[Bioperl-l] Bio::SearchIO blast_parsing
dot_at_the_end_of query_accession
James Wasmuth
james.wasmuth at ed.ac.uk
Wed Mar 17 16:10:53 EST 2004
Hi Jason, I work with Ralf, and sensibly he's gone home, but here's the
report file:
BLASTP 2.2.6 [Apr-09-2003]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= ZPP00163
(199 letters)
Database: swissall.fsa
1,218,016 sequences; 390,760,073 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
NUKM_CAEEL (Q94360) Probable NADH-ubiquinone oxidoreductase 20 k... 177 6e-44
Q9VAK5 (Q9VAK5) CG2014 protein 166 1e-40
NUKM_BOVIN (P42026) NADH-ubiquinone oxidoreductase 20 kDa subuni... 166 2e-40
Q9VXK7 (Q9VXK7) CG9172 protein (LD31474P) 165 4e-40
Q9BV17 (Q9BV17) Similar to CG9172 gene product (NADH:ubiquinone ... 163 1e-39
NUKM_HUMAN (O75251) NADH-ubiquinone oxidoreductase 20 kDa subuni... 163 1e-39
Q7PRW3 (Q7PRW3) ENSANGP00000019428 (Fragment) 162 2e-39
Q9DC70 (Q9DC70) 1010001M04Rik protein (RIKEN cDNA 1010001M04 gene) 159 2e-38
Q86EG3 (Q86EG3) Clone ZZD432 mRNA sequence 155 4e-37
Q7PQT1 (Q7PQT1) ENSANGP00000014787 (Fragment) 150 7e-36
Q7PQU6 (Q7PQU6) ENSANGP00000017108 (Fragment) 150 7e-36
NUKM_RECAM (O21272) NADH-ubiquinone oxidoreductase 20 kDa subuni... 146 2e-34
Q9G8U4 (Q9G8U4) NADH dehydrogenase subunit 10 (EC 1.6.5.3) 144 5e-34
Q8NAS7 (Q8NAS7) Hypothetical protein FLJ34850 144 9e-34
Q7RZB4 (Q7RZB4) Hypothetical protein 143 2e-33
NUKM_NEUCR (O47950) NADH-ubiquinone oxidoreductase 19.3 kDa subu... 143 2e-33
Q8W0E8 (Q8W0E8) Putative NADH dehydrogenase (Ubiquinone) chain PSST 141 6e-33
Q9TCA4 (Q9TCA4) NADH dehydrogenase subunit 10 (EC 1.6.5.3) 140 1e-32
Q9SP38 (Q9SP38) NADH ubiquinone oxidoreductase PSST subunit 139 2e-32
Q9LKG9 (Q9LKG9) NADH-ubiquinone oxidoreductase subunit PSST (Fra... 139 2e-32
NUKM_SOLTU (Q43844) NADH-ubiquinone oxidoreductase 20 kDa subuni... 139 2e-32
NUKM_BRAOL (P42027) NADH-ubiquinone oxidoreductase 20 kDa subuni... 139 2e-32
NUKM_ARATH (Q42577) NADH-ubiquinone oxidoreductase 20 kDa subuni... 138 5e-32
Q9LKH4 (Q9LKH4) NADH-ubiquinone oxidoreductase subunit PSST 137 1e-31
Q9UUT7 (Q9UUT7) Subunit NUKM of protein NADH:ubiquinone oxidored... 134 5e-31
Q7PBK3 (Q7PBK3) NADH dehydrogenase I chain B 134 9e-31
NUOB_RICCN (Q92ID6) NADH-quinone oxidoreductase chain B (EC 1.6.... 134 9e-31
>>NUKM_CAEEL (Q94360) Probable NADH-ubiquinone oxidoreductase 20 kDa
>
>
subunit, mitochondrial precursor (EC 1.6.5.3) (EC
1.6.99.3) (Complex I-20KD) (CI-20KD)
Length = 199
Score = 177 bits (450), Expect = 6e-44
Identities = 88/161 (54%), Positives = 106/161 (65%)
Query: 39 GKGVFGSPFVQSESKGEWALASLDDVINLCGKTSLWPLTFGLXXXXXXXXHFAAPRYDMD 98
G G+PF+ SK E+ALA LDDV+NL + S+WPLTFGL HFAAPRYDMD
Sbjct: 31 GIATTGTPFLNPSSKAEYALARLDDVLNLAQRGSIWPLTFGLACCAVEMMHFAAPRYDMD 90
Query: 99 HYGVVFHATPXQVNLILFTGTITNKMAPALHHIYNQMPKPKYVISMESYTNGSGYYHYTY 158
YGVVF A+P Q +LI GT+TNKMAPAL IY+QMP+ K+VISM S NG GYYHY Y
Sbjct: 91 RYGVVFRASPRQADLIFVAGTVTNKMAPALRRIYDQMPEAKWVISMGSCANGGGYYHYAY 150
Query: 159 SIVHNYNHMXXXXXXXXXXXXTAKXLLYNILQLQKKIKHSR 199
S++ + + TA+ LLY +LQLQKKIK R
Sbjct: 151 SVLRGCDRVIPVDIYVPGCPPTAEALLYGVLQLQKKIKRKR 191
>>Q9VAK5 (Q9VAK5) CG2014 protein
>
>
Length = 212
Score = 166 bits (421), Expect = 1e-40
Identities = 82/162 (50%), Positives = 103/162 (63%), Gaps = 3/162 (1%)
Query: 38 WGKGVFGSPFVQSESKGEWALASLDDVINLCGKTSLWPLTFGLXXXXXXXXHFAAPRYDM 97
WG FG ++ GEW A LDD++N K SLWPLTFGL H AAPRYDM
Sbjct: 46 WGYSAFGR---NQKTWGEWTCARLDDLLNWGRKGSLWPLTFGLACCAVEMMHIAAPRYDM 102
Query: 98 DHYGVVFHATPXQVNLILFTGTITNKMAPALHHIYNQMPKPKYVISMESYTNGSGYYHYT 157
D YGVVF A+P Q ++++ GT+TNKMAPA IY+QMP+P++VISM S NG GYYHY+
Sbjct: 103 DRYGVVFRASPRQADVLIVAGTLTNKMAPAFRKIYDQMPEPRWVISMGSCANGGGYYHYS 162
Query: 158 YSIVHNYNHMXXXXXXXXXXXXTAKXLLYNILQLQKKIKHSR 199
YS+V + + TA+ L+Y ILQLQKK+K R
Sbjct: 163 YSVVRGCDRIVPVDIYVPGCPPTAEALMYGILQLQKKVKRMR 204
Database: swissall.fsa
Posted date: Dec 5, 2003 3:22 PM
Number of letters in database: 390,760,073
Number of sequences in database: 1,218,016
Lambda K H
0.318 0.134 0.417
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 150,792,462
Number of Sequences: 1218016
Number of extensions: 5616912
Number of successful extensions: 15131
Number of sequences better than 1.0e-30: 27
Number of HSP's better than 0.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 15095
Number of HSP's gapped (non-prelim): 27
length of query: 199
length of database: 390,760,073
effective HSP length: 116
effective length of query: 83
effective length of database: 249,470,217
effective search space: 20706028011
effective search space used: 20706028011
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 336 (134.0 bits)
BLASTP 2.2.6 [Apr-09-2003]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= ZPP00036_1
(229 letters)
Database: swissall.fsa
1,218,016 sequences; 390,760,073 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Q95XJ0 (Q95XJ0) Hypothetical protein 256 2e-67
Q95XI9 (Q95XI9) Hypothetical protein 256 2e-67
ATPG_DROME (O01666) ATP synthase gamma chain, mitochondrial prec... 202 2e-51
Q7Q3N8 (Q7Q3N8) AgCP11416 (Fragment) 197 7e-50
ATPG_BOVIN (P05631) ATP synthase gamma chain, mitochondrial prec... 184 1e-45
Q9ERA8 (Q9ERA8) ATP synthase gamma-subunit precursor 178 4e-44
Q8TAS0 (Q8TAS0) Hypothetical protein (Fragment) 178 6e-44
ATPG_MOUSE (Q91VR2) ATP synthase gamma chain, mitochondrial prec... 178 6e-44
ATPG_HUMAN (P36542) ATP synthase gamma chain, mitochondrial prec... 178 6e-44
Q910C3 (Q910C3) Mitochondrial ATP synthase gamma-subunit 177 1e-43
Q9D9D7 (Q9D9D7) 1700094F02Rik protein 175 4e-43
Q86DM7 (Q86DM7) Hypothetical protein Y69A2AR.18 174 1e-42
Q8C2Q8 (Q8C2Q8) ATP synthase 172 2e-42
Q7ZXN3 (Q7ZXN3) Similar to ATP synthase, H+ transporting, mitoch... 172 4e-42
ATPG_RAT (P35435) ATP synthase gamma chain, mitochondrial (EC 3.... 169 2e-41
>>Q95XJ0 (Q95XJ0) Hypothetical protein
>
>
Length = 299
Score = 256 bits (653), Expect = 2e-67
Identities = 131/225 (58%), Positives = 164/225 (72%), Gaps = 4/225 (1%)
Query: 5 YGNVEQQRNFATLKDISIRLKSVKNIQKMTXXXXXXXXXXXXXXDRELKGARVYGEGAQA 64
+ N EQ R FATLKDISIRLKSVKNIQK+T +RELKGAR YG GA+
Sbjct: 16 FANAEQARGFATLKDISIRLKSVKNIQKITKSMKMVAAAKYAKAERELKGARAYGVGAKT 75
Query: 65 FYNNLAGDDAAVPKADASATTKKLLILMTSDSGLCGAVHTSIIKEAKNLIKNKPDNMEYK 124
F++N+ D V + + K++L+L+TSD GLCG VH+SI+KEAKN++ N D E +
Sbjct: 76 FFDNI---DPVVEGVEKQESKKQVLVLITSDRGLCGGVHSSIVKEAKNILNNAGDK-EIR 131
Query: 125 LVCIGDKSKAGMSRIYGNHILYTANEIGRLPPTFEDASIAALEILNSGYEFDEAEILYNR 184
+V IGDKS+AG+ R+Y N IL + NEIGR PP+F DASIAA IL+SGY+F+ IL+NR
Sbjct: 132 VVAIGDKSRAGLQRLYANSILLSGNEIGRAPPSFADASIAAKAILDSGYDFETGTILFNR 191
Query: 185 FKTVVSYQTSKLQVPPLATIKSNTKLYTYDSVDDDLLQSYAEYSL 229
FKTVVSY+TSKLQ+ PL IK+ L TYDSVDDD+LQSY+EYSL
Sbjct: 192 FKTVVSYETSKLQILPLEAIKAKEALSTYDSVDDDVLQSYSEYSL 236
>>Q95XI9 (Q95XI9) Hypothetical protein
>
>
Length = 313
Score = 256 bits (653), Expect = 2e-67
Identities = 131/225 (58%), Positives = 164/225 (72%), Gaps = 4/225 (1%)
Query: 5 YGNVEQQRNFATLKDISIRLKSVKNIQKMTXXXXXXXXXXXXXXDRELKGARVYGEGAQA 64
+ N EQ R FATLKDISIRLKSVKNIQK+T +RELKGAR YG GA+
Sbjct: 16 FANAEQARGFATLKDISIRLKSVKNIQKITKSMKMVAAAKYAKAERELKGARAYGVGAKT 75
Query: 65 FYNNLAGDDAAVPKADASATTKKLLILMTSDSGLCGAVHTSIIKEAKNLIKNKPDNMEYK 124
F++N+ D V + + K++L+L+TSD GLCG VH+SI+KEAKN++ N D E +
Sbjct: 76 FFDNI---DPVVEGVEKQESKKQVLVLITSDRGLCGGVHSSIVKEAKNILNNAGDK-EIR 131
Query: 125 LVCIGDKSKAGMSRIYGNHILYTANEIGRLPPTFEDASIAALEILNSGYEFDEAEILYNR 184
+V IGDKS+AG+ R+Y N IL + NEIGR PP+F DASIAA IL+SGY+F+ IL+NR
Sbjct: 132 VVAIGDKSRAGLQRLYANSILLSGNEIGRAPPSFADASIAAKAILDSGYDFETGTILFNR 191
Query: 185 FKTVVSYQTSKLQVPPLATIKSNTKLYTYDSVDDDLLQSYAEYSL 229
FKTVVSY+TSKLQ+ PL IK+ L TYDSVDDD+LQSY+EYSL
Sbjct: 192 FKTVVSYETSKLQILPLEAIKAKEALSTYDSVDDDVLQSYSEYSL 236
Database: swissall.fsa
Posted date: Dec 5, 2003 3:22 PM
Number of letters in database: 390,760,073
Number of sequences in database: 1,218,016
Lambda K H
0.314 0.132 0.358
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 148,369,851
Number of Sequences: 1218016
Number of extensions: 5173956
Number of successful extensions: 9119
Number of sequences better than 1.0e-30: 15
Number of HSP's better than 0.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 9087
Number of HSP's gapped (non-prelim): 15
length of query: 229
length of database: 390,760,073
effective HSP length: 118
effective length of query: 111
effective length of database: 247,034,185
effective search space: 27420794535
effective search space used: 27420794535
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 337 (134.4 bits)
BLASTP 2.2.6 [Apr-09-2003]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= ZPP00157
(124 letters)
Database: swissall.fsa
1,218,016 sequences; 390,760,073 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
RL23_CAEEL (P48158) 60S ribosomal protein L23 207 3e-53
Q7PMD8 (Q7PMD8) ENSANGP00000014430 (Fragment) 199 6e-51
RL23_AEDAE (Q9GNE2) 60S ribosomal protein L23 (L17A) 199 6e-51
Q9W1Y7 (Q9W1Y7) RPL17A protein 199 7e-51
RL23_BRUMA (Q93140) 60S ribosomal protein L23 196 6e-50
Q962Y9 (Q962Y9) Ribosomal protein L17/23 193 4e-49
Q7ZWJ5 (Q7ZWJ5) Hypothetical protein (Fragment) 191 2e-48
Q90YU5 (Q90YU5) Ribosomal protein L23 189 4e-48
Q8IT99 (Q8IT99) Ribosomal protein L17A (Fragment) 189 4e-48
Q9BTQ7 (Q9BTQ7) Similar to ribosomal protein L23 (Fragment) 189 4e-48
RL23_HUMAN (P23131) 60S ribosomal protein L23 (L17) 189 4e-48
Q9DFL3 (Q9DFL3) Ribosomal protein L23 189 6e-48
Q86D71 (Q86D71) Ribosomal protein L23 189 6e-48
RL23_DROME (P48159) 60S ribosomal protein L23 (L17A) 189 8e-48
Q9W6M3 (Q9W6M3) Ribosomal protein L17 188 1e-47
Q9CZE6 (Q9CZE6) 2810009A01Rik protein 188 1e-47
Q9DCQ4 (Q9DCQ4) 2810009A01Rik protein 186 4e-47
Q9XSU3 (Q9XSU3) Ribosomal protein 186 6e-47
Q9YHX0 (Q9YHX0) Ribosomal protein L17 homolog (Fragment) 182 5e-46
O22686 (O22686) F19P19.5 protein 179 6e-45
Q9ATF6 (Q9ATF6) Ribosomal protein L17 179 6e-45
RL23_TOBAC (Q07760) 60S ribosomal protein L23 179 6e-45
RL23_ARATH (P49690) 60S ribosomal protein L23 179 6e-45
Q7X9K1 (Q7X9K1) Ribosomal Pr 117 (Fragment) 178 1e-44
Q8L8P0 (Q8L8P0) Putative 60S ribosomal protein L17 178 1e-44
Q7XDL5 (Q7XDL5) 60S ribosomal protein L17 177 2e-44
Q9AV77 (Q9AV77) 60S ribosomal protein L17 177 2e-44
O65068 (O65068) 60S ribosomal protein L17 (Fragment) 176 5e-44
Q9SMI7 (Q9SMI7) 60S ribosomal protein L17 (Fragment) 174 2e-43
O96636 (O96636) Ribosomal protein L17 172 6e-43
RL23_SCHPO (O42867) 60S ribosomal protein L23 171 2e-42
RL23_YEAST (P04451) 60S ribosomal protein L23 (L17) 171 2e-42
RL23_TORRU (Q9XEK8) 60S ribosomal protein L23 (L17) 171 2e-42
Q7R814 (Q7R814) 60S ribosomal protein L23 164 3e-40
Q7SHJ9 (Q7SHJ9) Hypothetical protein 163 3e-40
Q873R3 (Q873R3) Alkaline serine protease (Fragment) 163 3e-40
Q8IE09 (Q8IE09) 60S ribosomal protein L23, putative 162 6e-40
Q98RY7 (Q98RY7) 60S ribosomal protein L23 154 2e-37
Q7QTA5 (Q7QTA5) GLP_15_22119_21691 149 9e-36
RL23_TRYCR (Q94776) 60S ribosomal protein L23 (L17) (TCEST082) 149 9e-36
Q9HIR9 (Q9HIR9) Probable 50S ribosomal protein L14 134 2e-31
Q97BW6 (Q97BW6) Ribosomal protein large subunit L23 133 4e-31
Q8SRA7 (Q8SRA7) Ribosomal protein L23 132 8e-31
>>RL23_CAEEL (P48158) 60S ribosomal protein L23
>
>
Length = 140
Score = 207 bits (526), Expect = 3e-53
Identities = 102/113 (90%), Positives = 105/113 (92%)
Query: 1 LSLPVGFXINXADNTGANNLFVIAVYGMRGRLNRLPSAGVGDMFVASVKKGKPELRKKVL 60
L LPVG +N ADNTGA NLFVI+VYG+RGRLNRLPSAGVGDMFV SVKKGKPELRKKVL
Sbjct: 18 LGLPVGAVMNCADNTGAKNLFVISVYGIRGRLNRLPSAGVGDMFVCSVKKGKPELRKKVL 77
Query: 61 QAVVIRQRKMFRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 113
Q VVIRQRK FRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP
Sbjct: 78 QGVVIRQRKQFRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 130
>>Q7PMD8 (Q7PMD8) ENSANGP00000014430 (Fragment)
>
>
Length = 135
Score = 199 bits (506), Expect = 6e-51
Identities = 97/113 (85%), Positives = 105/113 (92%)
Query: 1 LSLPVGFXINXADNTGANNLFVIAVYGMRGRLNRLPSAGVGDMFVASVKKGKPELRKKVL 60
L LPVG IN ADNTGA NL+VIAV+G+RGRLNRLP+AGVGDMFVA+VKKGKPELRKKV+
Sbjct: 13 LGLPVGAVINCADNTGAKNLYVIAVHGIRGRLNRLPAAGVGDMFVATVKKGKPELRKKVM 72
Query: 61 QAVVIRQRKMFRRKDGTFIYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 113
AVVIRQRK FRR+DG F+YFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP
Sbjct: 73 PAVVIRQRKPFRRRDGVFLYFEDNAGVIVNNKGEMKGSAITGPVAKECADLWP 125
Database: swissall.fsa
Posted date: Dec 5, 2003 3:22 PM
Number of letters in database: 390,760,073
Number of sequences in database: 1,218,016
Lambda K H
0.321 0.140 0.409
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 83,601,214
Number of Sequences: 1218016
Number of extensions: 3001107
Number of successful extensions: 5578
Number of sequences better than 1.0e-30: 43
Number of HSP's better than 0.0 without gapping: 42
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 5533
Number of HSP's gapped (non-prelim): 43
length of query: 124
length of database: 390,760,073
effective HSP length: 100
effective length of query: 24
effective length of database: 268,958,473
effective search space: 6455003352
effective search space used: 6455003352
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 332 (132.5 bits)
>
>
> Jason Stajich wrote:
>
>>ralf - can you send an example report - if I use your code and the
>>t/data/ecolitst.bls report in the bioperl disto I get this
>>jason at jason $ perl ralf_bug.pl
>>AAC73113.1
>>AAC73113.1
>>AAC73113.1
>>AAC73113.1
>>
>>also see below.
>>
>>-j
>>On Wed, 17 Mar 2004, Ralf Schmid wrote:
>>
>>
>>
>>>Hi,
>>>
>>>I have recently updated bioperl from 1.21 to 1.4 and this has broken one of my
>>>blast parsing scripts. Using the following snippet of code on a blast output (3
>>>input sequences, -b 2 option for retrieving only two alignments, otherwise
>>>standard) gives different results:
>>>
>>>=> code
>>>
>>>#!/usr/bin/perl -w
>>>use strict;
>>>use Bio::SearchIO;
>>>my $in = new Bio::SearchIO( -format => 'blast',
>>> -file => "test.out");
>>>my $prot = '';
>>>while( my $result = $in->next_result ) {
>>> while (my $hit = $result->next_hit) {
>>> $prot=$result->query_accession;
>>> print"$prot\n";
>>> }
>>>}
>>>
>>>
>>>=> output bioperl 1.21:
>>>
>>>ZPP00163
>>>ZPP00163
>>>ZPP00036_1
>>>ZPP00036_1
>>>ZPP00157
>>>ZPP00157
>>>
>>>- query accession is retrieved for each hit where there is an alignment
>>>
>>>=> output bioperl 1.4:
>>>
>>>ZPP00163.
>>>ZPP00163.
>>>ZPP00163.
>>>ZPP00163.
>>>ZPP00163.
>>>ZPP00163.
>>>ZPP00163.
>>>...
>>>
>>>- query_accession is retrieved for each hit regardless whether there is an
>>>alignment or not
>>>- each query_accession ends with a "."
>>>
>>>
>>>So far I have taken advantage of the blast -b option to set the number of hits
>>>to be parsed by bioperl, but I can see the ratio in changing bioperl from
>>>parsing every hit that has an alignment to parsing every hit.
>>>
>>>
>>>
>>This was a requested feature. You can add a little code which exists the
>>hit loop if the hit doesn't have any hsps
>>last if $hit->num_hsps == 0;
>>
>>
>>
>>>Looking at the diff between blast.pm 1.42.2.8 and blast.pm 1.76 and finding the
>>>helpful comment in line 769 makes me believe that there is the change in parsing
>>>coded, but I couldn't spot any reason for the "." at the end of each
>>>query_accession. Not sure whether the two are related anyway.
>>>
>>><SNIP>
>>># This is for the case when we specify -b 0 (or B=0 for WU-BLAST)
>>># and still want to construct minimal Hit objects
>>>while(my $v = shift @hit_signifs) {
>>>next unless defined $v;
>>>$self->start_element({ 'Name' => 'Hit'});
>>>...
>>><SNIP>
>>>
>>>So far I'm fixing the "dot" issue by an s/\.$// , but ...
>>>
>>>
>>>Cheers,
>>>
>>>Ralf
>>>
>>>
>>>
>>>
>>>
>>>
>>>------------------------------------------------------------------------------
>>>Dr. Ralf Schmid
>>>Nematode Bioinformatics
>>>Blaxter Nematode Genomics Group
>>>Institute of Cell, Animal and Population Biology
>>>Ashworth Labs
>>>University of Edinburgh
>>>King's Buildings
>>>Edinburgh
>>>EH9 3JT
>>>UK
>>>
>>>(+44)(0)131 650 7403
>>>
>>>
>>>
>>>
>>>
>>>_______________________________________________
>>>Bioperl-l mailing list
>>>Bioperl-l at portal.open-bio.org
>>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>>
>>>
>>>
>>
>>--
>>Jason Stajich
>>Duke University
>>jason at cgt.mc.duke.edu
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>
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