[Bioperl-l] parsing bl2seq alignment with Bio::AlignIO

[rich]

Hi,

i'm using Bio::AlignIO and specifically $aln = $report_align->next_aln() 
to read the 2 alignments from the bl2seq formatted file at the bottom of 
this mail.

Does anyone know why it only reads in the first alignment? ie

Query: 299  GEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRSGSGKSTIANLFTRFYDVDSGS 
358
           G++ VKD+T  Y       L ++SFSI  G+ V L+GR+GSGKST+ + F R  + + G
Sbjct: 1226 GQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLNTE-GE 
1284

Query: 359  ICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIAYAAEGEYTREQIEQAARQAHA 
418
           I +DG       L   R+ F ++ Q V +F+ T   N+      +++ ++I + A +
Sbjct: 1285 IQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLD--PYEQWSDQEIWKVADEVGL 
1342

Query: 419  MEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRDAPVLILDEATSALDTESERAI 
478
              IE  P  LD V+ + G  LS G +Q + +AR++L  A +L+LDE ++ LD  + + I
Sbjct: 1343 RSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQII 
1402

Query: 479  QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEGEI 515
           +  L +   + TV++  HR+  + +  + LV++E ++
Sbjct: 1403 RRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKV 1439

Any help appreciated,
thanks
Rich



use Bio::AlignIO;
use Bio::Align::AlignI;

my $report_align  = Bio::AlignIO->new(-file => '/tmp/align' ,
                                              '-format' => 'bl2seq');

my $loop_num=1;

while(my $aln = $report_align->next_aln()){
                   print $loop_num++,"\n";
  }


Query=
        (523 letters)

 >, 1498 aa.
         Length = 1498

Score =  117 bits (292), Expect = 4e-30
Identities = 68/217 (31%), Positives = 120/217 (55%), Gaps = 3/217 (1%)

Query: 299  GEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRSGSGKSTIANLFTRFYDVDSGS 
358
           G++ VKD+T  Y       L ++SFSI  G+ V L+GR+GSGKST+ + F R  + + G
Sbjct: 1226 GQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLLGRTGSGKSTLLSAFLRLLNTE-GE 
1284

Query: 359  ICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIAYAAEGEYTREQIEQAARQAHA 
418
           I +DG       L   R+ F ++ Q V +F+ T   N+      +++ ++I + A +
Sbjct: 1285 IQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLD--PYEQWSDQEIWKVADEVGL 
1342

Query: 419  MEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRDAPVLILDEATSALDTESERAI 
478
              IE  P  LD V+ + G  LS G +Q + +AR++L  A +L+LDE ++ LD  + + I
Sbjct: 1343 RSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTYQII 
1402

Query: 479  QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEGEI 515
           +  L +   + TV++  HR+  + +  + LV++E ++
Sbjct: 1403 RRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKV 1439



Score = 87.0 bits (214), Expect = 4e-21
Identities = 61/237 (25%), Positives = 116/237 (48%), Gaps = 20/237 (8%)

Query: 278 FGLMDLETERDNGKYEAERVNGEVDVKDVTFTYQGKEKPALSHVSFSIPQGKTVALVGRS 337
          FG +  + +++N   +    NG+  +    F+  G   P L  ++F I +G+ +A+ G +
Sbjct: 423 FGELFEKAKQNNNNRKTS--NGDDSLFFSNFSLLGT--PVLKDINFKIERGQLLAVAGST 478

Query: 338 GSGKSTIANLFTRFYDVDSGSICLDGHDVRDYKLTNLRRHFALVSQNVHLFNDTIANNIA 397
          G+GK+++  +     +   G I   G               +  SQ   +   TI  NI
Sbjct: 479 GAGKTSLLMVIMGELEPSEGKIKHSGR-------------ISFCSQFSWIMPGTIKENII 525

Query: 398 YAAEGEYTREQIEQAARQAHAMEFIENMPQGLDTVIGENGTSLSGGQRQRVAIARALLRD 457
          +     Y   +     +     E I    +  + V+GE G +LSGGQR R+++ARA+ +D
Sbjct: 526 FGVS--YDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQRARISLARAVYKD 583

Query: 458 APVLILDEATSALDTESERAI-QAALDELQKNKTVLVIAHRLSTIEQADEILVVDEG 513
          A + +LD     LD  +E+ I ++ + +L  NKT +++  ++  +++AD+IL++ EG
Sbjct: 584 ADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILHEG 640


Lambda     K      H
  0.322    0.136    0.384

Gapped
Lambda     K      H
  0.267   0.0410    0.140


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1908
Number of Sequences: 0
Number of extensions: 52
Number of successful extensions: 6
Number of sequences better than 10.0: 1
Number of HSP's better than 10.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 2
length of query: 523
length of database: 1498
effective HSP length: 43
effective length of query: 480
effective length of database: 1455
effective search space:   698400
effective search space used:   698400
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 30 (16.8 bits)
S2: 30 (16.2 bits)