Mercurial > repos > dfornika > blast_report_basic

changeset 23:8d92b3b58f5e draft

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Uploaded
author dfornika
date Tue, 03 Mar 2020 09:30:07 +0000
parents 261235bbd475
children 96aa497b13c1
files blast_report.py
diffstat 1 files changed, 8 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/blast_report.py	Tue Mar 03 09:29:50 2020 +0000
+++ b/blast_report.py	Tue Mar 03 09:30:07 2020 +0000
@@ -4,7 +4,7 @@
 
 '''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]]
+python blast_report.py input_tab cheetah_tmpl output_html output_tab [-i [min_identity]] [-f filterkw1,...,filterkwN]] [-b bin1_label=bin1_path[,...binN_label=binN_path]]
 '''
 
 import argparse
@@ -12,7 +12,7 @@
 import sys
 
 from Cheetah.Template import Template
-
+from pprint import pprint
 
 def stop_err( msg ):
     sys.stderr.write("%s\n" % msg)
@@ -81,7 +81,9 @@
                     dest='min_identity',
                     )
 parser.add_argument('-b', '--bins',
-                    dest='bins'
+                    dest='bins',
+                    action='append',
+                    nargs='+'
                     )
 parser.add_argument('-r', '--discard-redundant',
                     dest='discard_redundant',
@@ -92,8 +94,11 @@
 parser.add_argument('cheetah_tmpl')
 parser.add_argument('output_html')
 parser.add_argument('output_tab')
+
 args = parser.parse_args()
 
+pprint(bins)
+
 print('input_tab: %s    cheetah_tmpl: %s    output_html: %s    output_tab: %s' % (args.input_tab, args.cheetah_tmpl, args.output_html, args.output_tab))