diff imgt_loader/imgt_loader.py @ 0:afe85eb6572e draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/imgt_loader/imgt_loader.py	Mon Aug 29 05:41:20 2016 -0400
@@ -0,0 +1,147 @@
+import pandas as pd
+try:
+	pd.options.mode.chained_assignment = None  # default='warn'
+except:
+	pass
+import re
+import argparse
+import os
+
+def stop_err( msg, ret=1 ):
+    sys.stderr.write( msg )
+    sys.exit( ret )
+
+#docs.python.org/dev/library/argparse.html
+parser = argparse.ArgumentParser()
+parser.add_argument("--summ", help="The 1_Summary file from the imgt output")
+parser.add_argument("--aa", help="The 5_AA-Sequence file from the imgt output")
+parser.add_argument("--junction", help="The 6_Junction file from the imgt output")
+parser.add_argument("--output", help="Output file")
+
+args = parser.parse_args()
+
+old_summary_columns = [u'Sequence ID', u'JUNCTION frame', u'V-GENE and allele', u'D-GENE and allele', u'J-GENE and allele', u'CDR1-IMGT length', u'CDR2-IMGT length', u'CDR3-IMGT length', u'Orientation']
+old_sequence_columns = [u'CDR1-IMGT', u'CDR2-IMGT', u'CDR3-IMGT']
+old_junction_columns = [u'JUNCTION']
+
+added_summary_columns = [u'Functionality', u'V-REGION identity %', u'V-REGION identity nt', u'D-REGION reading frame', u'AA JUNCTION', u'Functionality comment', u'Sequence']
+added_sequence_columns = [u'FR1-IMGT', u'FR2-IMGT', u'FR3-IMGT', u'CDR3-IMGT', u'JUNCTION', u'J-REGION', u'FR4-IMGT']
+added_junction_columns = [u"P3'V-nt nb", u'N-REGION-nt nb', u'N1-REGION-nt nb', u"P5'D-nt nb", u"P3'D-nt nb", u'N2-REGION-nt nb', u"P5'J-nt nb", u"3'V-REGION trimmed-nt nb", 
+						  u"5'D-REGION trimmed-nt nb", u"3'D-REGION trimmed-nt nb", u"5'J-REGION trimmed-nt nb", u"N-REGION", u"N1-REGION", u"N2-REGION"]
+
+outFile = args.output
+
+#fSummary = pd.read_csv(triplets[0][0], sep="\t", low_memory=False)
+fSummary = pd.read_csv(args.summ, sep="\t", dtype=object)
+#fSequence = pd.read_csv(triplets[0][1], sep="\t", low_memory=False)
+fSequence = pd.read_csv(args.aa, sep="\t", dtype=object)
+#fJunction = pd.read_csv(triplets[0][2], sep="\t", low_memory=False)
+fJunction = pd.read_csv(args.junction, sep="\t", dtype=object)
+tmp = fSummary[["Sequence ID", "JUNCTION frame", "V-GENE and allele", "D-GENE and allele", "J-GENE and allele"]]
+
+tmp["CDR1 Seq"] = fSequence["CDR1-IMGT"]
+tmp["CDR1 Length"] = fSummary["CDR1-IMGT length"]
+
+tmp["CDR2 Seq"] = fSequence["CDR2-IMGT"]
+tmp["CDR2 Length"] = fSummary["CDR2-IMGT length"]
+
+tmp["CDR3 Seq"] = fSequence["CDR3-IMGT"]
+tmp["CDR3 Length"] = fSummary["CDR3-IMGT length"]
+
+tmp["CDR3 Seq DNA"] = fJunction["JUNCTION"]
+tmp["CDR3 Length DNA"] = '1'
+tmp["Strand"] = fSummary["Orientation"]
+tmp["CDR3 Found How"] = 'a'
+
+for col in added_summary_columns:
+    tmp[col] = fSummary[col]
+
+for col in added_sequence_columns:
+    tmp[col] = fSequence[col]
+
+for col in added_junction_columns:
+    tmp[col] = fJunction[col]
+
+outFrame = tmp
+
+outFrame.columns = [u'ID', u'VDJ Frame', u'Top V Gene', u'Top D Gene', u'Top J Gene', u'CDR1 Seq', u'CDR1 Length', u'CDR2 Seq', u'CDR2 Length', u'CDR3 Seq', u'CDR3 Length', 
+					u'CDR3 Seq DNA', u'CDR3 Length DNA', u'Strand', u'CDR3 Found How', u'Functionality', 'V-REGION identity %', 'V-REGION identity nt', 'D-REGION reading frame', 
+					'AA JUNCTION', 'Functionality comment', 'Sequence', 'FR1-IMGT', 'FR2-IMGT', 'FR3-IMGT', 'CDR3-IMGT', 'JUNCTION', 'J-REGION', 'FR4-IMGT', 'P3V-nt nb', 
+					'N-REGION-nt nb', 'N1-REGION-nt nb', 'P5D-nt nb', 'P3D-nt nb', 'N2-REGION-nt nb', 'P5J-nt nb', '3V-REGION trimmed-nt nb', '5D-REGION trimmed-nt nb', '3D-REGION trimmed-nt nb', 
+					'5J-REGION trimmed-nt nb', "N-REGION", "N1-REGION", "N2-REGION"]
+
+"""
+IGHV[0-9]-[0-9ab]+-?[0-9]?D?
+TRBV[0-9]{1,2}-?[0-9]?-?[123]?
+IGKV[0-3]D?-[0-9]{1,2}
+IGLV[0-9]-[0-9]{1,2}
+TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?
+TRGV[234589]
+TRDV[1-3]
+
+IGHD[0-9]-[0-9ab]+
+TRBD[12]
+TRDD[1-3]
+
+IGHJ[1-6]
+TRBJ[12]-[1-7]
+IGKJ[1-5]
+IGLJ[12367]
+TRAJ[0-9]{1,2}
+TRGJP?[12]
+TRDJ[1-4]
+"""
+
+vPattern = [r"(IGHV[0-9]-[0-9ab]+-?[0-9]?D?)",
+						r"(TRBV[0-9]{1,2}-?[0-9]?-?[123]?)",
+						r"(IGKV[0-3]D?-[0-9]{1,2})",
+						r"(IGLV[0-9]-[0-9]{1,2})",
+						r"(TRAV[0-9]{1,2}(-[1-46])?(/DV[45678])?)",
+						r"(TRGV[234589])",
+						r"(TRDV[1-3])",
+						r"(IGHV[0-9]S[0-9]+)"]
+
+dPattern = [r"(IGHD[0-9]-[0-9ab]+)",
+						r"(TRBD[12])",
+						r"(TRDD[1-3])"]
+						
+jPattern = [r"(IGHJ[1-6])",
+						r"(TRBJ[12]-[1-7])",
+						r"(IGKJ[1-5])",
+						r"(IGLJ[12367])",
+						r"(TRAJ[0-9]{1,2})",
+						r"(TRGJP?[12])",
+						r"(TRDJ[1-4])"]
+
+vPattern = re.compile(r"|".join(vPattern))
+
+dPattern = re.compile(r"|".join(dPattern))
+
+jPattern = re.compile(r"|".join(jPattern))
+
+
+def filterGenes(s, pattern):
+    if type(s) is not str:
+        return "NA"
+    res = pattern.search(s)
+    if res:
+        return res.group(0)
+    return "NA"
+
+
+
+outFrame["Top V Gene"] = outFrame["Top V Gene"].apply(lambda x: filterGenes(x, vPattern))
+outFrame["Top D Gene"] = outFrame["Top D Gene"].apply(lambda x: filterGenes(x, dPattern))
+outFrame["Top J Gene"] = outFrame["Top J Gene"].apply(lambda x: filterGenes(x, jPattern))
+
+
+tmp = outFrame["VDJ Frame"]
+tmp = tmp.replace("in-frame", "In-frame")
+tmp = tmp.replace("null", "Out-of-frame")
+tmp = tmp.replace("out-of-frame", "Out-of-frame")
+outFrame["VDJ Frame"] = tmp
+outFrame["CDR3 Length DNA"] = outFrame["CDR3 Seq DNA"].map(str).map(len)
+safeLength = lambda x: len(x) if type(x) == str else 0
+#outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows?
+#outFrame = outFrame[(outFrame["CDR3 Seq DNA"].map(safeLength) > 0) & (outFrame["Top V Gene"] != "NA") & (outFrame["Top D Gene"] != "NA") & (outFrame["Top J Gene"] != "NA")] #filter out weird rows?
+outFrame.to_csv(outFile, sep="\t", index=False, index_label="index")