Difference between revisions of "BuKyung Create a FASTA file with a sequence. Open it and reverse the sequence of it and print it out in another FASTA file"
imported>Baik BuKyung (Created page with "<p>Back to Baik BuKyung</p> <hr /> <p> </p>") |
imported>Baik BuKyung |
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− | <p> </p> | + | <p><span style="font-size:24px">Source code:</span></p> |
+ | |||
+ | <hr /> | ||
+ | <div> | ||
+ | <div>#!/usr/bin/perl<br /> | ||
+ | use strict;<br /> | ||
+ | use warnings;<br /> | ||
+ | open FH, ">", "outer.fasta" or die "$!\n";<br /> | ||
+ | while(<>){<br /> | ||
+ | if($_=~ />/){<br /> | ||
+ | my $name=$_;<br /> | ||
+ | $name=~ s/>/rev_/;<br /> | ||
+ | print FH ">",$name,"\n"<br /> | ||
+ | }<br /> | ||
+ | else{<br /> | ||
+ | my $rv=reverse $_;<br /> | ||
+ | print FH ( $rv,"\n");<br /> | ||
+ | }<br /> | ||
+ | }</div> | ||
+ | </div> | ||
+ | |||
+ | <div> | ||
+ | <hr /> | ||
+ | <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9816.PNG" style="height:228px; width:306px" /></p> | ||
+ | </div> | ||
+ | |||
+ | <div> | ||
+ | <hr /> | ||
+ | <p><span style="font-size:24px">Result</span></p> | ||
+ | |||
+ | <p><img alt="" src="/ckfinder/userfiles/images/%EC%BA%A1%EC%B2%9817.PNG" style="height:24px; width:361px" /></p> | ||
+ | |||
+ | <p><span style="font-size:16px">After the 5.pl is executed with the tert_Human.fasta file, the outer.fasta file is generated.</span></p> | ||
+ | |||
+ | <p><span style="font-size:16px">The original content in the tert_Human.fasta file is</span></p> | ||
+ | |||
+ | <p><em>>sp|O14746|TERT_HUMAN Telomerase reverse transcriptase OS=Homo sapiens GN=TERT PE=1 SV=1<br /> | ||
+ | MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRALVAQCLVCVPWDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTTSVRSYLPNTVTDALRGSGAWGLLLRRVGDDVLVHLLARCALFVLVAPSCAYQVCGPPLYQLGAATQARPPPHASGPRRRLGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLPLPKRPRRGAAPEPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGTRHSHPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRPSFLLSSLRPSLTGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKTHCPLRAAVTPAAGVCAREKPQGSVAAPEEEDTDPRRLVQLLRQHSSPWQVYGFVRACLRRLVPPGLWGSRHNERRFLRNTKKFISLGKHAKLSLQELTWKMSVRDCAWLRRSPGVGCVPAAEHRLREEILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSIGIRQHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMDYVVGARTFRREKRAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDIHRAWRTFVLRVRAQDPPPELYFVKVDVTGAYDTIPQDRLTEVIASIIKPQNTYCVRRYAVVQKAAHGHVRKAFKSHVSTLTDLQPYMRQFVAHLQETSPLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKSYVQCQGIPQGSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKTFLRTLVRGVPEYGCVVNLRKTVVNFPVEDEALGGTAFVQMPAHGLFPWCGLLLDTRTLEVQSDYSSYARTSIRASLTFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYKILLLQAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAAGPLPSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANPALPSDFKTILD</em></p> | ||
+ | |||
+ | <p><span style="font-size:16px">The content of outer.fasta file is</span></p> | ||
+ | |||
+ | <div><em>>rev_sp|O14746|TERT_HUMAN Telomerase reverse transcriptase OS=Homo sapiens GN=TERT PE=1 SV=1</em></div> | ||
+ | |||
+ | <div> </div> | ||
+ | |||
+ | <div><em>DLITKFDSPLAPNAAAELATLTTGPLKRSLQTQATRLSGLLPVYTVRHRTLKLLFAQHCLWQVAESPLPGAAGKAGLSMGANKAKLISYCLSATDSIVRLFFTPNKWVQQHFPLQLVCAHFRYAQLLLIKYINTCVTQLSNVQLDLFLSHCKLRLVGFLKRRMNRGAKFGRNFTLSARISTRAYSSYDSQVELTRTDLLLGCWPFLGHAPMQVFATGGLAEDEVPFNVVTKRLNVVCGYEPVGRVLTRLFTKAHTLHPTVLLFDDVLRLLLGDRRIGAFLKNEMDGYCLSCLLTSLISGQPIGQCQVYSKGRIRVAHHCMFRLFVDFLGSSAENLSSSQEIVVADRLPSTEQLHAVFQRMYPQLDTLTSVHSKFAKRVHGHAAKQVVAYRRVCYTNQPKIISAIVETLRDQPITDYAGTVDVKVFYLEPPPDQARVRLVFTRWARHIDDLGLVSAGLLGPRRAREYNLVSFLAKVRSTLREARKERRFTRAGVVYDMNVIPRLGDPKPIFRLRSTLLAPRAERHQRVEAESLERLQVRKLHQRIGISQLKSWVSKRYFFLRNKQFTTETVYFFSRLLEVVYVSMLWHLFKALIEERLRHEAAPVCGVGPSRRLWACDRVSMKWTLEQLSLKAHKGLSIFKKTNRLFRRENHRSGWLGPPVLRRLCARVFGYVQWPSSHQRLLQVLRRPDTDEEEPAAVSGQPKERACVGAAPTVAARLPCHTKLLVGYPCQAHNGLLELFLPRMQWYRQPLRPLRRPTGPMWPRSGLFITEVLRRAGTLSPRLSSLLFSPRLQEKDGSSYLFHKTEAYVPPCPTDWPRPPRSTSPPGAHHQRGVSPHSHRTGSLAGELSTAEEAPRAPSVVCFGRDSPGRTRGPHAWSGQGVPTREPEPAAGRRPRKPLPLSRSASGGRRRAGPAPLGLPVGAERVSHNWARECGLRRRPGSAHPPPRAQTAAGLQYLPPGCVQYACSPAVLVFLACRALLHVLVDDGVRRLLLGWAGSGRLADTVTNPLYSRVSTTFAEPPGGRAGDLLAFGFALVNKAGRECLRQLVRAVLEKLCSVQRFSPAAPPPRADWPVCVLCQAVLARFAAPDGRQVLRWGQPGLRRVFTALPLVERYHSRLLSRVARCRPARPM</em></div> | ||
+ | |||
+ | <div> </div> | ||
+ | |||
+ | <div> </div> | ||
+ | |||
+ | <div><span style="font-size:16px">I just add prefix 'rev_' to the gene name so as to show that this is the reverse sequence of certain sequence.</span></div> | ||
+ | </div> |
Revision as of 19:27, 14 June 2016
Back to Baik BuKyung
Source code:
use strict;
use warnings;
open FH, ">", "outer.fasta" or die "$!\n";
while(<>){
if($_=~ />/){
my $name=$_;
$name=~ s/>/rev_/;
print FH ">",$name,"\n"
}
else{
my $rv=reverse $_;
print FH ( $rv,"\n");
}
Result
After the 5.pl is executed with the tert_Human.fasta file, the outer.fasta file is generated.
The original content in the tert_Human.fasta file is
>sp|O14746|TERT_HUMAN Telomerase reverse transcriptase OS=Homo sapiens GN=TERT PE=1 SV=1
MPRAPRCRAVRSLLRSHYREVLPLATFVRRLGPQGWRLVQRGDPAAFRALVAQCLVCVPWDARPPPAAPSFRQVSCLKELVARVLQRLCERGAKNVLAFGFALLDGARGGPPEAFTTSVRSYLPNTVTDALRGSGAWGLLLRRVGDDVLVHLLARCALFVLVAPSCAYQVCGPPLYQLGAATQARPPPHASGPRRRLGCERAWNHSVREAGVPLGLPAPGARRRGGSASRSLPLPKRPRRGAAPEPERTPVGQGSWAHPGRTRGPSDRGFCVVSPARPAEEATSLEGALSGTRHSHPSVGRQHHAGPPSTSRPPRPWDTPCPPVYAETKHFLYSSGDKEQLRPSFLLSSLRPSLTGARRLVETIFLGSRPWMPGTPRRLPRLPQRYWQMRPLFLELLGNHAQCPYGVLLKTHCPLRAAVTPAAGVCAREKPQGSVAAPEEEDTDPRRLVQLLRQHSSPWQVYGFVRACLRRLVPPGLWGSRHNERRFLRNTKKFISLGKHAKLSLQELTWKMSVRDCAWLRRSPGVGCVPAAEHRLREEILAKFLHWLMSVYVVELLRSFFYVTETTFQKNRLFFYRKSVWSKLQSIGIRQHLKRVQLRELSEAEVRQHREARPALLTSRLRFIPKPDGLRPIVNMDYVVGARTFRREKRAERLTSRVKALFSVLNYERARRPGLLGASVLGLDDIHRAWRTFVLRVRAQDPPPELYFVKVDVTGAYDTIPQDRLTEVIASIIKPQNTYCVRRYAVVQKAAHGHVRKAFKSHVSTLTDLQPYMRQFVAHLQETSPLRDAVVIEQSSSLNEASSGLFDVFLRFMCHHAVRIRGKSYVQCQGIPQGSILSTLLCSLCYGDMENKLFAGIRRDGLLLRLVDDFLLVTPHLTHAKTFLRTLVRGVPEYGCVVNLRKTVVNFPVEDEALGGTAFVQMPAHGLFPWCGLLLDTRTLEVQSDYSSYARTSIRASLTFNRGFKAGRNMRRKLFGVLRLKCHSLFLDLQVNSLQTVCTNIYKILLLQAYRFHACVLQLPFHQQVWKNPTFFLRVISDTASLCYSILKAKNAGMSLGAKGAAGPLPSEAVQWLCHQAFLLKLTRHRVTYVPLLGSLRTAQTQLSRKLPGTTLTALEAAANPALPSDFKTILD
The content of outer.fasta file is