Re: How to match the sequences with headers

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Re^2: How to match the sequences with headers by anonym (Acolyte) on Oct 23, 2011 at 14:43 UTC
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..	[reply] [d/l] [select]
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]