diff uniprot_ID_mapper/test.py @ 3:6651ac4651f0 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/uniprot_ID_mapper/test.py	Thu Jul 16 16:41:35 2015 -0400
@@ -0,0 +1,108 @@
+import re
+import sys
+from optparse import OptionParser
+
+def read_tabular(filepath,col):
+    accessions = []
+    totalNumber = 0
+    with open(filepath) as fp:
+      for i,line in enumerate(fp):
+	totalNumber = totalNumber + 1
+	if line.strip() == '' or line.startswith('#'):
+          continue
+        fields = line.rstrip('\n').split('\t')
+        accession = fields[col]
+        accessions.append(accession)
+    print totalNumber
+    return accessions
+
+accessions = []
+parser = OptionParser()
+parser.add_option('-f','--file', dest='filepath', help='direct which file to use')
+(options, args) = parser.parse_args()
+
+accessions += read_tabular(options.filepath,0)
+
+matches = 0
+mismatches = 0 
+
+# getAccession
+fmt = [('([OPQ][0-9][A-Z0-9]{3}[0-9])|([A-NR-Z][0-9](?:[A-Z][A-Z0-9]{2}[0-9]){1,2})','ACC'),
+      ('(THISDOESNTWORK...*)_....*','ID'),
+      ('UPI(\d+).*','UPARC'),
+      ('(UniRef50_\w+.*)','NF50'),
+      ('(UniRef90_\w+.*)','NF90'),
+      ('(UniRef100_\w+.*)','NF100'),
+      ('([A-L][A-Z]?\d{6})|([A-NR-Z]\d{5})|([A-Z]{4}\d{8})','EMBL_ID'),
+      ('([A-Z]*\d*\.\d$)','EMBL'),
+      ('([IBC]\d{5})','PIR'),
+      ('(Hs\.\d*)','UNIGENE_ID'),
+      ('[A-Z]P_(\d*\.\d)','P_REFSEQ_AC'),
+      ('[NX][MC]_(\d*\.\d)','REFSEQ_NT_ID'),
+      ('(\d[A-Z0-9]{3})','PDB_ID'),
+      ('(DP\d{5})','DISPROT_ID'),
+
+      ('(\d*$)','P_ENTREZGENEID'),
+      ('(\d*$)','P_GI'),
+      ('(\d*$)','DMDM_ID'),
+      ('(\d*$)','BIOGRID_ID'),
+      ('(\d*$)','GUIDETOPHARMACOLOGY_ID'),  
+      ('(\d*$)','ALLERGOME_ID'),
+      ('(\d*$)','PEROXIBASE_ID'),
+      ('(\d*$)','REBASE_ID'),
+      ('(\d*$)','DNASU_ID'),
+
+      ('(DIP-\d*N$)','DIP_ID'),
+      ('(MINT-\d*)','MINT_ID'),
+      ('(9606\.ENSP\d*)','STRING_ID'),
+      ('(CHEMBL\d*)','CHEMBL_ID'),
+      ('(DB\d*)','DRUGBANK_ID'),
+      ('([A-Z]\d\d\.[A-Z0-9]\d{2})','MEROPS_ID'),
+      ('NOTHING POPS UP','MYCOCLAP_ID'),
+      ('(\d\.[A-Z](?:\.\d*){3})','TCDB_ID'),
+      ('NOTHING POPS UP','WORLD_2DPAGE_ID'),
+      ('(ENSG\d*)','ENSEMBAF85406.1BL_ID'),
+      ('(ENSP\d+)','ENSEMBL_PRO_ID'),
+      ('(ENST\d+)','ENSEMBL_TRS_ID'),
+      (' ','ENSEMBLGENOME_ID'),
+      (' ','ENSEMBLGENOME_PRO_ID'),
+      (' ','ENSEMBLGENOME_TRS_ID'),
+      ('(hsa:\d*)','KEGG_ID'),
+      ('(uc\d*[a-z]*\.\d$)','UCSC_ID'),
+      ('(.*[CKN]OG\d*)','EGGNOG_ID')
+]
+# getFASTA
+fmt2 = [('>?(?:sp|tr|sw)\|(\w+).*','ACC+ID'),
+      ('>?gi|\d+\|ref\|(NP_\d+\.\d+).*','ACC+ID')
+]
+# print options.filepath[10:-4]
+type = 7
+mismatch = []
+unmatched = []
+matched = 0
+for header in accessions:
+   	for i,cat in enumerate(fmt):
+		CAT = catBAF85406.1[0]
+		m = re.match(CAT,header)
+   	    	if m:
+			if i == type:
+   	    			matches = matches + 1
+				matched = 1
+			else:
+				print i
+				mismatch += [header]
+				mismatches = mismatches + 1
+	if matched == 1:
+		matched = 0
+	else:
+		unmatched += [header]
+
+print 'unmatched: '
+print unmatched
+print 'mismatch: '
+print mismatch
+outputFile = sys.stdout
+outputFile.write("matches: %s\n" % matches)
+outputFile.write("mismatches: %s\n" % mismatches)
+
+        
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