Need help for bioinformatics work
So I am an undergrad student and my prof has given a assignment where I have to extract the DNA sequences from a file. I am able to extract the sequences and their relative positions in the file but I am unable to extract the sequences.
Let me give you an example:
>lcl|NZ_LR134363.1_prot_WP_026427009.1_1 [locus_tag=EL266_RS00005] [protein=hypothetical protein] [protein_id=WP_026427009.1] [location=1..210] [gbkey=CDS]
MCRPVTCRTCGKTTWAGCGQHVDQVMRDVAPAQRCTCERDAPSDSGGDSGGQARGAGLFSRLLGRGGGS
>lcl|NZ_LR134363.1_prot_WP_034514895.1_2 [locus_tag=EL266_RS00010] [protein=metal-sensitive transcriptional regulator] [protein_id=WP_034514895.1] [location=248..517] [gbkey=CDS]
MGTALDPADLRPTLARLKRARGQLDGVIRMLEEGRDCEETVVQIAAVSKAVNRAGLAVIASGMRTCLSEDPTGQTMDTRR
LERLLMSLA
>lcl|NZ_LR134363.1_prot_WP_026427010.1_3 [locus_tag=EL266_RS00015] [protein=pyridoxal phosphate-dependent aminotransferase] [protein_id=WP_026427010.1] [location=588..1802] [gbkey=CDS]
MTPAPQTRVSARLAAIAPSATLAVDAKAKALKAAGRPVIGFGAGEPDFATPDYIVEAAIASAKDPASHKYSPAKGLPALR
EAIAAKTLRDSGYEVSAEDILVTNGGKQAVFQAFAAIIGPGDEVLLPAPYWTTYPEVVALAGGTTVEVFAGAEQDYKVTV
AQLEAARTDRTKALLVCSPSNPTGSVYTPEELTEIGRWALEHGVWVITDEIYEHLLYDGAAAAHIVALVPELAEQTIVLN
GVAKTYAMTGWRVGWMIGPSDVIKAATNFQSHLSSNVANVCQAAALAAVSGDLTAVEEMRGAFDRRRRTMVELLTAIEGL
TVPVPRGAFYAYPSAEALIGRNLRGTAIDSSATLAGLILEHAEVAVVPGEAFGPSGFLRLSYALGDEDLAEGVGRMASLLAEVE
This is a typical sequence that we have to work with and the lines containing ">" (the ones in bold) are called headers. Now I can extract the headers as well the sequence (ones in italics lines) just after that but I have to extract lines till the next ">" arrives and I am unable to do so. I am a noob coder in every sense of the word, I just started a month back and therefore I am not very good at it. This is a file operation where we have to input a file tat contains thousands of such sequences and based on that we need to be able to find sequences of our interest. Please help me out, I swear that I am not trying to outsource my assignment. Jut need to know how to read and print the lines till the next ">" arrives.
My output ideally should look like:
>lcl|NZ_LR134363.1_prot_WP_232012119.1_980 [locus_tag=EL266_RS04980] [protein=histidine kinase] [protein_id=WP_232012119.1] [location=complement(1218761..1219630)] [gbkey=CDS]
MLLSRGHPRRTIYPAAAAHALALIIYASQTPDGPFFGTLATAIIATPCLTAGEMVRLHRQATARTELERQERLERQR
RLVISELHDTVVRDLSHAVMLAEQARLTHPDDELLHRELAAVTAPVRSAIKQLRNSLKAMSAAKGDDALLLLASS
PPPPLSETIERVRASLAQRDTVLLVEGLELLDHQSITPGVHQQLVRVIGELITNASKYAPPSTKVSLLIETDDRTVEC
MCVNAIGPDTPPSTALSSKIGLEGARRRIETLGGTFTVSKTAERWSVVFSVPIQDDDAT
>lcl|NZ_LR134363.1_prot_WP_026428191.1_981 [locus_tag=EL266_RS04985]_[protein=histidine kinase] [protein_id=WP_026428191.1] [location=complement(1220180..1221349)] [gbkey=CDS]
MTGLLAPTRLTVWTPRLRTHLLCLACATLLTLAAVAALVPDRRTDAFYMVTLLISGLGVAVLSVAPLISSGLCLGTLY
AFLLALGDAAPAGPSLPAIGPWLCASVLLTRGFSRLSAYGLVLISLGGSVIGHHSNVVSNSALATDFTYTMLVGTIC
LIVAELMRQPRMEAEAAARRHEADMRNQRLLIVSELHDTVVRDLTQAVMRAEQARLAQPDAPLVGELGAMTSS
VRTAVDQLRSSLRSMNDMADQVPLDVLASSAPRSLTEVVDETRRTLAARGISLETAGLEALESARIGPGLRQQLV
RMLGELTTNMAKHAAPGPARLVVEHDGMSLEAMSSNTVDAGTEADPVASSGLGLVGVRRRVEALGGTLNVSRT
PDRFTVVLSVPVV
Notice how both headers contain [protein=histidine kinase]. I have the isolate the headers with histidine kinase in them and the sequence beneath it, till the next header arrives, which can be recognized by a ">" at the start of the line.
Thank you for your help in advance.