print from pattern1 to pattern2 but not pattern2

[wuermchen]

hi, i have a problem with a fasta file.

i look for id's in this file, they look like

>id001 blablabla

the id is folowed by some lines with proteinsequenzes
after this it comes the next id

>id002 blablbla

so a short fasta file look like

-->
>104K_THEAN
MKFLVLLFNILCLFPILGADELVMSPIPTTDVQPKVTFDINSEVSSGPLYLNPVEMAGVK
YLQLQRQPGVQVHKVVEGDIVIWENEEMPLYTCAIVTQNEVPYMAYVELLEDPDLIFFLK
EGDQWAPIPEDQYLARLQQLRQQIHTESFFSLNLSFQHENYKYEMVSSFQHSIKMVVFTP
KNGHICKMVYDKNIRIFKALYNEYVTSVIGFFRGLKLLLLNIFVIDDRGMIGNKYFQLLD
DKYAPISVQGYVATIPKLKDFAEPYHPIILDISDIDYVNFYLGDATYHDPGFKIVPKTPQ
CITKVVDGNEVIYESSNPSVECVYKVTYYDKKNESMLRLDLNHSPPSYTSYYAKREGVWV
TSTYIDLEEKIEELQDHRSTEL
>104K_THEPA
MKFLILLFNILCLFPVLAADNHGVGPQGASGVDPITFDINSNQTGPAFLTAVEMAGVKYL
QVQHGSNVNIHRLVEGNVVIWENASTPLYTGAIVTNNDGPYMAYVEVLGDPNLQFFIKSG
DAWVTLSEHEYLAKLQEIRQAVHIESVFSLNMAFQLENNKYEVETHAKNGANMVTFIPRN
GHICKMVYHKNVRIYKATGNDTVTSVVGFFRGLRLLLINVFSIDDNGMMSNRYFQHVDDK
YVPISQKNYETGIVKLKDY
>108_LYCES
MASVKSSSSSSSSSFISLLLLILLVIVLQSQVIECQPQQSCTASLTGLNVCAPFLVPGSP
TASTECCNAVQSINHDCMCNTMRIAAQIPAQCNLPPLSCSAN
>10KD_VIGUN
MEKKSIAGLCFLFLVLFVAQEVVVQSEAKTCENLVDTYRGPCFTTGSCDDHCKNKEHLLS
GRCRDDVRCWCTRNC
>110KD_PLAKN
FNSNMLRGSVCEEDVSLMTSIDNMIEEIDFYEKEIYKGSHSGGVIKGMDYDLEDDENDED
EMTEQMVEEVADHITQDMIDEVAHHVLDNITHDMAHMEEIVHGLSGDVTQIKEIVQKVNV
AVEKVKHIVETEETQKTVEPEQIEETQNTVEPEQTEETQKTVEPEQTEETQNTVEPEQIE
ETQKTVEPEQTEEAQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTE
ETQKTVEPEQTEETQKTVEPEQTEETQKTVEPEQTEETQNTVEPEPTQETQNTVEP
>11S2_SESIN
MVAFKFLLALSLSLLVSAAIAQTREPRLTQGQQCRFQRISGAQPSLRIQSEGGTTELWDE
RQEQFQCAGIVAMRSTIRPNGLSLPNYHPSPRLVYIERGQGLISIMVPGCAETYQVHRSQ
RTMERTEASEQQDRGSVRDL
>11S3_HELAN
MASKATLLLAFTLLFATCIARHQQRQQQQNQCQLQNIEALEPIEVIQAEAGVTEIWDAYD
QQFQCAWSILFDTGFNLVAFSCLPTSTPLFWPSSREGVILPGCRRTYEYSQEQQFSGEGG
RRGGGEGTFRTVIRKLENLKEGDVVAIPTGTAHWLHNDGNTELVVVFLDTQNHENQLDEN
QRRFFLAGNPQAQAQSQQQQQRQPRQQSPQRQRQRQRQGQGQNAGNIFNGFTPELIAQSF
NVDQETAQKLQGQNDQRGHIVNVGQDLQIVRPPQDRRSPRQQQEQATSPRQQQEQQQGRR
<--

i use the following script to read only special sequence

-->
BEGIN {
string=ARGV[2]
ARGV[2]=0
pr=0
print "looking for \"" string "\" in file: " file
}
$0 ~ string {pr=1; print; next}
pr == 1
/^>/ {
if(pr==1)
exit
}
<--

i call this programm like

awk -f search4ids.awk file.fast 11S2_SESIN

and the output is

-->
>11S2_SESIN
MVAFKFLLALSLSLLVSAAIAQTREPRLTQGQQCRFQRISGAQPSLRIQSEGGTTELWDE
RQEQFQCAGIVAMRSTIRPNGLSLPNYHPSPRLVYIERGQGLISIMVPGCAETYQVHRSQ
RTMERTEASEQQDRGSVRDL
>11S3_HELAN
<--

but i need only the first id and the sequence..... not the next id...


sorry for my bad english, i hope everybody understand me...

 

[Ygor]

Perhaps try...

awk '$1~s' RS='>' s='11S2_SESIN' file.fast

Which gives...

11S2_SESIN
MVAFKFLLALSLSLLVSAAIAQTREPRLTQGQQCRFQRISGAQPSLRIQSEGGTTELWDE
RQEQFQCAGIVAMRSTIRPNGLSLPNYHPSPRLVYIERGQGLISIMVPGCAETYQVHRSQ
RTMERTEASEQQDRGSVRD

 

[PHV]

-->
BEGIN {
string=ARGV[2]
ARGV[2]=0
pr=0
print "looking for \"" string "\" in file: " file
}
$0 ~ string {pr=1; print; next}
[!]pr == 1[/!]
/^>/ {
if(pr==1)
exit
}
[!]pr == 1[/!]
<--

Hope This Helps, PH.
Want to get great answers to your Tek-Tips questions? Have a look at FAQ219-2884 or FAQ181-2886