[Bioperl-l] Re: [Bioperl-guts-l] Notification: incoming/1002

Jason Stajich jason@chg.mc.duke.edu
Tue, 4 Sep 2001 08:49:04 -0400 (EDT)


Need more info - what version of perl are you running under, what OS, what
does the data file look like.  You also have a typo in your code 
The following line should be changed
<     $in  = Bio::AlignIO->newFh('-format' => $format2 );
to
>     $in  = Bio::AlignIO->newFh('-format' => $format1 );

Here behavior on FreeBSD-4.4 perl 5.005 bioperl 0.7.1
19 magrathea bioperl-live $ cat test_alignio.pl
#!/usr/bin/perl
 
    $format1 = shift;
    $format2 = shift || die "Usage: reformat format1 format2 < input >
output";
 
    use Bio::AlignIO;
    $in  = Bio::AlignIO->newFh('-format' => $format1 );
    $out = Bio::AlignIO->newFh('-format' => $format2 );
 
 
    print $out $_ while <$in>;
20 magrathea bioperl-live $ perl test_alignio.pl stockholm clustalw < 
 t/data/testaln.stockholm > newalgn.clustal
21 magrathea bioperl-live $ cat newalgn.clustal
CLUSTAL W(1.4) multiple sequence alignment


1433_LYCES/9-246       REENVYMAKLADRAESDEEMVEFMEKVSNSLGS.EELTVEERNLLSVAYK
1434_LYCES/6-243       REENVYLAKLAEQAERYEEMIEFMEKVAKTADV.EELTVEERNLLSVAYK
143R_ARATH/7-245       RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATPAEELTVEERNLLSVAYK
143B_VICFA/7-242       RENFVYIAKLAEQAERYEEMVDSMKNVANLDV...ELTIEERNLLSVGYK
143E_HUMAN/4-239       REDLVYQAKLAEQAERYDEMVESMKKVAGMDV...ELTVEERNLLSVAYK
BMH1_YEAST/4-240       REDSVYLAKLAEQAERYEEMVENMKTVASSGQ...ELSVEERNLLSVAYK
RA24_SCHPO/6-241       REDAVYLAKLAEQAERYEGMVENMKSVASTDQ...ELTVEERNLLSVAYK
RA25_SCHPO/5-240       RENSVYLAKLAEQAERYEEMVENMKKVACSND...KLSVEERNLLSVAYK
1431_ENTHI/4-239       REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA...ELSIEERNLLSVAYK
1432_ENTHI/4-238       REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT...ELSVEERNLISVAYK
1433_CAEEL/5-237       VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ...ELSNEERNLLSVAYK
143Z_DROME/6-239       KEELVQKAKLAEQSERYDDMAQAMKSVTETGV...ELSNEERNLLSVAYK
1433_XENLA/1-227       .......AKLSEQAERYDDMAASMKAVTELGA...ELSNEERNLLSVAYK
143T_HUMAN/3-236       KTELIQKAKLAEQAERYDDMATCMKAVTEQGA...ELSNEERNLLSVAYK
143F_MOUSE/3-240       REQLLQRARLAEQAERYDDMASAMKAVTELNE...PLSNEDRNLLSVAYK
143S_HUMAN/3-238       RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE...ELSCEERNLLSVAYK


1433_LYCES/9-246       NVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKICDG
1434_LYCES/6-243       NVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKICDG
143R_ARATH/7-245       NVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVCSG
143B_VICFA/7-242       NVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNICID
143E_HUMAN/4-239       NVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLICCD
BMH1_YEAST/4-240       NVIGARRASWRIVSSIEQKEESKEKSEHQVELICSYRSKIETELTKISDD
RA24_SCHPO/6-241       NVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTICQD
RA25_SCHPO/5-240       NIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDICHD
1431_ENTHI/4-239       NVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCCDD
1432_ENTHI/4-238       NVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKCDD
1433_CAEEL/5-237       NVVGARRSSWRVISSIEQKTEG...SEKKQQLAKEYRVKVEQELNDICQD
143Z_DROME/6-239       NVVGARRSSWRVISSIEQKTEA...SARKQQLAREYRERVEKELREICYE
1433_XENLA/1-227       NVVGARRSSWRVISSIEQKTEG...NDKRQQMAREYREKVETELQDICKD
143T_HUMAN/3-236       NVVGGRRSAWRVISSIEQKTDT...SDKKLQLIKDYREKVESELRSICTT
143F_MOUSE/3-240       NVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVCND
143S_HUMAN/3-238       NVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVCDT


1433_LYCES/9-246       ILKLLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFKTGAERKEAAES
1434_LYCES/6-243       ILSLLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFKTGTERKEAAEN
143R_ARATH/7-245       ILKLLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFKSGDERKTAAED
143B_VICFA/7-242       VMRVIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFKTGNEKKEAGDQ
143E_HUMAN/4-239       ILDVLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFATGNDRKEAAEN
BMH1_YEAST/4-240       ILSVLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFSSGDAREKATNA
RA24_SCHPO/6-241       ILTVLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFAVGEKRQHSADQ
RA25_SCHPO/5-240       VLSVLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFTVGEVCKEAADS
1431_ENTHI/4-239       VLKVIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFTVDEKRKEVADK
1432_ENTHI/4-238       VLKIITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFTVDEKRKEVADK
1433_CAEEL/5-237       VLKLLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVAS.EDRAAVVEK
143Z_DROME/6-239       VLGLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVATGDARNTVVDD
1433_XENLA/1-227       VLDLLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVASGDSKQETVAS
143T_HUMAN/3-236       VLELLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVACGDDRKQTIDN
143F_MOUSE/3-240       VLALLDKFLIKNCNDFQYESKVFYLKMKGDYYRYLAEVASGEKKNSVVEA
143S_HUMAN/3-238       VLGLLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVATGDDKKRIIDS


1433_LYCES/9-246       TLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQ
1434_LYCES/6-243       TLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYYEILNSPDRACNLAKQ
143R_ARATH/7-245       TMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYYEILNSSDKACNMAKQ
143B_VICFA/7-242       SMKAYESATTAAEAELPPTHPIRLGLALNFSVFYYEILNSPERACHLAKQ
143E_HUMAN/4-239       SLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYYEILNSPDRACRLAKA
BMH1_YEAST/4-240       SLEAYKTASEIATTELPPTHPIRLGLALNFSVFYYEIQNSPDKACHLAKQ
RA24_SCHPO/6-241       SLEGYKAASEIATAELAPTHPIRLGLALNFSVFYYEILNSPDRACYLAKQ
RA25_SCHPO/5-240       SLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYYEILDSPESACHLAKQ
1431_ENTHI/4-239       SLAAYTEATEISNAELAPTHPIRLGLALNFSVFYFEIMNDADKACQLAKQ
1432_ENTHI/4-238       SLAAYQEATDTA.ASLVPTHPIRLGLALNFSVFYYQIMNDADKACQLAKE
1433_CAEEL/5-237       SQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYYEILNTPEHACQLAKQ
143Z_DROME/6-239       SQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYYEILNSPDKACQLAKQ
1433_XENLA/1-227       SQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKS
143T_HUMAN/3-236       SQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYYEILNNPELACTLAKT
143F_MOUSE/3-240       SEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYYEIQNAPEQACLLAKQ
143S_HUMAN/3-238       ARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHYEIANSPEEAISLAKT
 
 
1433_LYCES/9-246       AFDEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDMQDDG
1434_LYCES/6-243       AFDEAISELDTLGEESYKDSTLIMQLLRDNLTLWTSDNADDV
143R_ARATH/7-245       AFEEAIAELDTLGEESYKDSTLIMQLLRDNLTLWTSDYAGAD
143B_VICFA/7-242       AFDEAISELDTLNEESYKDSTLIMQLLRDNLTLWTSDIPEDG
143E_HUMAN/4-239       AFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMQGDG
BMH1_YEAST/4-240       AFDDAIAELDTLSEESYKDSTLIMQLLRDNLTLWTSDMSESG
RA24_SCHPO/6-241       AFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYSA
RA25_SCHPO/5-240       VFDEAISELDSLSEESYKDSTLIMQLLRDNLTLWTSDAEYNQ
1431_ENTHI/4-239       AFDDAIAKLDEVPENMYKDSTLIMQLLRDNLTLWTSDACDEE
1432_ENTHI/4-238       AFDEAIQKLDEVPEESYKESTLIMQLLRDNLTLWTSDMGDDE
1433_CAEEL/5-237       AFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDVGAED
143Z_DROME/6-239       AFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDTQGDE
1433_XENLA/1-227       AFDEAIRELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGEE
143T_HUMAN/3-236       AFDEAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDSAGEE
143F_MOUSE/3-240       AFDDAIAELDTLNEDSYKDSTLIMQLLRDNLTLWTSDQQDEE
143S_HUMAN/3-238       TFDEAMADLHTLSEDSYKDSTLIMQLLRDNLTLWTADNAGEE

On Tue, 4 Sep 2001 bioperl-bugs@bioperl.org wrote:

> JitterBug notification
> 
> new message incoming/1002
> 
> Message summary for PR#1002
> 	From: tali@kimura.tau.ac.il
> 	Subject: clustalw format in AlignIO
> 	Date: Tue, 4 Sep 2001 07:41:05 -0400
> 	0 replies 	0 followups
> 
> ====> ORIGINAL MESSAGE FOLLOWS <====
> 
> >From tali@kimura.tau.ac.il Tue Sep  4 07:41:05 2001
> Received: from localhost (localhost [127.0.0.1])
> 	by pw600a.bioperl.org (8.11.2/8.11.2) with ESMTP id f84Bf5B06650
> 	for <bioperl-bugs@pw600a.bioperl.org>; Tue, 4 Sep 2001 07:41:05 -0400
> Date: Tue, 4 Sep 2001 07:41:05 -0400
> Message-Id: <200109041141.f84Bf5B06650@pw600a.bioperl.org>
> From: tali@kimura.tau.ac.il
> To: bioperl-bugs@bioperl.org
> Subject: clustalw format in AlignIO
> 
> Full_Name: Tal Dagan
> Module: AlignIO
> Version: 0.7.1
> PerlVer: 5.005
> OS: IRIX
> Submission from: proxym.tau.ac.il (132.66.16.23)
> 
> 
> reading alignment in clustalw format using AlignIO
> dosent work. There are no error messages, and the 
> output file is empty.
> 
> script:
> 
> #!/usr/bin/perl
>  
> use lib "/usr/local0/bioperl-0.7.1";
> use lib "/usr/local0/bioperl-0.7.1/Bio";
> 
> 
>     $format1 = shift;
>     $format2 = shift || die "Usage: reformat format1 format2 < input > output";
> 
>     use Bio::AlignIO;
>     $in  = Bio::AlignIO->newFh('-format' => $format2 );
>     $out = Bio::AlignIO->newFh('-format' => $format2 );
>    
> 
>     print $out $_ while <$in>;
> 
> 
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