# HG changeset patch
# User dfornika
# Date 1583194474 0
# Node ID 5dfd8490752166dcd0dc9d240de0a5065ac911ce
planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/blast_report_basic commit bc359460bb66db7946cc68ccbd47cd479624c4a1-dirty
diff -r 000000000000 -r 5dfd84907521 blast_report.py
--- /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()
diff -r 000000000000 -r 5dfd84907521 blast_report_basic.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_report_basic.xml Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,86 @@
+
+ Produce an HTML table report of BLAST results
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+.. class:: infomark
+
+**What it does**
+
+This tool produces a HTML report for each query in a tabular BLAST file.
+
+----
+
+**Tabular BLAST results**
+
+One or more query's BLAST results in extended 26 column tabular format.
+
+----
+
+**Report template**
+
+The report template dictates the format of the HTML report.
+Note that changing the template from the standard "Top 20 hits shown, toggle remainder" to "Euzby results shown first" causes
+the order of the results in the HTML report and the tabular BLAST results (if outputted) to be inconsistent with each other.
+
+----
+
+**Minimum percentage identity**
+
+Filter by percentage identity. This filter is applied before the description keyword filters.
+
+----
+
+**Comma-separated list of description keyword filters**
+
+Filter by description keywords. Do not include spaces (unless your keyword is two words). These are applied
+after the percentage identity filter.
+
+----
+
+**Database bins**
+
+Bin the results by accession number into "database bins."
+
+----
+
+**Throw out redundant hits?**
+
+Only the first hit for any accession number will be reported.
+
+----
+
+**Output tabular BLAST results?**
+
+This option produces a tabular BLAST file with the same results as those shown in the report.
+
+
+
diff -r 000000000000 -r 5dfd84907521 templates/template1.tmpl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/template1.tmpl Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,108 @@
+#silent import time
+#set $display_m = 20
+#set $header = ''
+
+
+
+
+
+
+ #set $q = 0
+ #for $query in $queries
+ #set $bin_symbols = dict([($bin,$i) for $i, $bin in enumerate($query.bins, 1)])
+ #set $m = 0
+ $query.query_id
+
+
+ #if len($query.matches) == 0:
+
+
+ #else:
+ $header
+ #for $match in $query.matches:
+ #if $m == $display_m
+
+ Displaying ${display_m}/$m matches. Show the remaining results. |
+ Hide the last #echo $m - $display_m # results. |
+
+
+ #end if
+
+ #if len($bin_symbols) > 0:
+ #echo ', '.join(['%s %s'%($bin_symbols[$bin],$bin) for $bin in $query.bins])#
+ #end if
+ #end if
+ #if $query.pident_filtered > 0:
+ $query.pident_filtered results filtered by % Identity.
+ #end if
+ #if $query.kw_filtered > 0:
+ $query.kw_filtered results filtered by description keywords: #echo ', '.join(list(["%s matches to '%s'" % (str($query.kw_filtered_breakdown[$kw]),$kw) for $kw in $query.kw_filtered_breakdown])) #.
+ #end if
+ Report produced on #echo time.strftime("%d/%m/%Y") #.
+
+ #set $q += 1
+ #end for
+
+
diff -r 000000000000 -r 5dfd84907521 templates/template2.tmpl
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/templates/template2.tmpl Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,127 @@
+#silent import time
+#set $display_m = 20
+#set $header = ''
+
+
+
+
+
+
+ #set $q = 0
+ #for $query in $queries
+ #set $bin_symbols = dict([($bin,$i) for $i, $bin in enumerate($query.bins, 1)])
+ #set $m = 0
+ $query.query_id
+
+
+ #set $num_of_euzby = -1
+ #if len($query.matches) == 0:
+
+
+ #else:
+ $header
+ #try
+ #set $priority = $query.bins['Euzby']
+ #set $front = []
+ #for $i in reversed($priority)
+ #silent $front.append($query.matches.pop($i))
+ #end for
+ #set $num_of_euzby = len($front)
+ #silent $front.reverse()
+ #silent $front.extend($query.matches)
+ #set $query.matches = $front
+ #except
+ #pass
+ #end try
+ #for $match in $query.matches:
+ #if $m == $display_m
+
+ Displaying ${display_m}/$m matches. Show the remaining results. |
+ Hide the last #echo $m - $display_m # results. |
+
+
+ #end if
+
+ #if len($bin_symbols) > 0:
+ #echo ', '.join(['%s %s'%($bin_symbols[$bin],$bin) for $bin in $query.bins])#
+ #end if
+ #end if
+ #if $query.pident_filtered > 0:
+ $query.pident_filtered results filtered by % Identity.
+ #end if
+ #if $query.kw_filtered > 0:
+ $query.kw_filtered results filtered by description keywords: #echo ', '.join(list(["%s matches to '%s'" % (str($query.kw_filtered_breakdown[$kw]),$kw) for $kw in $query.kw_filtered_breakdown])) #.
+ #end if
+ Report produced on #echo time.strftime("%d/%m/%Y") #.
+
+ #set $q += 1
+ #end for
+
+
diff -r 000000000000 -r 5dfd84907521 tool-data/blast_reference_bins.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/blast_reference_bins.loc.sample Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,7 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB, consider using a UUID but any unique value will work)
+# - name (Galaxy shows this in the UI)
+# - path (Path to the blast reference bin file)
+#
+# e.g.
+# f45ee89a-d456-469a-8aeb-54cdfea821ec16S Microbial NCBI/path/to/16S_Microbial_NCBI.tab
diff -r 000000000000 -r 5dfd84907521 tool-data/blast_report_templates.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/blast_report_templates.loc.sample Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,7 @@
+# Expect three columns, tab separated, as follows:
+# - value (Galaxy records this in the Galaxy DB, consider using a UUID but any unique value will work)
+# - name (Galaxy shows this in the UI)
+# - path (Path to the blast report template (cheetah format))
+#
+# e.g.
+# f45ee89a-d456-469a-8aeb-54cdfea821ecDefault BLAST Report Template/path/to/template.tmpl
diff -r 000000000000 -r 5dfd84907521 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+
diff -r 000000000000 -r 5dfd84907521 tool_data_table_conf.xml.test
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.test Tue Mar 03 00:14:34 2020 +0000
@@ -0,0 +1,8 @@
+
+
+
+
+