From 720dea16dc102e7900a12228c59bfaa03d11583a Mon Sep 17 00:00:00 2001 From: Peter Cock Date: Wed, 18 May 2011 18:43:46 +0100 Subject: [PATCH] Fix for BLAST XML to tabular when both query and subject have XXX masking --- tools/ncbi_blast_plus/blastxml_to_tabular.py | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/tools/ncbi_blast_plus/blastxml_to_tabular.py b/tools/ncbi_blast_plus/blastxml_to_tabular.py index 41d8e582c0a..795abebe892 100644 --- a/tools/ncbi_blast_plus/blastxml_to_tabular.py +++ b/tools/ncbi_blast_plus/blastxml_to_tabular.py @@ -176,16 +176,19 @@ for event, elem in context: expected_mismatch = len(q_seq) \ - sum(1 for q,h in zip(q_seq, h_seq) \ if q == h or q == "-" or h == "-") - assert expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch, \ - "%s vs %s mismatches, expected %i <= %i <= %i" \ - % (qseqid, sseqid, expected_mismatch - q_seq.count("X"), int(mismatch), expected_mismatch) + xx = sum(1 for q,h in zip(q_seq, h_seq) if q=="X" and h=="X") + if not (expected_mismatch - q_seq.count("X") <= int(mismatch) <= expected_mismatch + xx): + stop_err("%s vs %s mismatches, expected %i <= %i <= %i" \ + % (qseqid, sseqid, expected_mismatch - q_seq.count("X"), + int(mismatch), expected_mismatch)) #TODO - Remove this alternative identity calculation and test #once satisifed there are no problems - expected_idendity = sum(1 for q,h in zip(q_seq, h_seq) if q == h) - assert expected_idendity <= int(nident) <= expected_idendity + q_seq.count("X"), \ - "%s vs %s identities, expected %i <= %i <= %i" \ - % (qseqid, sseqid, expected_idendity, int(identity), expected_idendity + q_seq.count("X")) + expected_identity = sum(1 for q,h in zip(q_seq, h_seq) if q == h) + if not (expected_identity - xx <= int(nident) <= expected_identity + q_seq.count("X")): + stop_err("%s vs %s identities, expected %i <= %i <= %i" \ + % (qseqid, sseqid, expected_identity, int(nident), + expected_identity + q_seq.count("X"))) evalue = hsp.findtext("Hsp_evalue")