Splitting fasta file into smaller files based on header pattern I have to split this fasta files into smaller files and write them into individual files my files  

&gt;lcl|CP000522.1_prot_ABO13860.1_1 [locus_tag=A1S_3471] [protein=hypothetical protein] [protein_id=ABO13860.1] [location=1..957] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13850.1_2 [locus_tag=A1S_3461] [protein=DNA replication protein] [protein_id=ABO13850.1] [location=950..1504] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13851.1_3 [locus_tag=A1S_3462] [protein=hypothetical protein] [protein_id=ABO13851.1] [location=complement(2523..3437)] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13852.1_4 [locus_tag=A1S_3463] [protein=YPPCP.09C-like protein] [protein_id=ABO13852.1] [location=3538..4788] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13853.1_5 [locus_tag=A1S_3464] [protein=Cro-like protein] [protein_id=ABO13853.1] [location=5039..5629] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13854.1_6 [locus_tag=A1S_3465] [protein=hypothetical protein] [protein_id=ABO13854.1] [location=complement(6340..6906)] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13855.1_7 [locus_tag=A1S_3466] [protein=Resolvase] [protein_id=ABO13855.1] [location=complement(7074..7685)] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13856.1_8 [locus_tag=A1S_3467] [protein=hypothetical protein] [protein_id=ABO13856.1] [location=complement(8602..9732)] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13857.1_9 [locus_tag=A1S_3468] [protein=putative lipoprotein] [protein_id=ABO13857.1] [location=complement(10072..10374)] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13858.1_10 [locus_tag=A1S_3469] [protein=Diaminopimelate decarboxylase] [protein_id=ABO13858.1] [location=complement(10367..10723)] [gbkey=CDS]
&gt;lcl|CP000522.1_prot_ABO13859.1_11 [locus_tag=A1S_3470] [protein=regulatory protein LysR] [protein_id=ABO13859.1] [location=complement(12076..12444)] [gbkey=CDS]


The other pattern is 

&gt;lcl|CP000523.1_prot_ABO13861.1_1 [locus_tag=A1S_3472] [protein=DNA replication protein] [protein_id=ABO13861.1] [location=1..951] [gbkey=CDS]
&gt;lcl|CP000523.1_prot_ABO13862.1_2 [locus_tag=A1S_3473] [protein=hypothetical protein] [protein_id=ABO13862.1] [location=3048..4262] [gbkey=CDS]
&gt;lcl|CP000523.1_prot_ABO13863.1_3 [locus_tag=A1S_3474] [protein=hypothetical protein] [protein_id=ABO13863.1] [location=4357..5133] [gbkey=CDS]
&gt;lcl|CP000523.1_prot_ABO13864.1_4 [locus_tag=A1S_3475] [protein=hypothetical protein] [protein_id=ABO13864.1] [location=6197..8608] [gbkey=CDS]
&gt;lcl|CP000523.1_prot_ABO13865.1_5 [locus_tag=A1S_3476] [protein=secretory lipase] [protein_id=ABO13865.1] [location=8705..9403] [gbkey=CDS]


So now my idea is how do i parse and write them into individual files such that CP000522 output written to one file and CP000523 written to another file so forth and so on.

So far what i understand is i have to match the pattern after >lcl 
so there are other patterns like "LN997847" in the file 

Not sure how to proceed tried it in R but failed 

it can be done with awk and sed which i tried but i can;t define something that parse all header like takes into account CP as well as LN .

Any suggestion or help would be highly appreciated .
here is my file
Here's a simple awk approach:

awk '{if(/^&gt;/){split($1,a,"[|.]")}print &gt;&gt; a[2]".fa"}' Protein_FASTA.txt 


Or, more concisely, just:

awk '/^&gt;/{split($1,a,"[|.]")}{print &gt;&gt; a[2]".fa"}' Protein_FASTA.txt 


When run on the file linked to in your question, that results in the following files:

$ ls
AP014650.fa  CP003848.fa  CP007713.fa  CP012005.fa  CP015122.fa  CP017645.fa  CP018422.fa  CP020594.fa  CP023021.fa  CP024577.fa  CP026712.fa  CP027245.fa  CP030108.fa
CP000522.fa  CP003850.fa  CP007714.fa  CP012007.fa  CP015365.fa  CP017647.fa  CP018678.fa  CP020596.fa  CP023023.fa  CP024578.fa  CP026748.fa  CP027529.fa  CP030109.fa
CP000523.fa  CP003887.fa  CP008707.fa  CP012008.fa  CP015366.fa  CP017649.fa  CP018679.fa  CP021322.fa  CP023024.fa  CP025267.fa  CP026749.fa  CP027531.fa  CU459137.fa
CP000864.fa  CP003888.fa  CP008708.fa  CP012953.fa  CP015484.fa  CP017651.fa  CP019218.fa  CP021327.fa  CP023025.fa  CP026126.fa  CP027121.fa  CP027532.fa  CU459138.fa
CP000865.fa  CP003907.fa  CP008709.fa  CP012954.fa  CP015485.fa  CP017653.fa  CP020573.fa  CP021348.fa  CP023027.fa  CP026127.fa  CP027122.fa  CP027608.fa  CU459139.fa
CP001183.fa  CP003908.fa  CP008850.fa  CP012955.fa  CP015486.fa  CP017655.fa  CP020575.fa  CP021783.fa  CP023028.fa  CP026128.fa  CP027124.fa  CP027609.fa  CU459140.fa
CP001922.fa  CP003968.fa  CP008851.fa  CP012956.fa  CP016296.fa  CP017657.fa  CP020576.fa  CP021784.fa  CP023030.fa  CP026129.fa  CP027179.fa  CP027610.fa  JN377410.fa
CP001923.fa  CP004359.fa  CP010398.fa  CP013925.fa  CP016297.fa  CP018144.fa  CP020577.fa  CP021785.fa  CP023032.fa  CP026339.fa  CP027180.fa  CP029570.fa  LN865144.fa
CP001938.fa  CP006769.fa  CP010399.fa  CP014216.fa  CP016299.fa  CP018255.fa  CP020580.fa  CP021786.fa  CP023033.fa  CP026340.fa  CP027181.fa  CP029571.fa  LN997847.fa
CP002523.fa  CP007578.fa  CP010400.fa  CP014217.fa  CP016301.fa  CP018257.fa  CP020585.fa  CP021787.fa  CP023035.fa  CP026705.fa  CP027182.fa  CP029572.fa  LT594096.fa
CP002524.fa  CP007579.fa  CP010780.fa  CP014292.fa  CP016302.fa  CP018333.fa  CP020589.fa  CP022284.fa  CP024125.fa  CP026706.fa  CP027243.fa  CP029573.fa  Protein_FASTA.txt
CP003501.fa  CP007580.fa  CP010782.fa  CP014293.fa  CP017643.fa  CP018334.fa  CP020593.fa  CP022285.fa  CP024419.fa  CP026708.fa  CP027244.fa  CP030107.fa


Explanation


if(/^&gt;/){split($1,a,"[|.]") : if this line starts with a &gt;, split the first field on any occurrence of either | or . and save the results in the array a. Since your header lines all start with &gt;lcl|, then the string you are looking for and a ., this means that the second value in the a array will be your target string. 
print &gt;&gt; a[2]".fa" : print (append, &gt;&gt;) the current line to a file called "whatever the name of this sequence is" (a[2]) and .fa. This is run for every line in your input file. Note that if you run the same command again, you will need to first delete the files created the first time. If you don't, because I am using the &gt;&gt;, you will just append to the existing files.