add orthofinder parse script

scripts/orthofinder_parse.py

+import pandas as pd
+from Bio import SeqIO
+from Bio.SeqRecord import SeqRecord
+from Bio.Seq import Seq
+import click
+
+
+@click.command(context_settings={'help_option_names': ('-h', '--help'), "max_content_width": 800})
+@click.option('--orthogroups_table', '-t', default=None,
+              type=click.Path(exists=True, file_okay=True, dir_okay=False, readable=True, resolve_path=True),
+              required=True, show_default=True, help='Path to input orthogroups table file')
+@click.option('--strain_name', '-n', default=None,
+              type=click.STRING, required=True)
+@click.option('--output1', '-f', default=None,
+              type=click.Path(exists=False, file_okay=True, dir_okay=False, readable=True, resolve_path=True),
+              required=True, show_default=True, help='Path to output specific proteins sequences fasta file')
+@click.option('--output2', '-c', default=None,
+              type=click.Path(exists=False, file_okay=True, dir_okay=False, readable=True, resolve_path=True),
+              required=True, show_default=True, help='Path to output specific orthogroups csv file')
+@click.option('--path_seq', '-p', default=None,
+              type=click.STRING, help='path to orthogroup sequences', required=True)
+
+def main(orthogroups_table, strain_name, path_seq, output1, output2):
+    gene_counts = pd.read_table(orthogroups_table, sep='\t')
+    specific = gene_counts[gene_counts[strain_name] != 0]
+    specific = specific[specific["Total"] == specific[strain_name]]
+
+    file = ""
+    list_record = []
+
+    for name in specific["Orthogroup"]:
+        file = str(path_seq) + str(name) + ".fa"
+        for record in SeqIO.parse(file, "fasta"):
+            list_record.append(record)
+
+    SeqIO.write(list_record, str(output1), "fasta")
+    specific.to_csv(str(output2))
+
+
+if __name__ == '__main__':
+    main()
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