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 AAGAAGGAAGAAGAGGGTAGAGGAGAAGTGCAGCAAGGGTGGAGGGAGGTGCCCGCGCTGGGTCGGAGGAGCAGGAGTAT GGAGGGAAGACTCCTGGGTGGCATGGAGCTCTTGCACCTCTAGGCACTGCCCAGCCCTGTGTCAGCCAGGGCTGAACCCCCACAGGATAAGGAACCTGTGTGTGTGACCAACAATCAAAG CTACATCTGTGACACAACAGGACACTGCTATGGGCAGTCTCAGTTCTGGCTCGCGTGGACCATCACCATCA TCCTGAGCTGCTGCTGTGTCTGCCACCACAGCCAAGCCAGCCCTCAAGTCCAGCAGTAGCAACATGAAATCAA CCTGCCTGCCTATCCAGAAGCCCGCAATTACTCAGTGCTACCATTTTATTTCACCAAACTATTTATTACCTT CTTATGAGGAAGTGGTGAAC AAGAAGGAAGCAGAGGGAAGAAGAAATGAAGGAGGAGGGTGATAGTGCCATGGTGGAGAAACAGGAGGAG CAGGGGCAGGGGCACTCTACACTGGACACTGTAGTGGACAGTCTCAGTGCTCCAGCTCTGAA TTCTGGTATAAGTCCTTGCCTAGGGAGTTATTGGCATCCCAGGGTCTCAGTTACTGCCTCTGCTCCACAGGCAGAGG AAAGCATGGGGTGTCCAGCCTTTTCTCACTCTTAGGGACAATGTTGACTTCTGACTGATGTGGACCATCATCATCT TCCGGAGCTGCTGCTGTGTCTGCCACCAATGCTGAGCCCAGGCACTGCCTTCAGACCCAGCAATGACAGCATGAAATCAA ATTGATGGCCTACCAGGAAGCCCACAATTACTCATCACTGCCATTTTAGTTCAGGTTTTTGCCAAACTATTTATTACCTC 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]
