search

ash211 / gtfold

GTfold is a fast, scalable multicore code for predicting RNA secondary structure and is one to two orders of magnitude faster than the de facto standard programs and achieves comparable accuracy of prediction.
http://gtfold.sourceforge.net/
5 stars 18 forks source link

rewrite branch is not handling a fasta file properly #27

Closed shelswenson closed 13 years ago

shelswenson commented 13 years ago

old gtfold ran fine on:

HIV-1-HXB2: Weeks sequence GGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACUAGGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCUCAAAGUAGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCAGACCCUUUUAGUCAGUGUGGAAAAUCUCUAGCAGUGGCGCCCGAACAGGGACUUGAAAGCGAAAGUAAAGCCAGAGGAGAUCUCUCGACGCAGGACUCGGCUUGCUGAAGCGCGCACGGCAAGAGGCGAGGGGCGGCGACUGGUGAGUACGCCAAAAAUUUUGACUAGCGGAGGCUAGAAGGAGAGAGAUGGGUGCGAGAGCGUCGGUAUUAAGCGGGGGAGAAUUAGAUAAAUGGGAAAAAAUUCGGUUAAGGCCAGGGGGAAAGAAACAAUAUAAACUAAAACAUAUAGUAUGGGCAAGCAGGGAGCUAGAACGAUUCGCAGUUAAUCCUGGCCUUUUAGAGACAUCAGAAGGCUGUAGACAAAUACUGGGACAGCUACAACCAUCCCUUCAGACAGGAUCAGAAGAACUUAGAUCAUUAUAUAAUACAAUAGCAGUCCUCUAUUGUGUGCAUCAAAGGAUAGAUGUAAAAGACACCAAGGAAGCCUUAGAUAAGAUAGAGGAAGAGCAAAACAAAAGUAAGAAAAAGGCACAGCAAGCAGCAGCUGACACAGGAAACAACAGCCAGGUCAGCCAAAAUUACCCUAUAGUGCAGAACCUCCAGGGGCAAAUGGUACAUCAGGCCAUAUCACCUAGAACUUUAAAUGCAUGGGUAAAAGUAGUAGAAGAGAAGGCUUUCAGCCCAGAAGUAAUACCCAUGUUUUCAGCAUUAUCAGAAGGAGCCACCCCACAAGAUUUAAAUACCAUGCUAAACACAGUGGGGGGACAUCAAGCAGCCAUGCAAAUGUUAAAAGAGACCAUCAAUGAGGAAGCUGCAGAAUGGGAUAGAUUGCAUCCAGUGCAUGCAGGGCCUAUUGCACCAGGCCAGAUGAGAGAACCAAGGGGAAGUGACAUAGCAGGAACUACUAGUACCCUUCAGGAACAAAUAGGAUGGAUGACACAUAAUCCACCUAUCCCAGUAGGAGAAAUCUAUAAAAGAUGGAUAAUCCUGGGAUUAAAUAAAAUAGUAAGAAUGUAUAGCCCUACCAGCAUUCUGGACAUAAGACAAGGACCAAAGGAACCCUUUAGAGACUAUGUAGACCGAUUCUAUAAAACUCUAAGAGCCGAGCAAGCUUCACAAGAGGUAAAAAAUUGGAUGACAGAAACCUUGUUGGUCCAAAAUGCGAACCCAGAUUGUAAGACUAUUUUAAAAGCAUUGGGACCAGGAGCGACACUAGAAGAAAUGAUGACAGCAUGUCAGGGAGUGGGGGGACCCGGCCAUAAAGCAAGAGUUUUGGCUGAAGCAAUGAGCCAAGUAACAAAUCCAGCUACCAUAAUGAUACAGAAAGGCAAUUUUAGGAACCAAAGAAAGA

ash211 commented 13 years ago

The problem is that this sequence contains a newline character and a space character in it. I'll fix the input reader to ignore all spaces and newlines in the sequence file.

ash211 commented 13 years ago

Ignore spaces in the sequence file

Closed by 1c2cd71b4e3d1db909f701d54f73539da4fed7d1