use ncbi table to convert from id to name for fasta

src/change_ncbi_to_name_fasta.py

@@ -0,0 +1,32 @@
+import sys
+import seq
+import os
+import argparse as ap
+
+def generate_argparser():
+    parser = ap.ArgumentParser(prog="change_ncbi_to_name_fasta.py",
+        formatter_class=ap.ArgumentDefaultsHelpFormatter)
+    parser = ap.ArgumentParser()
+    parser.add_argument("-t", "--table", type=str, help="NCBI translation table", required=True)
+    parser.add_argument("-i", "--infile", type=str, help="Input fasta alignment", required=True)
+    parser.add_argument("-o", "--outfile", type=str, help="Output fasta alignment", required=True)
+    return parser
+
+if __name__ == "__main__":
+    parser = generate_argparser()
+    if len(sys.argv[1:]) == 0:
+        sys.argv.append("-h")
+    args = parser.parse_args(sys.argv[1:])
+
+    tab = open(args.table, "r")
+    idn = {}
+    for i in tab:
+        spls = i.strip().split("\t")
+        idn[spls[1]] = spls[4]
+    tab.close()
+    outf = open(args.outfile, "w")
+    for i in seq.read_fasta_file_iter(args.infile):
+        i.name = idn[i.name].replace(" ", "_")
+        outf.write(i.get_fasta())
+    outf.close()
+