diff blast_report.py @ 0:5dfd84907521 draft

planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_report.py	Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,209 @@
+#!/usr/bin/env python
+'''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
+
+from Cheetah.Template import Template
+
+
+def stop_err( msg ):
+    sys.stderr.write("%s\n" % msg)
+    sys.exit(1)
+
+
+class BLASTBin:
+    def __init__(self, label, file):
+        self.label = label
+        self.dict = {}
+        
+        file_in = open(file)
+        for line in file_in:
+            self.dict[line.rstrip().split('.')[0]] = ''
+        file_in.close()
+    
+    def __str__(self):
+        return "label: %s    dict: %s" % (self.label, str(self.dict))
+
+
+class BLASTQuery:
+    def __init__(self, query_id):
+        self.query_id = query_id
+        self.matches = []
+        self.match_accessions = {}
+        self.bins = {} #{bin(label):[match indexes]}
+        self.pident_filtered = 0
+        self.kw_filtered = 0
+        self.kw_filtered_breakdown = {} #{kw:count}
+        
+    def __str__(self):
+        return "query_id: %s    len(matches): %s    bins (labels only): %s    pident_filtered: %s    kw_filtered: %s    kw_filtered_breakdown: %s" \
+            % (self.query_id,
+               str(len(self.matches)),
+               str([bin.label for bin in bins]),
+               str(self.pident_filtered),
+               str(self.kw_filtered),
+               str(self.kw_filtered_breakdown))
+
+
+class BLASTMatch:
+    def __init__(self, subject_acc, subject_descr, score, p_cov, p_ident, subject_bins):
+        self.subject_acc = subject_acc
+        self.subject_descr = subject_descr
+        self.score = score
+        self.p_cov = p_cov
+        self.p_ident = p_ident
+        self.bins = subject_bins
+        
+    def __str__(self):
+        return "subject_acc: %s    subject_descr: %s    score: %s    p-cov: %s    p-ident: %s" \
+            % (self.subject_acc,
+               self.subject_descr,
+               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',
+                    type='string',
+                    dest='filter',
+                    )
+parser.add_argument('-b', '--bins',
+                    type='string',
+                    dest='bins'
+                    )
+parser.add_argument('-r', '--redundant',
+                    dest='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.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))
+
+        try:
+            accs = cols[SUBJ_ID_COL].split('|')[1::2][1::2]
+        except IndexError as e:
+            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 accs[0] in queries[-1].match_accessions:
+                continue #don't save the result and skip to the next
+            else:
+                queries[-1].match_accessions[accs[0]] = ''
+
+
+        p_ident = float(cols[PIDENT_COL])
+        #FILTER BY PIDENT
+        if p_ident < filter_pident: #if we are not filtering, filter_pident == 0 and this will never evaluate to True
+            queries[-1].pident_filtered += 1
+            continue
+        
+        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:
+                    queries[-1].kw_filtered_breakdown[kw] = 1
+        if filter_by_kw: #if we are not filtering, for loop will not be entered and this will never be True
+            queries[-1].kw_filtered += 1
+            continue
+        descr = descrs.split(';')[0]
+        
+        #ATTEMPT BIN
+        subj_bins = []
+        for bin in bins: #if we are not binning, bins = [] so for loop not entered
+            for acc in accs:
+                if acc.split('.')[0] in bin.dict:
+                    try:
+                        queries[-1].bins[bin.label].append(len(queries[-1].matches))
+                    except:
+                        queries[-1].bins[bin.label] = [len(queries[-1].matches)]
+                    subj_bins.append(bin.label)
+                    break #this result has been binned to this bin so break
+        acc = accs[0]
+        
+        score = int(float(cols[SCORE_COL]))
+        p_cov = float(cols[PCOV_COL])
+        
+        #SAVE RESULT
+        queries[-1].matches.append(
+            BLASTMatch(acc, descr, score, p_cov, p_ident, subj_bins)
+        )
+        output_tab.write(line)            
+input_tab.close()
+output_tab.close()
+
+'''
+for query in queries:
+    print(query)
+    for match in query.matches:
+        print('    %s' % str(match))
+    for bin in query.bins:
+        print('    bin: %s' % bin)
+        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__':
+    main()