diff kraken_summarize.py @ 14:fd27c97c8366 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken_summarize.py	Mon May 18 15:55:47 2015 -0400
@@ -0,0 +1,101 @@
+#!/usr/bin/env python
+import sys
+import subprocess
+import argparse
+
+from collections import Counter
+
+from Bio import Entrez
+
+
+
+# U	HWI-ST933:109:C2A2NACXX:5:1101:1311:2013	0	50	Q:0
+def fetchTaxonomyData(ids, email='[e-mail]'):
+    Entrez.email = email
+    handle = Entrez.efetch(db='Taxonomy', id=','.join(ids), retmode='xml')
+    records = Entrez.read(handle)
+    return records
+
+def writeKronaInput(fi, taxInfo, unclassified=0):
+    if unclassified:
+        fi.write('%i\tUnclassified\n' % unclassified)
+    for tid in sorted(taxInfo, key=lambda x:taxInfo[x][0]['Lineage']):
+        fi.write('%i\t%s\n' % (taxInfo[tid][1], '; '.join([taxInfo[tid][0]['Lineage'].strip(), taxInfoDict[tid][0]['ScientificName']]).replace('; ', '\t').strip('\t')))
+    pass
+
+def writeOutput(out, taxInfoDict, c):
+    for tid in sorted(taxInfoDict, reverse=True, key=lambda x:taxInfoDict[x][1]):
+        data = [tid, taxInfoDict[tid][1], taxInfoDict[tid][0]['TaxId'], taxInfoDict[tid][0]['Lineage'], taxInfoDict[tid][0]['ScientificName']]
+        out.write('\t'.join(data) + '\n')
+    data = (sum(c.values()) - c['0'], sum(c.values()), (sum(c.values()) - c['0']) / float(sum(c.values())) * 100, c['0'])
+    out.write('%i/%i (%.5f%%) classified, %i unclassified\n' % data)
+
+
+def main(argv):
+
+    parser = argparse.ArgumentParser(description='')
+    parser.add_argument('--krona-output', type=str, default='')
+    parser.add_argument('--output', type=str)
+    parser.add_argument('--call-krona', type=str)
+    parser.add_argument('--include-unclassified')
+    parser.add_argument('kraken_summary_tsv', type=str)
+    args = parser.parse_args()
+
+    c = Counter(line.strip().split()[2] for line in open(sys.argv[1]))
+    taxids = sorted(c.keys(), key=lambda x:c[x], reverse=True)
+    taxData = fetchTaxonomyData(taxids)
+    taxInfoDict = {tinfo['TaxId']: [tinfo, c[tinfo['TaxId']]] for tinfo in taxData}
+
+    kr_out = None
+    if 'krona_output' in args:
+        with open(args.krona_output, 'wb') as kr_out:
+            if 'include_unclassified' in args:
+                writeKronaInput(kr_out, taxInfoDict, unclassified=c['0'])
+            else:
+                writeKronaInput(kr_out, taxInfoDict)
+
+        if 'call_krona' in args:
+            p = subprocess.Popen('source krona_tools-2.4; ktImportText -o %s %s' % (args.call_krona, args.krona_output), shell=True, stdout=subprocess.PIPE)
+            p.communicate()
+
+    if 'output' in args:
+        if args.output == '-':
+            writeOutput(sys.stdout, taxInfoDict, c)
+        else:
+            with open(args.output, 'wb') as out:
+                writeOutput(out, taxInfoDict, c)
+
+
+
+
+
+
+
+
+"""
+2	Fats	Saturated fat
+3	Fats	Unsaturated fat	Monounsaturated fat
+3	Fats	Unsaturated fat	Polyunsaturated fat
+13	Carbohydrates	Sugars
+4	Carbohydrates	Dietary fiber
+21	Carbohydrates
+5	Protein
+4
+"""
+
+
+
+"""
+handle = Entrez.efetch(db="Taxonomy", id="1323524", retmode="xml")
+records  = Entrez.read(handle)
+records[0]["Lineage"]
+'Viruses; dsRNA viruses; Partitiviridae; Betapartitivirus'
+records[0]["LineageEx"]
+[{u'ScientificName': 'Viruses', u'TaxId': '10239', u'Rank': 'superkingdom'}, {u'ScientificName': 'dsRNA viruses', u'TaxId': '35325', u'Rank': 'no rank'}, {u'ScientificName': 'Partitiviridae', u'TaxId': '11012', u'Rank': 'family'}, {u'ScientificName': 'Betapartitivirus', u'TaxId': '1511809', u'Rank': 'genus'}]
+"""
+
+"""
+{u'Lineage': 'Viruses; dsDNA viruses, no RNA stage; Iridoviridae; unclassified Iridoviridae', u'Division': 'Viruses', u'ParentTaxId': '180169', u'PubDate': '2014/03/16 07:01:27', u'LineageEx': [{u'ScientificName': 'Viruses', u'TaxId': '10239', u'Rank': 'superkingdom'}, {u'ScientificName': 'dsDNA viruses, no RNA stage', u'TaxId': '35237', u'Rank': 'no rank'}, {u'ScientificName': 'Iridoviridae', u'TaxId': '10486', u'Rank': 'family'}, {u'ScientificName': 'unclassified Iridoviridae', u'TaxId': '180169', u'Rank': 'no rank'}], u'CreateDate': '2014/02/24 15:56:28', u'TaxId': '1465751', u'Rank': 'species', u'GeneticCode': {u'GCId': '1', u'GCName': 'Standard'},
+u'ScientificName': 'Anopheles minimus irodovirus', u'MitoGeneticCode': {u'MGCId': '0', u'MGCName': 'Unspecified'}, u'UpdateDate': '2014/02/24 15:56:29'}
+
+"""