S Wang wrote: > > 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
perl -i~ pe'/^[acgt]+$/i and chomp' yourfile John -- use Perl; program fulfillment -- To unsubscribe, e-mail: [EMAIL PROTECTED] For additional commands, e-mail: [EMAIL PROTECTED]
