Bioperl-guts: Problems with Blast Examples in 0.05

Greg Colello gcolello@scibizsw.com
Mon, 29 Mar 1999 09:26:06 -0800


I sent a separate email to Steve Chervitz (Hi Steve), because I know
he's the Blast man, but I also know you folks want an historical problem
log too, so...

I am trying to run the examples listed in parse_blast.pl in the
Prerelease 0.05 and the first few I tried came up with problems.

I found solutions to a couple of these as indicated, but I gave up on
#3, because it appeared to involve an upstream problem from where the
error occurred.

Greg Colello
-------------------------------------

Here are the problems:

------------------------
1. The system appears to not be handling compressed file input. I cured
the
following error by uncompressing blastp.2.gz and specifying the
uncompressed
version.

[gcolello@ls2 blast]$ perl parse_blast.pl out/blastp.2.gz -signif 1e-15
-table
1 -exponent -desc

Parsing Blast report file(s).
Odd number of elements in hash list at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Root/Object.pm

line 515.
.

*** 1 Blast reports produced fatal errors:

FILE: out/blastp.2.gz

*** Trouble creating Blast object:

-------------------- EXCEPTION --------------------
MSG: seek failed to seek 0 on FileHandle.
CONTEXT: Error in object Bio::Root::Utilities "Static Utilities object"
SCRIPT: parse_blast.pl
STACK:
Bio::Root::Utilities::taste_file(951)
Bio::Root::Utilities::get_newline(877)
Bio::Tools::Blast::_parse_blast_stream(1555)
Bio::Tools::Blast::parse(1404)
Bio::Tools::SeqAnal::_initialize(286)
Bio::Root::Object::new(455)
main::create_blast(521)
main::parse_blast.pl(134)
---


        main::create_blast called at parse_blast.pl line 134
        eval {...} called at parse_blast.pl line 130


-------------------------------------
2. Argument '.' is not numeric. This lead me to a defective do-while
loop. I
rearranged the loop so it does the loop test before the enclosed logic
statement. It fixed the problem.

[gcolello@ls2 blast]$ perl parse_blast.pl out/blastp.2 -signif 1e-15
-table 1
-exponent -desc

Parsing Blast report file(s).
Odd number of elements in hash list at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Root/Object.pm

line 515.
.
7 SIGNIFICANT HITS.
DONE PARSING DESCRIPTIONS.
Argument "." isn't numeric in eq at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Tools/Blast/Sbjct.pm

line 2297, <GEN1> chunk 9.
Argument "." isn't numeric in eq at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Tools/Blast/Sbjct.pm

line 2297, <GEN1> chunk 10.
QUERY   Q_LEN   SBJCT   S_LEN   EXPCT   SCORE   BITS    HSPS    IDEN
CONSV
Q_ALN    S_ALN   Q_GAP   S_GAP   Q_BEG   Q_END   S_BEG   S_END   Q_STR
S_STR  FRAM     DESC
-----   -----   -----   -----   -----   -----   -----   -----   -----
-----
-----    -----   -----   -----   -----   -----   -----   -----   -----
-----  -----    -----
Argument "." isn't numeric in eq at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Tools/Blast/Sbjct.pm

line 2297.
Argument "." isn't numeric in eq at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Tools/Blast/Sbjct.pm

line 2297.
Argument "." isn't numeric in eq at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Tools/Blast/Sbjct.pm

line 2297.
YER020W 449     1GIA    353     -77     716     283     1       0.44
0.64
326      322     2       6       122     447     31
352                    G


-----------------------------------------
3. Undefined array pointer. I gave up on this one, because there was no
stack
listing generated. The stack listings are really useful for speeding up
debugging.

[gcolello@ls2 blast]$ perl parse_blast.pl out/blastp.2.wu -check_all
-filt_func '\$hit->gaps == 0' -table 2

Parsing Blast report file(s).
Odd number of elements in hash list at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Root/Object.pm

line 515.
.
12 SIGNIFICANT HITS.
DONE PARSING DESCRIPTIONS.
QUERY   Q_LEN   SBJCT   S_LEN   EXPCT   SCORE   BITS    HSPS    FR_ID
FR_CN
FR_ALQ   FR_ALS  Q_ALN   S_ALN   Q_GAP   S_GAP   Q_BEG   Q_END   S_BEG
S_END  AMBIG
-----   -----   ------  -----   -----   -----   -----   -----   -----
-----
-----    -----   -----   -----   -----   -----   -----   -----   -----
-----  -----
.

*** 1 Blast reports produced fatal errors:

FILE: out/blastp.2.wu
Can't use an undefined value as an ARRAY reference at
/hosts/kinetic/dust/users/gcolello/bioperl/bioperl-0.05.pre/Bio/Tools/Blast.pm

line 2833.




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