| # setup an empty list | ||
| sequences = [] | ||
| # iterate for each record | ||
| for record in SeqIO.parse(args['input'], "fasta"): | ||
| # add this record to the list | ||
| sequences.append(fastatrim(record,record.seq)) | ||
| # export to fasta | ||
| SeqIO.write(sequences, args['output'], "fasta") | ||
| else: | ||
| # 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 = fastatrim(record,record.seq) | ||
| # export to fasta | ||
| SeqIO.write(sequence, "".join([filename.split(".")[0],"_","trimmed",".fasta"]), "fasta") | ||
|
|
||
| if __name__ == '__main__': | ||
| main() |
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