changeset 3:386a88793078 draft

Uploaded

--- a/blast_report.py	Tue Mar 03 01:04:15 2020 +0000
+++ b/blast_report.py	Tue Mar 03 01:09:56 2020 +0000
@@ -1,8 +1,12 @@
 #!/usr/bin/env python
+
+from __future__ import print_function
+
 '''Report on BLAST results.
 
 python blast_report.py input_tab cheetah_tmpl output_html output_tab [-f [filter_pident]:[filterkw1,...,filterkwN]] [-b bin1_label=bin1_path[,...binN_label=binN_path]]
 '''
+
 import argparse
 import re
 import sys
@@ -72,15 +76,14 @@
 parser = argparse.ArgumentParser()
 
 parser.add_argument('-f', '--filter',
-                    type='string',
                     dest='filter',
                     )
 parser.add_argument('-b', '--bins',
-                    type='string',
                     dest='bins'
                     )
-parser.add_argument('-r', '--redundant',
-                    dest='redundant',
+parser.add_argument('-r', '--discard-redundant',
+                    dest='discard_redundant',
+                    type=bool,
                     default=False,
                     action='store_true'
                     )
@@ -108,7 +111,7 @@
     filter_kws = pident_kws[-1].split(',')
 print('filter_pident: %s    filter_kws: %s' % (str(filter_pident), str(filter_kws)))
 
-if args.redundant:
+if args.discard_redundant:
     print('Throwing out redundant hits...')
 
 #RESULTS!
@@ -134,7 +137,7 @@
             stop_err("Problem with splitting:" + cols[SUBJ_ID_COL])
 
         #hsp option: keep best (first) hit only for each query and accession id.
-        if args.redundant:
+        if args.discard_redundant:
             if accs[0] in queries[-1].match_accessions:
                 continue #don't save the result and skip to the next
             else: