Mercurial > repos > dfornika > blast_report

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_report.py	Tue Sep 10 12:51:57 2019 -0400
@@ -0,0 +1,198 @@
+#!/usr/bin/env python
+from __future__ import print_function
+
+'''Report on BLAST results.
+
+python bccdc_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 optparse
+import re
+import sys
+
+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 = optparse.OptionParser(description='Report on BLAST results.',
+                               usage='python bccdc_blast_report_generator.py input_tabut cheetah_tmpl output_html [output_id output_dir] [options]')
+
+parser.add_option('-f', '--filter',
+                    type='string',
+                    dest='filter',
+                    )
+parser.add_option('-b', '--bins',
+                    type='string',
+                    dest='bins'
+                    )
+parser.add_option('-r', '--redundant',
+                    dest='hsp',
+                    default=False,
+                    action='store_true'
+                    )
+options, 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 options.bins != None:
+    bins = list([BLASTBin(label_file.split('=')[0],label_file.split('=')[-1]) for label_file in options.bins.split(',')])
+print('database bins: %s' % str([bin.label for bin in bins]))
+
+#FILTERS
+filter_pident = 0
+filter_kws = []
+if options.filter != None:
+    pident_kws = options.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 options.hsp:
+    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 options.hsp:
+            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]))
+'''
+
+from Cheetah.Template import Template
+namespace = {'queries': queries}
+html = Template(file=cheetah_tmpl, searchList=[namespace])
+out_html = open(output_html, 'w')
+out_html.write(str(html))
+out_html.close()
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/blast_report.xml	Tue Sep 10 12:51:57 2019 -0400
@@ -0,0 +1,102 @@
+<tool id="blast_report" name="BLAST report" force_history_refresh="true" version="1.1.0">
+    <description>Report on BLAST results</description>
+    <command >
+        <![CDATA[
+          '$__tool_directory__/blast_report.py'
+          '${in_tab}'
+          '${tmpl}'
+          '${out_html}'
+          '${out_tab}'
+          -f '{$filter_pident}:$filter_kws'
+          #if str($bins) == "None"
+            #pass
+          #else
+          -b "${bins}"
+          #end if
+          #if $hsp_bool
+            -r
+          #end if
+        ]]>
+    </command>
+    <inputs>
+        <param name="in_tab" type="data" format="tabular" label="Tabular BLAST results (extended 26 columns)"/>
+        <param name="tmpl" type="select" optional="false" label="Report template">
+            <options from_file="bccdc_blast_report_templates.loc">
+                <column name="value" index="1"/>
+                <column name="name" index="0"/>
+            </options>
+        </param>
+        <param name="filter_pident" type="integer" min="90" max="100" value="97" label="Minimum percentage identity"/>
+        <param name="filter_kws" type="text" size="50" label="Comma-separated list of description keyword filters" value="bovine,clone,environmental,swine,uncultivated,uncultured,unidentified"/>
+        <param name="bins" type="select" label="Database bins" multiple="true" display="checkboxes">
+            <options from_file="bccdc_blast_bins.loc">
+                <column name="value" index="1"/>
+                <column name="name" index="0"/>
+            </options>
+        </param>
+        <!--<repeat name="hist_bins" title="History database bins">
+            <param name="filter" type="data" format="csv" label="History database bin"/>
+        </repeat>-->
+        <param name="hsp_bool" type="boolean" label="Throw out redundant hits?"/>
+        <param name="tab_bool" type="boolean" label="Output tabular file?"/>
+    </inputs>
+    <outputs>
+        <data name="out_html" format="html" label="$tool.name on data $in_tab.hid: report"/>
+        <data name="out_tab" format="tabular" label="$tool.name on data $in_tab.hid: tabular results">
+            <filter> tab_bool </filter>
+        </data>
+    </outputs>
+    <help>
+.. 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.
+
+    </help>
+</tool>