A simple, if not elegant, way of doing it assumes that you have each sequence in its own variable, say in an array. Then:
$sequence =~ s/\n//g; #remove ALL newlines $sequence .= "\n"; #re-add the terminal newline >===== Original Message From "Prachi Shah" <[EMAIL PROTECTED]> ===== >Hmmm. One way of doing it could be to read each sequence in the file, >reading the header and the actual sequence in different variables. And then, >format the sequence variable to remove all newlines using a regular >expression. And then write them back to another file. > >Hope this helps. > >Prachi. > > >----Original Message Follows---- >From: s wang <[EMAIL PROTECTED]> >To: [EMAIL PROTECTED] >Subject: how can i get rid of these new line characters? >Date: Fri, 4 Oct 2002 08:00:19 -0700 (PDT) > > >i have just started writing some scripts in PERL and i am trying to catch a >deadline, i really wish i could get some help for this problem. any >suggestion is greatly appreciated. > >i have a set of files with sequences aligned in the following format. i >wonder how i can eliminate the new line characters within each sequence >without touching those between sequences? > >..... > >2 chr1 10761 10775 chr19 46520370 46520384 + 941 >acaGGAAAAGAACAA >acaggaaaagaaggg > >3 chr1 10776 11241 chrUn 45411478 45411944 - 12857 >AAGAAGGAAGAAGAGGGTAGAGGAGAAGTGCAGCAAGGGTGGAGGGAGGTGCCCGCGCTGGGTCGGAGGAGCAGGAG TAT >GGAGGGAAGACTCCTGGGTGGCATGGAGCTCTTGCACCTCTAGGCACTGCCCAGCCCTGTGTCAGCCAGGGCTGAAC CCCCACAGGATAAGGAACCTGTGTGTGTGACCAACAATCAAAG >CTACATCTGTGACACAACAGGACACTGCTATGGGCAGTCTCAGTTCTGGCTCGCGTGGACCATCACCATCA >TCCTGAGCTGCTGCTGTGTCTGCCACCACAGCCAAGCCAGCCCTCAAGTCCAGCAGTAGCAACATGAAATCAA >CCTGCCTGCCTATCCAGAAGCCCGCAATTACTCAGTGCTACCATTTTATTTCACCAAACTATTTATTACCTT >CTTATGAGGAAGTGGTGAAC >AAGAAGGAAGCAGAGGGAAGAAGAAATGAAGGAGGAGGGTGATAGTGCCATGGTGGAGAAACAGGAGGAG >CAGGGGCAGGGGCACTCTACACTGGACACTGTAGTGGACAGTCTCAGTGCTCCAGCTCTGAA >TTCTGGTATAAGTCCTTGCCTAGGGAGTTATTGGCATCCCAGGGTCTCAGTTACTGCCTCTGCTCCACAGGCAGAGG >AAAGCATGGGGTGTCCAGCCTTTTCTCACTCTTAGGGACAATGTTGACTTCTGACTGATGTGGACCATCATCATCT >TCCGGAGCTGCTGCTGTGTCTGCCACCAATGCTGAGCCCAGGCACTGCCTTCAGACCCAGCAATGACAGCATGAAAT CAA >ATTGATGGCCTACCAGGAAGCCCACAATTACTCATCACTGCCATTTTAGTTCAGGTTTTTGCCAAACTATTTATTAC CTC >CTTATGAGGAAGTGATGAAC > >4 11242 11268 25467376 25467402 - 294 >TAACCTCCACCTGTTTCCCTCCCTGTC >ATCTTCCAATCCCTTCCCCACCCTACC > > > > > > >--------------------------------- >Do you Yahoo!? >New DSL Internet Access from SBC & Yahoo! > > > > >_________________________________________________________________ >MSN Photos is the easiest way to share and print your photos: >http://photos.msn.com/support/worldwide.aspx > > >-- >To unsubscribe, e-mail: [EMAIL PROTECTED] >For additional commands, e-mail: [EMAIL PROTECTED] "Ain't no blood in my body, it's liquid soul in my veins" ~Roots Manuva -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
