Adding a script aiming to help alex on his work

ab1_to_blast.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+
+from Bio import SeqIO
+from Bio.Blast import NCBIWWW
+import sys
+
+input_file = sys.argv[1]
+input_name = input_file.split(".")[0]
+
+records = SeqIO.parse(input_file,"abi")
+count = SeqIO.write(records, input_name+".fastq", "fastq")
+print("Converted %i records" % count)
+input_name = "teste"
+# h37rv 16s portion
+# fasta_string = "ggaattcctggtgtagcggtggaatgcgcagatatcaggaggaacaccggtggcgaaggcgggtctctgggcagtaactgacgctgaggagcgaaagcgtggggagcgaacaggattagataccctggtagtccacgccgtaaacggtgggtactaggtgtgggtttccttccttgggat"
+fasta_string = open(input_name+".fasta").read()
+result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string, format_type="Text")
+
+with open(input_name+"_blast_result.txt", "w") as out_handle:
+     out_handle.write(result_handle.read())
+     result_handle.close()
+