[Biopython-dev] Notification: incoming/77

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new message incoming/77

Message summary for PR#77
	From: zakano at hotmail.com
	Subject: Blast bug
	Date: Thu, 1 Aug 2002 17:13:06 -0400
	0 replies 	0 followups

====> ORIGINAL MESSAGE FOLLOWS <====

>From zakano at hotmail.com Thu Aug  1 17:13:06 2002
Received: from localhost (localhost [127.0.0.1])
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Date: Thu, 1 Aug 2002 17:13:06 -0400
Message-Id: <200208012113.g71LD6JD009191 at pw600a.bioperl.org>
From: zakano at hotmail.com
To: biopython-bugs at bioperl.org
Subject: Blast bug

Full_Name: Courtney Harper
Module: NCBIWWW.py
Version: ?
OS: windows
Submission from: leopard.cgl.ucsf.edu (128.218.21.28)


THERE ARE TWO PROBLEMS CAUSED BY A CHANGE IN BLAST OUTPUT SINCE THE RELEASE OF
THE BIOPYTHON VERSION I DOWNLOADED LAST WEEK.

PROBLEM #1, IN:
    def _scan_database_info(self, uhandle, consumer):

THE FOLLOWING IS EXPECTED:
<b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences 
           1,357,022 sequences; 6,227,440,795 total letters

BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
<b>Database:</b> All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS,
GSS, or phase 0, 1 or 2 HTGS sequences) 
           1,357,022 sequences; 6,227,440,795 total letters

TO FIX THIS, I CHANGED THIS CODE:
        read_and_call(uhandle, consumer.database_info, contains='Database')
        read_and_call(uhandle, consumer.database_info, contains='sequences')
        read_and_call(uhandle, consumer.noevent, blank=1)

TO THIS CODE:
        read_and_call(uhandle, consumer.database_info, contains='Database')
        read_and_call(uhandle, consumer.database_info, contains='sequences')
        read_and_call(uhandle, consumer.database_info, contains='total')
        read_and_call(uhandle, consumer.noevent, blank=1)


PROBLEM #2, IN:
    def _scan_database_report(self, uhandle, consumer):

THE FOLLOWING IS EXPECTED:
<PRE>
   Database: Non-redundant SwissProt sequences
     Posted date:  Dec 18, 1999  8:26 PM

BLAST OUTPUT HAS BEEN CHANGED TO THE FOLLOWING:
<PRE>
  Database: All GenBank+EMBL+DDBJ+PDB sequences (but no EST, STS, GSS,
  or phase 0, 1 or 2 HTGS sequences)
    Posted date:  Aug 1, 2002 12:00 AM

TO FIX THIS, I CHANGED THIS CODE:
        read_and_call(uhandle, consumer.noevent, start='<PRE>')
        read_and_call(uhandle, consumer.noevent, start='  Database')
        read_and_call(uhandle, consumer.posted_date, start='    Posted')

TO THIS CODE:
        read_and_call(uhandle, consumer.noevent, start='<PRE>')
        read_and_call(uhandle, consumer.noevent, start='  Database')
        read_and_call(uhandle, consumer.database, start='  or')
        read_and_call(uhandle, consumer.posted_date, start='    Posted')