Hi !
It is often very useful to read a text files by blocks of lines, using
another line separator than '\n'.
Especially in bio-informatics, for example DNA or Protein FASTA sequences
are separated by '\n>' (see uniprot.txt attached).
In Perl, it is possible to change the line separator using :
local $/ = '\n>'
for example.
In Julia I did not found how to do that :
line by line :
julia> f = open("uniprot.txt")
IOStream(<file uniprot.txt>)
julia> readline(f, '\n>' )
ERROR: syntax: invalid character literal
all lines in an array (I prefer line by line because some files do not fit
into RAM) :
julia> readdlm("uniprot.txt", '\n>' )
ERROR: syntax: invalid character literal
readdlm("uniprot.txt", '>' ) # works but does not give the expected result
So I suppose that this feature is currently not implemented in Julia ?
Thanks in advance for your comments !
>sp|P31946|1433B_HUMAN 14-3-3 protein beta/alpha OS=Homo sapiens GN=YWHAB PE=1
>SV=3
MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVGARRSS
WRVISSIEQKTERNEKKQQMGKEYREKIEAELQDICNDVLELLDKYLIPNATQPESKVFY
LKMKGDYFRYLSEVASGDNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFY
YEILNSPEKACSLAKTAFDEAIAELDTLNEESYKDSTLIMQLLRDNLTLWTSENQGDEGD
AGEGEN
>sp|P04439|1A03_HUMAN HLA class I histocompatibility antigen, A-3 alpha chain
>OS=Homo sapiens GN=HLA-A PE=1 SV=2
MAVMAPRTLLLLLSGALALTQTWAGSHSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASQRMEPRAPWIEQEGPEYWDQETRNVKAQSQTDRVDLGTLRGYYNQSEAGSHTIQ
IMYGCDVGSDGRFLRGYRQDAYDGKDYIALNEDLRSWTAADMAAQITKRKWEAAHEAEQL
RAYLDGTCVEWLRRYLENGKETLQRTDPPKTHMTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEL
SSQPTIPIVGIIAGLVLLGAVITGAVVAAVMWRRKSSDRKGGSYTQAASSDSAQGSDVSL
TACKV
>sp|P01889|1B07_HUMAN HLA class I histocompatibility antigen, B-7 alpha chain
>OS=Homo sapiens GN=HLA-B PE=1 SV=3
MLVMAPRTVLLLLSAALALTETWAGSHSMRYFYTSVSRPGRGEPRFISVGYVDDTQFVRF
DSDAASPREEPRAPWIEQEGPEYWDRNTQIYKAQAQTDRESLRNLRGYYNQSEAGSHTLQ
SMYGCDVGPDGRLLRGHDQYAYDGKDYIALNEDLRSWTAADTAAQITQRKWEAAREAEQR
RAYLEGECVEWLRRYLENGKDKLERADPPKTHVTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
SSQSTVPIVGIVAGLAVLAVVVIGAVVAAVMCRRKSSGGKGGSYSQAACSDSAQGSDVSL
TA
>sp|P30464|1B15_HUMAN HLA class I histocompatibility antigen, B-15 alpha chain
>OS=Homo sapiens GN=HLA-B PE=1 SV=2
MRVTAPRTVLLLLSGALALTETWAGSHSMRYFYTAMSRPGRGEPRFIAVGYVDDTQFVRF
DSDAASPRMAPRAPWIEQEGPEYWDRETQISKTNTQTYRESLRNLRGYYNQSEAGSHTLQ
RMYGCDVGPDGRLLRGHDQSAYDGKDYIALNEDLSSWTAADTAAQITQRKWEAAREAEQW
RAYLEGLCVEWLRRYLENGKETLQRADPPKTHVTHHPISDHEATLRCWALGFYPAEITLT
WQRDGEDQTQDTELVETRPAGDRTFQKWAAVVVPSGEEQRYTCHVQHEGLPKPLTLRWEP
SSQSTIPIVGIVAGLAVLAVVVIGAVVATVMCRRKSSGGKGGSYSQAASSDSAQGSDVSL
TA
