Re^2: How to match the sequences with headers

The sample input is:

>101M:A:sequence
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVKHLKTEAEMKASEDLKKHGVTVL
+TALGA
ILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAA
+KYKEL
GYQG                                            

>101M:A:secstr
    HHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHH GGGGGG TTTTT  SHHHHHH HHHHHHHHHHH
+HHHHH
HHTTTT  HHHHHHHHHHHHHTS   HHHHHHHHHHHHHHHHHH GGG SHHHHHHHHHHHHHHHHHHHH
+HHHHT
T

>102L:A:sequence
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQ
+DVDAA
VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPN
+RAKRV
ITTFRTGTWDAYKNL

>102L:A:secstr
  HHHHHHHHH  EEEEEE TTS EEEETTEEEESSS TTTHHHHHHHHHHTS  TTB  HHHHHHHHHH
+HHHHH
HHHHHH TTHHHHHHHS HHHHHHHHHHHHHHHHHHHHT HHHHHHHHTT HHHHHHHHHSSHHHHHSHH
+HHHHH
HHHHHHSSSGGG
[download]

The first output should be all protein fasta sequences like:

>101M:A:sequence
MVLSEGEWQLVLHVWAKVEADVAGHGQDILIRLFKSHPETLEKFDRVKHLKTEAEMKASEDLKKHGVTVL
+TALGA
ILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISEAIIHVLHSRHPGNFGADAQGAMNKALELFRKDIAA
+KYKEL
GYQG

>102L:A:sequence
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAAKSELDKAIGRNTNGVITKDEAEKLFNQ
+DVDAA
VRGILRNAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPN
+RAKRV
ITTFRTGTWDAYKNL
[download]

The second Output file should hav secondary structures:

>101M:A:secstr
    HHHHHHHHHHHHHHGGGHHHHHHHHHHHHHHH GGGGGG TTTTT  SHHHHHH HHHHHHHHHHH
+HHHHH
HHTTTT  HHHHHHHHHHHHHTS   HHHHHHHHHHHHHHHHHH GGG SHHHHHHHHHHHHHHHHHHHH
+HHHHT
T

>102L:A:secstr
  HHHHHHHHH  EEEEEE TTS EEEETTEEEESSS TTTHHHHHHHHHHTS  TTB  HHHHHHHHHH
+HHHHH
HHHHHH TTHHHHHHHS HHHHHHHHHHHHHHHHHHHHT HHHHHHHHTT HHHHHHHHHSSHHHHHSHH
+HHHHH
HHHHHHSSSGGG
[download]

Thanks..

Comment on Re^2: How to match the sequences with headers Select or Download Code

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Re^3: How to match the sequences with headers by Lotus1 (Vicar) on Oct 23, 2011 at 16:07 UTC
At the beginning of your program put in `$/="\n\n";` Then inside the while loop if $_ matches 'sequence' print $_ to out1; if it matches 'secstr' print $_ to out2.	[reply] [d/l]