[Bioperl-l] Fwd: Problem with using blast and blastp in one single program
jonas s
jonas_schaer at gmx.de
Thu Feb 11 15:05:12 UTC 2010
Hi,
I have a problem using the online blast applications.
I wrote two scripts in PERL (with your help btw, thanks again :) ).
One of these calls at some point a subroutine that submitts blast requests
and stores the recieved reports.
parameters:
########################################################################################################
my $prog = 'blastp';
my $db = 'nr';
my $e_val= '1e-10';
my @params = ( '-prog' => $prog,
'-data' => $db,
'-expect' => $e_val,
'-readmethod' => 'SearchIO' );
my $factory = Bio::Tools::Run::RemoteBlast->new(@params);
$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
$Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
$Bio::Tools::Run::RemoteBlast::HEADER{'COMPOSITION_BASED_STATISTICS'} = '2';
my %put = (
WORD_SIZE => 3,
HITLIST_SIZE => 100,
THRESHOLD => 11,
FILTER => 'R', #''L'' for Low Complexity, ''R'' for Human Repeats, ''m''
for Mask for Lookup
GENETIC_CODE => 1
);
########################################################################################################
The other one does almost the same thing, except it uses blastp to
search for conserved domains:
parameters:
########################################################################################################
my $cddprog = 'blastp';
my $cdddb = 'cdsearch/cdd';
my $cdde_val= '0.010';
my @cddparams = ( '-prog' => $cddprog,
'-data' => $cdddb,
'-expect' => $cdde_val,
'-readmethod' => 'SearchIO' );
my $cddfactory = Bio::Tools::Run::RemoteBlast->new(@cddparams);
$Bio::Tools::Run::RemoteBlast::HEADER{'GAPCOSTS'} = '11 1';
$Bio::Tools::Run::RemoteBlast::HEADER{'MAX_NUM_SEQ'} = '100';
$Bio::Tools::Run::RemoteBlast::HEADER{'EXPECT'} = '10';
$Bio::Tools::Run::RemoteBlast::HEADER{'SERVICE'} = 'rpsblast';
my %cddput = (
WORD_SIZE => 3,
HITLIST_SIZE => 100,
THRESHOLD => 11,
FILTER => 'R', #''L'' for Low Complexity, ''R'' for Human Repeats, ''m''
for Mask for Lookup
GENETIC_CODE => 1
);
########################################################################################################
Both skripts work fine, but i need to combine them to one single
programm and if i do that the first subroutine works but the second one
doesn't (it doesn't matter which one is called first, its always the
second one that crashes instead submitting the requests). Instead of submitting the same sequences again
to recieve the other blast_reports, there is some output one my screen,
the end of it is this:
url=http%3A//blast.ncbi.nlm.nih.gov/Blast.cgi%3FALIGNMENTS%3D50%26ALIGNMENT%5FVI
EW%3DPairwise%26CMD%3DPut%26COMPOSITION%5FBASED%5FSTATISTICS%3D2%26DATABASE%3Dnr
%26DESCRIPTIONS%3D100%26ERROR%3D%26EXPECT%3D10%26FILTER%3DR%26FORMAT%5FOBJECT%3D
Alignment%26FORMAT%5FTYPE%3DText%26GAPCOSTS%3D11%2B1%26GENETIC%5FCODE%3D1%26HITL
IST%5FSIZE%3D100%26MAX%5FNUM%5FSEQ%3D100%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblas
tp%26QUERY%3D%253Ejgi%257CChlre4%257C522274%257Cau5.g11876%5Ft1%2B%250AMASLLAGKP
LMGGLKLQRSAKMAVPAVAVPRVATAAAARVGLKGGLGERPFAPKPVEKKPLAPAPQAASGDAPAPEPKKFLGFEPITWA
KILPLGAMFFCILFNYTILRDTKDVLVVTAPGSGAEIIPFLKTWVNLPMAIGFTIMYSALSNRLSSEALFYTCIIPFIAF
FGAFAALMYPMRDALHPTEFCQNLLEQMGPRFAGPIAILRNWTFCLFYVMAELWGSVVVSVLFWGFANQITTVEEASQFY
PLFGLGANVALIFSGQAVKYFSQVRAGLPPDVDGWGVSLNGLMGMVVIGGLLIIGIYFSLQRLVVPKLKSLREGKKKKNK
TKMSVGESFAFLAQSSYIRDMATLVVAYGISINLVEVTWKGKLKAQFPNPNDYSSFMGEFSTATGTVTFTMMILSRWIFK
QFGWGVAALITPIMLLITGLLFFTLVLAGDTVKPALAAWGMTPLYAAVLVGAAQNVFSKSSKYSLFDPCKEMAYIPLEDE
VKTKGKAAIDVICNPLGKSGGALIQQFMIIGLGSLAASTPYLGAILCVIIVAWINAAASLNKQFTALQEETGMYITGEKP
ANKSEKKD%2A%26SERVICE%3Drpsblast%26THRESHOLD%3D11%26USER%5FTYPE%3D0%26WORD%5FSIZ
E%3D3" title="Click to register for an
account"onclick="MyNCBI_auto_submit('http
://www.ncbi.nlm.nih.gov/sites/myncbi/register/?back_url=http%3A//blast.ncbi.nlm.
nih.gov/Blast.cgi%3FALIGNMENTS%3D50%26ALIGNMENT%5FVIEW%3DPairwise%26CMD%3DPut%26
COMPOSITION%5FBASED%5FSTATISTICS%3D2%26DATABASE%3Dnr%26DESCRIPTIONS%3D100%26ERRO
R%3D%26EXPECT%3D10%26FILTER%3DR%26FORMAT%5FOBJECT%3DAlignment%26FORMAT%5FTYPE%3D
Text%26GAPCOSTS%3D11%2B1%26GENETIC%5FCODE%3D1%26HITLIST%5FSIZE%3D100%26MAX%5FNUM
%5FSEQ%3D100%26MYNCBI%5FUSER%3D%2D1%26PROGRAM%3Dblastp%26QUERY%3D%253Ejgi%257CCh
lre4%257C522274%257Cau5.g11876%5Ft1%2B%250AMASLLAGKPLMGGLKLQRSAKMAVPAVAVPRVATAAA
ARVGLKGGLGERPFAPKPVEKKPLAPAPQAASGDAPAPEPKKFLGFEPITWAKILPLGAMFFCILFNYTILRDTKDVLVV
TAPGSGAEIIPFLKTWVNLPMAIGFTIMYSALSNRLSSEALFYTCIIPFIAFFGAFAALMYPMRDALHPTEFCQNLLEQM
GPRFAGPIAILRNWTFCLFYVMAELWGSVVVSVLFWGFANQITTVEEASQFYPLFGLGANVALIFSGQAVKYFSQVRAGL
PPDVDGWGVSLNGLMGMVVIGGLLIIGIYFSLQRLVVPKLKSLREGKKKKNKTKMSVGESFAFLAQSSYIRDMATLVVAY
GISINLVEVTWKGKLKAQFPNPNDYSSFMGEFSTATGTVTFTMMILSRWIFKQFGWGVAALITPIMLLITGLLFFTLVLA
GDTVKPALAAWGMTPLYAAVLVGAAQNVFSKSSKYSLFDPCKEMAYIPLEDEVKTKGKAAIDVICNPLGKSGGALIQQFM
IIGLGSLAASTPYLGAILCVIIVAWINAAASLNKQFTALQEETGMYITGEKPANKSEKKD%2A%26SERVICE%3Drpsb
last%26THRESHOLD%3D11%26USER%5FTYPE%3D0%26WORD%5FSIZE%3D3');return
false;">[Regi
ster]</a></td></tr></table></div> </div>
<ul id="nav"> <li class="first "><a href="Blast.cgi?CMD=Web&
PAGE_TYPE=BlastHome" title="BLAST Home">Home</a></li> <li class=
"recent"><a href="Blast.cgi?CMD=GetSaved&RECENT_RESULTS=on"
title="Unexpire
d BLAST jobs">Recent Results</a></li> <li class=
"saved"><a href="Blast.cgi?CMD=GetSaved" title="Saved sets of BLAST
search para
meters">Saved Strategies</a></li> <li class= "last documentation
"> <a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs" title="BLAST
documentati
on">Help</a></li> </ul> </div> <div id=
"content-wrap"> <!-- %%% Add breadcrumb text --> <
div id="breadcrumb"> <a href="http://www.ncbi.nlm.nih.gov/">NC
BI</a>/<a href="Blast.cgi?CMD=Web&PAGE_TYPE=BlastHome">BLAST<
/a>/<strong>Format Request</strong>
</div> <!-- Do errors t
his way --> <!--<ul
class="msg"><li class="error"><p></p></li></ul>-->
<ul id="msgR" class="msg"><li class="error"><div class="error
msInf">Message ID#
35 Error: Cannot validate the Blast options: Compositional adjustments
are only
supported with blastp or tblastn<a class="helplink hiding shown
errorHelp error
" title="help" href="#" id="errorHelp0"><span>[?]</span></a><div
toggle="errorHe
lp0" class="helpbox hidden">This error message indicates that the
combination of
options for this Blast search is inconsistent or invalid. This can
happen when
the selected Blast program does not support one of the options provided,
when tw
o or more options have conflicting values, etc. If you are using URL
API, please
check the options mentioned in the error message string and re-submit
your sear
ch. Please note that the current version of the Blast CGI application is
stricte
r at validating Blast options than it has been historically. If this
error persi
sts, please, contact<a
href="mailto:blast-help at ncbi.nlm.nih.gov">Blast-help at ncb
i.nlm.nih.gov</a> for more help.</div></div></li></ul> <div id="c
ontent"> <form action="Blast.cgi" enctype="applic
ation/x-www-form-urlencoded" method="post" name="FormatForm"
id="FormatForm">
<script language="JavaScript"> <!--//document.images['Bl
astHeaderGif'].src = 'html/head_formating.gif';// --></script><!--
<p class='info'><strong>Job submitted.</strong>We estimate that results
will b
e ready in 16 seconds or less.</p>--><div class="fbtn"><!--<a
href="javascript:d
ocument.forms[0].submit();"><img align="middle" alt="Format button"
border="0" s
rc="FormatPage_files/format_but.gif"></a>--></div><dl class="summary
db"><dd></
dd><!--<span class=" db">--><!--<span class="hidden
query"><dt>Query</dt><dd>
</dd></span> --><dt class="hidden query">Query</dt><dd class="hidden
query"></dd
><dt class="hidden db">Database</dt><dd class="hidden db">nr</dd><dt
class="hidd
en title">Job title</dt><dd class="hidden title"></dd><dt class="hidden
entrez">
Entrez Query</dt><dd class="hidden entrez"><span class="note
entrez">Note: Your
search is limited to records matching this Entrez query</span></dd><!--
</span>
--><dt><label for="rid">Request ID</label></dt><dd><input name="RID"
size="50" t
ype="text" value="" id="rid" /><input type="submit" value="View report"
name="Vi
ewReport" class="button" /><!--<img border="0" id="viewRpButton"
src="images/ve
iwRpButton.jpg" class="viewReport" alt="View report"
mouseovImg="images/veiwRp
ButtonOver.jpg" mouseoutImg="images/veiwRpButton.jpg"
mousedownImg="images/veiwR
pButtonDown.jpg" mouseupImg="images/veiwRpButtonOver.jpg" />--><input
type="che
ckbox" name="NEWWINRES" form="FormatForm" winType="const" id="nw"
class="newwin
" /><label for="nw">Show results in a new
window</label></dd><dt>Format<br/><!-
-<a class='help' href="#">[Help]</a></dt> --><dd><table class="options
blastp ">
<tr class="paramSet xgl"><td class="hd"><label
for="FORMAT_OBJECT">Show</label><
/td><td><div class="fi"><select id="FORMAT_OBJECT" class="reset"
name="FORMAT_OB
JECT" defVal="Alignment"><option value="Alignment"
selected="selected">Alignment
</option><option value="PSSM">PSSM</option><option
value="PSSM_Scoremat">PssmW
ithParameters</option><option value="Bioseq"
>Bioseq</option></select><label fo
r="FORMAT_TYPE">as</label><select name="FORMAT_TYPE" id="FORMAT_TYPE"
class="res
et" defVal="HTML"><option value="HTML">HTML</option><option
value="Text" selec
ted="selected">Plain text</option><option value="ASN.1"
>ASN.1</option><option
value="XML">XML</option></select><input name="PSSM_FORMAT_TYPE"
value="Text"
size="3" id="pssmFormat" type="text" class="hidden dispType" /><input
name="BIOS
EQ_FORMAT_TYPE" value="ASN.1" size="3" id="bioseqFormat" type="text"
class="hidd
en dispType" /><input name="PSSM_SC_FORMAT_TYPE" value="ASN.1" size="3"
id="pssm
ScFormat" type="text" class="hidden dispType" /><span id="advView"
class=""><inp
ut name="NEW_VIEW" id="NEW_VIEW" type="checkbox" class="cb reset"
defVal="checke
d" /><label for="NEW_VIEW">Advanced View</label><span class=""><input
name="OLD
_BLAST" id="OLD_BLAST" type="checkbox" class="cb reset"
defVal="unchecked" /><l
abel for="OLD_BLAST">Use old BLAST report format</label></span></span><a
class="
resetAll" id="resetAll">Reset form to defaults</a><a class="helplink
hiding" ti
tle="Alignments object formatting help" id="formatHelp"
href="#"><span>[?]</span
></a><p toggle="formatHelp" class="helpbox hidden" id="hlp1">These
options contr
ol formatting of alignments in results pages. Thedefault is HTML, but
other form
ats (including plain text) are available.PSSM and PssmWithParameters are
represe
ntations of Position Specific Scoring Matrices and are only available
for PSI-BL
AST. The Advanced view option allows the database descriptions to be
sorted by v
arious indices in a table.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihel
p.shtml#format_object" target="helpWin" title="Additional alignments
object form
atting help">more...</a></p></div></td></tr><tr class="odd paramSet"><td
class="
hd"><label for="ALIGNMENT_VIEW">Alignment View</label></td><td><div
class="fi"><
select name="ALIGNMENT_VIEW" id="ALIGNMENT_VIEW" defVal="Pairwise"
class="reset"
><option value="Pairwise" selected="selected">Pairwise</option><option
value="P
airwiseWithIdentities">Pairwise with dots for
identities</option><option value
="QueryAnchored">Query-anchored with dots for
identities</option><option value
="QueryAnchoredNoIdentities">Query-anchored with letters for
identities</optio
n><option value="FlatQueryAnchored">Flat query-anchored with dots for
identiti
es</option><option value="FlatQueryAnchoredNoIdentities">Flat
query-anchored w
ith letters for identities</option><option value="Tabular">Hit
Table</option><
/select><a class="helplink hiding" title="Alignments view options help"
id="alnV
iewHelp" href="#"><span>[?]</span></a><p toggle="alnViewHelp"
class="helpbox hid
den" id="hlp2">Choose how to view alignments.The default "pairwise" view
shows h
ow each subject sequence alignsindividually to the query sequence. The
"query-an
chored" view shows howall subject sequences align to the query sequence.
For eac
h view type,you can choose to show "identities" (matching residues) as
letters o
rdots.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#alignment_vi
ew" target="helpWin" title="Additional alignments view options
help">more...</a>
</p></div></td></tr><tr class="paramSet"><td
class="hd"><label>Display</label></
td><td class="cb"><div class="fi"><input name="SHOW_OVERVIEW"
id="SHOW_OVERVIEW"
type="checkbox" class="cb reset" defVal="checked" checked="checked"
/><label cl
ass="rb" for="SHOW_OVERVIEW">Graphical Overview</label><input
name="SHOW_LINKOUT
" id="SHOW_LINKOUT" type="checkbox" class="cb reset" defVal="checked"
checked="c
hecked" /><label class="rb" for="SHOW_LINKOUT">Linkout</label><input
name="GET_S
EQUENCE" id="GET_SEQUENCE" type="checkbox" class="cb reset"
defVal="checked" che
cked="checked" /><label class="rb" for="GET_SEQUENCE">Sequence
Retrieval</label>
<input name="NCBI_GI" id="NCBI_GI" type="checkbox" class="cb reset"
defVal="unch
ecked" /><label class="rb" for="NCBI_GI">NCBI-gi</label><input
name="SHOW_CDS_F
EATURE" id="SHOW_CDS_FEATURE" type="checkbox" class="cb reset blastn"
defVal="un
checked" /><label for="SHOW_CDS_FEATURE" class="blastn">CDS
feature</label><a c
lass="helplink hiding" title="Alignments display options help"
id="displayHelp"
href="#"><span>[?]</span></a><ul toggle="displayHelp" class="helpbox
hidden" id=
"hlp3"><li>Graphical Overview: Graphical Overview: Show graph of similar
sequenc
e regions aligned to query.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgih
elp.shtml#show_overview" target="helpWin" title="Graphical Overview
help">more..
.</a></li><li>Database LinkOuts: Show links from matching sequences to
entries i
n specialized NCBI databases.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgi
help.shtml#show_linkout" title="LinkOut help" target="helpWin"
>more...</a></li>
<li>Sequence Retrieval: Show buttons to download matching sequences.<a
href="htt
p://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#get_sequence"
title="Sequence
Retrieval help" target="helpWin">more...</a></li><li>NCBI-gi: Show NCBI
gi iden
tifiers.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#ncbi_gi" t
itle="NCBI-gi help" target="helpWin">more...</a></li><li>CDS feature:
Show anno
tated coding region and translation.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/b
lastcgihelp.shtml#show_cds_feature" title="CDS feature help"
target="helpWin">m
ore...</a></li></ul></div></td></tr><tr class="paramSet odd xgl"><td
class="hd">
<label>Masking</label></td><td><div class="fi"><label for="MASK_CHAR">
Character
:</label><select name="MASK_CHAR" id="MASK_CHAR" class="reset"
defVal="2"><opt
ion value="0">X for protein, n for nucleotide</option><option value="2"
select
ed="selected">Lower Case</option></select><label for="MASK_COLOR">
Color:</labe
l><select name="MASK_COLOR" id="MASK_COLOR" class="reset"
defVal="1"><option val
ue="0">Black</option><option value="1" selected="selected"
>Grey</option><opti
on value="2">Red</option></select><a class="helplink hiding"
title="Alignments
masking help" id="maskingHelp" href="#"><span>[?]</span></a><ul
toggle="masking
Help" class="helpbox hidden" id="hlp4"><li>Masking Character: Display
masked (fi
ltered) sequence regions as lower-case or as specific letters (N for
nucleotide,
P for protein).</li><li>Masking Color: Display masked sequence regions
in the g
iven color.</li></ul></div></td></tr><tr class="paramSet xgl"><td
class="hd"><la
bel>Limit results</label></td><td><div class="fi"><label
for="FRM_DESCRIPTIONS">
Descriptions:</label><select name="DESCRIPTIONS" id="FRM_DESCRIPTIONS"
class="re
set" defVal="100"><option value="0">0</option><option value="10">10</
option><option value="50">50</option><option value="100" selected="select
ed">100</option><option value="250">250</option><option value="500">500
</option><option value="1000">1000</option><option value="5000">5000</opti
on><option value="10000">10000</option><option value="20000"
>20000</option><
/select><label for="FRM_NUM_OVERVIEW">Graphical overview:</label><select
name="N
UM_OVERVIEW" id="FRM_NUM_OVERVIEW" class="reset" defVal="100"><option
value="0"
>0</option><option value="10">10</option><option value="50">50</opti
on><option value="100" selected="selected">100</option><option
value="250">
250</option><option value="500">500</option><option value="1000"
>1000</optio
n></select><label for="FRM_ALIGNMENTS">Alignments:</label><select
name="ALIGNMEN
TS" id="FRM_ALIGNMENTS" class="reset" defVal="100"><option value="0">0</op
tion><option value="10">10</option><option value="50" selected="selected
">50</option><option value="100">100</option><option value="250">250</o
ption><option value="500">500</option><option value="1000">1000</option><
option value="5000">5000</option><option value="10000"
>10000</option><optio
n value="20000">20000</option></select><a class="helplink hiding"
title="Limit
number of descriptions/alignments help" id="numHelp"
href="#"><span>[?]</span><
/a><ul toggle="numHelp" class="helpbox hidden"
id="hlp5"><li>Descriptions: Show
short descriptions for up to the given number of sequences.</li>
<li>Alignments
: Show alignments for up to the given number of sequences, in order of
statisti
cal significance.</li></ul></div></td></tr><tr class="paramSet odd
xgl"><td clas
s="hd"></td><td><div class="fi"><label
for="qorganism">Organism</label><span cla
ss="instr">Type common name, binomial, taxid, or group name. Only 20 top
taxa wi
ll be shown.</span><input name="FORMAT_ORGANISM" size="55"
id="qorganism" sgDic
t="taxids_sg" value="" sgStyle="SG_green" class="reset" /><a
class="helplink hi
ding" title="Limit results by organism help" id="organismHelp"
href="#"><span>[?
]</span></a><p toggle="organismHelp" class="helpbox hidden"
id="hlp6">Show only
sequences from the given organism.</p></div></td></tr><tr
class="paramSet xgl"><
td class="hd"></td><td><div class="fi"><label
for="FORMAT_EQ_TEXT">Entrez query:
</label><input name="FORMAT_EQ_TEXT" id="FORMAT_EQ_TEXT" size="60"
type="text" v
alue="" class="reset" /><a class="helplink hiding" title="Limit results
by Entre
z query help" id="entrezHelp" href="#"><span>[?]</span></a><p
toggle="entrezHelp
" class="helpbox hidden" id="hlp7">Show only those sequences that match
the give
n Entrez query.<a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#lim
it_result" target="helpWin" title="Additional limit results by Entrez
query help
" target="helpWin">more...</a></p></div></td></tr><tr class="paramSet
odd xgl">
<td class="hd"></td><td><div class="fi"><label for="EXPECT_LOW">Expect
Min:</lab
el> <input name="EXPECT_LOW" id="EXPECT_LOW" size="10" type="text"
value="" clas
s="reset"/><label for="EXPECT_HIGH">Expect Max:</label> <input
name="EXPECT_HIGH
" id="EXPECT_HIGH" size="10" type="text" value="" class="reset" /><a
class="help
link hiding" title="Limit results by expect value range help"
id="expectHelp" hr
ef="#"><span>[?]</span></a><p toggle="expectHelp" class="helpbox hidden"
id="hlp
8">Show only sequences with expect values in the given range.<a
href="http://www
.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#expect_range"
target="helpWin" title=
"Additional limit results by expect value range
help">more...</a></p></div></td>
</tr><tr class="psiBlast paramSet xgl"><td class="hd"><label>Format
for</label><
/td><td><div class="fi"><input name="RUN_PSIBLAST_FORM"
id="RUN_PSIBLAST" type="
checkbox" class="cb psiBlast" /><label class="rb psiBlast"
for="RUN_PSIBLAST">P
SI-BLAST</label><label for="I_THRESH">with inclusion
threshold:</label><input na
me="I_THRESH" id="I_THRESH" size="10" type="text" value=""
defVal="0.005" /><a c
lass="helplink hiding" title="PSI BLAST formatting help" id="psiHelp"
href="#"><
span>[?]</span></a><ul toggle="psiHelp" class="helpbox hidden"
id="hlp9"><li>For
mat for PSI-BLAST: The Position-Specific Iterated BLAST (PSI-BLAST)
program perf
orms iterative searches with a protein query, in which sequences found
in one ro
und of search are used to build a custom score model for the next
round.</li><a
href="http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml#psiblast"
target="hel
pWin" title="Additional PSI BLAST formatting
help">more...</a><li>Inclusion Thre
shold: This sets the statistical significance threshold for including a
sequence
in the model used by PSI-BLAST to create the PSSM on the next
iteration.</li> <
/ul></div></td></tr></table></dd></dl><input name="RID" value=""
type="hidden" /
><input name="CDD_RID" value="" type="hidden" /><input
name="CDD_SEARCH_STATE" t
ype="hidden" value="" /><input name="STEP_NUMBER" value=""
id="stepNumber" type=
"hidden" /><input name="CMD" value="Get" type="hidden" /><input
name="FORMAT_EQ_
OP" value="AND" type="hidden" /><input name="RESULTS_PAGE_TARGET"
type="hidden"
id="resPageTarget" value="Blast_Results_for_1661104373" /><input
name="QUERY_INF
O" type="hidden" value="" /> <input name="ENTREZ_QUER
Y" type="hidden" value="" /><input name="QUERY_INDEX" type="hidden"
value="0"/><
!-- Those params are set in the template (blastn.dat, blastp.dat etc.
--><input
name="BLAST_PROGRAMS" type="hidden" value="blastp"/><input name="PAGE"
type="hid
den" value="Proteins"/><input name="PROGRAM" type="hidden"
value="blastp"/><inpu
t name="MEGABLAST" type="hidden" value="" /><input name="RUN_PSIBLAST"
type="hid
den" value="" /><input name="BLAST_SPEC" id="blastSpec" type="hidden"
value=""/>
<input name="QUERY" type="hidden"
value=">jgi|Chlre4|522274|au5.g11876_t1 MASLLA
GKPLMGGLKLQRSAKMAVPAVAVPRVATAAAARVGLKGGLGERPFAPKPVEKKPLAPAPQAASGDAPAPEPKKFLGFEPI
TWAKILPLGAMFFCILFNYTILRDTKDVLVVTAPGSGAEIIPFLKTWVNLPMAIGFTIMYSALSNRLSSEALFYTCIIPF
IAFFGAFAALMYPMRDALHPTEFCQNLLEQMGPRFAGPIAILRNWTFCLFYVMAELWGSVVVSVLFWGFANQITTVEEAS
QFYPLFGLGANVALIFSGQAVKYFSQVRAGLPPDVDGWGVSLNGLMGMVVIGGLLIIGIYFSLQRLVVPKLKSLREGKKK
KNKTKMSVGESFAFLAQSSYIRDMATLVVAYGISINLVEVTWKGKLKAQFPNPNDYSSFMGEFSTATGTVTFTMMILSRW
IFKQFGWGVAALITPIMLLITGLLFFTLVLAGDTVKPALAAWGMTPLYAAVLVGAAQNVFSKSSKYSLFDPCKEMAYIPL
EDEVKTKGKAAIDVICNPLGKSGGALIQQFMIIGLGSLAASTPYLGAILCVIIVAWINAAASLNKQFTALQEETGMYITG
EKPANKSEKKD*"/><input name="JOB_TITLE" type="hidden" value=""/><input
name="QUER
Y_TO" type="hidden" value=""/><input name="QUERY_FROM" type="hidden"
value=""/><
input name="EQ_TEXT" type="hidden" value=""/><input name="ORGN"
type="hidden" va
lue=""/><input name="EQ_MENU" type="hidden" value=""/><input
name="ORG_EXCLUDE"
type="hidden" value=""/><input name="PHI_PATTERN" type="hidden"
value=""/><input
name="EXPECT" type="hidden" value="10"/>
<input name="DATABASE" type="hidden" value="nr"/
><input name="DB_GROUP" type="hidden" value=""/><input
name="SUBGROUP_NAME" type
="hidden" value=""/><input name="GENETIC_CODE" type="hidden"
value="1"/><input n
ame="WORD_SIZE" type="hidden" value="3"/><input name="MATCH_SCORES"
type="hidden
" value=""/> <input name="MATRIX_NAME" type="hidden" value=""
/> <input name="GAPCOSTS" type="hidden" value="11 1
"/><input name="MAX_NUM_SEQ" id="maxNumSeq" type="hidden" value="100"/>
<input name="COMPOSITION_BASED_STATISTICS" type="hidden"
value="2"/> <input name="NEWWIN" type="hidden" value=""/><in
put name="SHORT_QUERY_ADJUST" type="hidden" value=""/><input
name="FILTER" type=
"hidden" value="R;"/><input name="REPEATS" type="hidden"
value=""/><input name="
ID_FOR_PSSM" type="hidden" value=""/><input name="EXCLUDE_MODELS"
type="hidden"
value=""/><input name="EXCLUDE_SEQ_UNCULT" type="hidden"
value=""/><input name="
NUM_ORG" type="hidden" value = "1" /><!-- PSSM --><input
name="LCASE_MASK" type=
"hidden" value=""/><input name="TEMPLATE_TYPE" type="hidden"
value=""/><input na
me="TEMPLATE_LENGTH" type="hidden" value=""/><input name="I_THRESH"
type="hidden
" value=""/><input name="ADJUSTED_FOR_SHORT_QUERY" type="hidden"
value=""/><inpu
t name="MIXED_QUERIES" type="hidden" value=""/><!--QBlastInfoBegin RID =
RTOE = QBlastInfoEnd--></form>
</div><!-- /#con
tent --> </div><!-- /#content-wrap --> <div id="footer"
> <p id="orgns"> <a href="http://www.ncbi.nlm.nih.gov/" title="National C
enter for Biotechnology Information">NCBI</a> |<a href="http://www.nlm.nih
.gov/" title="National Library of Medicine">NLM</a> |<a href="http://www.n
ih.gov/" title="National Institutes of Health">NIH</a> |<a href="http://ww
w.hhs.gov/" title="US Department of Health and Human Services">DHHS</a> </p>
<p> <a href='http://ncbi.nlm.nih.gov/About/disclaimer.html' title=
'NCBI intellectual property statement'>Copyright</a> |<a href='http://ncb
i.nlm.nih.gov/About/disclaimer.html#disclaimer' title='About liability, end
orsements, external links, pop-up advertisements'>Disclaimer</a> |<a href
='http://www.nlm.nih.gov/privacy.html' title='NLM privacy policy'>Privacy</
a> |<a href='http://ncbi.nlm.nih.gov/About/accessibility.html' title
='About using NCBI resources with assistive technology'>Accessibility</a> |
<a href='http://www.ncbi.nlm.nih.gov/About/glance/contact_info.html' title
='How to get help, submit data, or provide feedback'>Contact</a> |<a href=
'mailto:blast-help at ncbi.nlm.nih.gov' title='How to get help, submit data, o
r provide feedback'>Send feedback</a> </p></div> </div><!--/#w
rap--><script type="text/javascript"
src="http://www.ncbi.nlm.nih.gov/coreweb/ja
vascript/nsuggest/nsuggest_loader.js"></script></body></html>
---------------------------------------------------
########################################################################################################
After printing that text the program continues normally, so it actually
doesnt "crash", but submitting the requests for a second time is abortet.
Again: both skripts work fine individually, but as soon as they are combined there is this problem...
I really need to put theses two subroutines in one single program.
Can you please tell me why this doesn´t work?
Thanks in advance, Jonas Schaer
More information about the Bioperl-l
mailing list