diff format_fasta_hairpins.py @ 3:ee99c6374a3b draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/mircounts commit af48e9f6df2717ffd3731a974be1ec36e4eff779"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/format_fasta_hairpins.py	Fri Oct 18 19:18:17 2019 -0400
@@ -0,0 +1,64 @@
+import argparse
+import gzip
+
+
+def Parser():
+    the_parser = argparse.ArgumentParser()
+    the_parser.add_argument(
+        '--hairpins_path', action="store", type=str,
+        help="BASE url. ex: /pub/mirbase/22/")
+    the_parser.add_argument(
+        '--output', action="store", type=str,
+        help="parsed hairpin output in fasta format")
+    the_parser.add_argument(
+        '--basename', action="store", type=str,
+        help="genome basename of the parsed fasta")
+    args = the_parser.parse_args()
+    return args
+
+
+def get_fasta_dic(gzipfile):
+    '''
+    gzipfile value example : 'mirbase/22/hairpin.fa.gz'
+    '''
+    item_dic = {}
+    with gzip.open(gzipfile, 'rb') as f:
+        current_item = ''
+        stringlist = []
+        for line in f:
+            line = line.decode('utf-8').strip('\n')
+            if (line[0] == ">"):
+                # dump the sequence of the previous item
+                if current_item and stringlist:
+                    item_dic[current_item] = "".join(stringlist)
+                # take first word of item '''
+                current_item = line[1:].split()[0]
+                stringlist = []
+            else:
+                stringlist.append(line)
+        item_dic[current_item] = "".join(stringlist)  # for the last item
+    return item_dic
+
+
+def convert_and_print_hairpins(gzipfile, basename, fasta_output):
+    raw_fasta_dict = get_fasta_dic(gzipfile)
+    parsed_fasta_dict = {}
+    for head in raw_fasta_dict:
+        if basename in head:
+            parsed_fasta_dict[head] = raw_fasta_dict[head]
+            parsed_fasta_dict[head] = ''.join(
+                [i if i != 'u' else 't' for i in parsed_fasta_dict[head]])
+            parsed_fasta_dict[head] = ''.join(
+                [i if i != 'U' else 'T' for i in parsed_fasta_dict[head]])
+    with open(fasta_output, "w") as output:
+        for head in sorted(parsed_fasta_dict):
+            output.write('>%s\n%s\n' % (head, parsed_fasta_dict[head]))
+
+
+def main(hairpins_path, basename, outfile):
+    convert_and_print_hairpins(hairpins_path, basename, outfile)
+
+
+if __name__ == "__main__":
+    args = Parser()
+    main(args.hairpins_path, args.basename, args.output)