[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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