diff fasta_header_converter.py @ 0:4f9e5110914b draft

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/TreeBest commit 136cba2b8c8a2ac2465e7e9420314f2511b991f2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/fasta_header_converter.py	Tue Dec 20 16:32:25 2016 -0500
@@ -0,0 +1,39 @@
+from __future__ import print_function
+
+import json
+import optparse
+
+
+def read_gene_info(gene_info):
+    transcript_species_dict = dict()
+    for gene_dict in gene_info.values():
+        for transcript in gene_dict['Transcript']:
+            transcript_species_dict[transcript['id']] = transcript['species'].replace("_", "")
+    return transcript_species_dict
+
+
+parser = optparse.OptionParser()
+parser.add_option('-j', '--json', dest="input_gene_filename",
+                  help='Gene feature information in JSON format')
+parser.add_option('-f', '--fasta', dest="input_fasta_filename",
+                  help='Sequences in FASTA format')
+options, args = parser.parse_args()
+
+if options.input_gene_filename is None:
+    raise Exception('-j option must be specified')
+
+if options.input_fasta_filename is None:
+    raise Exception('-f option must be specified')
+
+with open(options.input_gene_filename) as json_fh:
+    gene_info = json.load(json_fh)
+transcript_species_dict = read_gene_info(gene_info)
+
+with open(options.input_fasta_filename) as fasta_fh:
+    for line in fasta_fh:
+        line = line.rstrip()
+        if line.startswith(">"):
+            name = line[1:].lstrip()
+            print(">" + name + "_" + transcript_species_dict[name])
+        else:
+            print(line)