comparison blast_report.py @ 7:445a1923bb97 draft

Uploaded

6:b8a3578b6445

               str(self.score),
               str(round(self.p_cov,2)),
               str(round(self.p_ident, 2)))



#PARSE OPTIONS AND ARGUMENTS
parser = argparse.ArgumentParser()

parser.add_argument('-f', '--filter',
                    dest='filter',
                    )
parser.add_argument('-b', '--bins',
                    dest='bins'
                    )
parser.add_argument('-r', '--discard-redundant',
                    dest='discard_redundant',
                    default=False,
                    action='store_true'
                    )
args = parser.parse_args()

try:
    input_tab, cheetah_tmpl, output_html, output_tab = args
except:
    stop_err('you must supply the arguments input_tab, cheetah_tmpl and output_html.')
# print('input_tab: %s    cheetah_tmpl: %s    output_html: %s    output_tab: %s' % (input_tab, cheetah_tmpl, output_html, output_tab))


#BINS
bins=[]
if args.bins != None:
    bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in args.bins.split(',')])
print('database bins: %s' % str([bin.label for bin in bins]))

    #FILTERS
filter_pident = 0
filter_kws = []
if args.filter != None:
    pident_kws = args.filter.split(':')
    filter_pident = float(pident_kws[0])
    filter_kws = pident_kws[-1].split(',')
print('filter_pident: %s    filter_kws: %s' % (str(filter_pident), str(filter_kws)))

if args.discard_redundant:
    print('Throwing out redundant hits...')

#RESULTS!
PIDENT_COL = 2
DESCR_COL = 25
SUBJ_ID_COL = 12
SCORE_COL = 11
PCOV_COL = 24
queries = []
current_query = ''
output_tab = open(output_tab, 'w')
    
with open(input_tab) as input_tab:
    for line in input_tab:
        cols = line.split('\t')
        if cols[0] != current_query:
            current_query = cols[0]
            queries.append(BLASTQuery(current_query))

        
        descrs = cols[DESCR_COL]
        #FILTER BY KEY WORDS
        filter_by_kw = False
        for kw in filter_kws:
            kw = kw.strip() #Fix by Damion D Nov 2013
            if kw != '' and re.search(kw, descrs, re.IGNORECASE):
                filter_by_kw = True
                try:
                    queries[-1].kw_filtered_breakdown[kw] += 1
                except:

        for x in query.bins[bin]:
            print('        %s' % str(query.matches[x]))
'''

namespace = {'queries': queries}
html = Template(file=cheetah_tmpl, searchList=[namespace])
out_html = open(output_html, 'w')
out_html.write(str(html))
out_html.close()


if __name__ == '__main__':

7:445a1923bb97

               str(self.score),
               str(round(self.p_cov,2)),
               str(round(self.p_ident, 2)))


#PARSE OPTIONS AND ARGUMENTS
parser = argparse.ArgumentParser()

parser.add_argument('-f', '--filter-keywords',
                    dest='filter_keywords',
                    )
parser.add_argument('-i', '--min-identity',
                    dest='min_identity',
                    )
parser.add_argument('-b', '--bins',
                    dest='bins'
                    )
parser.add_argument('-r', '--discard-redundant',
                    dest='discard_redundant',
                    default=False,
                    action='store_true'
                    )
parser.add_argument('input_tab')
parser.add_argument('cheetah_tmpl')
parser.add_argument('output_html')
parser.add_argument('output_tab')
args = parser.parse_args()

try:
    input_tab, cheetah_tmpl, output_html, output_tab = args
except:
    stop_err('you must supply the arguments input_tab, cheetah_tmpl and output_html.')
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))


#BINS
bins=[]
if args.bins != None:
    bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in args.bins.split(',')])
print('database bins: %s' % str([bin.label for bin in bins]))

#FILTERS
filter_pident = 0
filter_kws = []
if args.keyword_filter:
    filter_kws = args.keyword_filter.split(',')
print('minimum percent identity: %s    filter_kws: %s' % (str(args.min_identity), str(filter_kws)))

if args.discard_redundant:
    print('Throwing out redundant hits...')


PIDENT_COL = 2
DESCR_COL = 25
SUBJ_ID_COL = 12
SCORE_COL = 11
PCOV_COL = 24
queries = []
current_query = ''
output_tab = open(args.output_tab, 'w')
    
with open(args.input_tab) as input_tab:
    for line in input_tab:
        cols = line.split('\t')
        if cols[0] != current_query:
            current_query = cols[0]
            queries.append(BLASTQuery(current_query))

        
        descrs = cols[DESCR_COL]
        #FILTER BY KEY WORDS
        filter_by_kw = False
        for kw in filter_kws:
            kw = kw.strip()
            if kw != '' and re.search(kw, descrs, re.IGNORECASE):
                filter_by_kw = True
                try:
                    queries[-1].kw_filtered_breakdown[kw] += 1
                except:

        for x in query.bins[bin]:
            print('        %s' % str(query.matches[x]))
'''

namespace = {'queries': queries}
html = Template(file=args.cheetah_tmpl, searchList=[namespace])
out_html = open(args.output_html, 'w')
out_html.write(str(html))
out_html.close()


if __name__ == '__main__':