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wurmlab / genevalidatorapp

A web wrapper for GeneValidator
GNU Affero General Public License v3.0
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erroneously cuts at newline?? #10

Closed yannickwurm closed 9 years ago

yannickwurm commented 9 years ago

The following two sequences are not treated identically:

>test
MLPQTPDIIPTTLNQQKCVKARALYDNIAEAPDELAFRKGDVLTVLEQNTAGLEGWWLCALRGRQGICPGNRLRLLVGQYDTGGCLVGSRPDLTISEDGIQRHGKRRSWHVQPNRVVTPQKCGDVYLYDLPASRGSPAPPSRHDSPLNSNNEHLHNSGRYTTSSRNSVDNGGDVSDCYDVPPRAIPVIPSPASSPSPAPSCYDIPRPPTSCTPISNCSGGSGVTPLDCYDVPRPLQPLTPSSSASSLTNDGSLSGSNRSSLAAPDYDVPRSRLPASSLPSRHNTPVPKTPTPPPPPQTQQIYDVPVSKELPLELDSALEGLQRLQSEASAAIARLLGFVSPVWRTPQRLDATLMDLRLAALRLRTSLHDLAEFAEGTLGNAGKAPDKGLATKLRPLVKALRDSDKLVQEAATELDAMEWDAGKLCRGGGDTPTPTNGPPSTILPPAQPDPLDQLIACARALTEDVRQVASFIQGNSTLLFKRSSIISTGSSNNSGAGEDYDYVNLDSREVVAKQREEVRASLPQELRSNYDLLVSESDNATIQMPPTTPTPMDPNDKQLLAFYAAQVITHGNHLTHAIDAFMQTVEHNQPPKVFLAHGKFVVLSAHRLVHIGDTVHRNVIRNDVKTRVLECANALNEALKQTVSKTKQAAQFFPSVSAVQEMVDSVVDVSHLAKDLKVAIINGAQQPMEVTSSNFQEVLVELDEILKNATFLCIDGEFTGLNSGPDGGVFDTPAQYYAKLRTGSMDFLLIQFGLSVFTFNKEMQKYNQRSYNFYVFPRPLNRMAPDCRFMCQTSSISFLASQGFDFNKLFKLGIPYLTTNEEEKLMKRLEEKQRIRDEGTEILPISDVERPQIEEICSRIDEFVTSETEELLIEKCNAFIRRLVYQEVKLRWPNKLKVESKMNNFGCILVVQRLGTKEEEEQREIEKREREKTEIQQAVGLSILMRKIADSGKLIVGHNMLLDLCHIVHQFFGQLPESYFEFKSLVHSLFPRILDTKIICHSQQFKENIPSSNLGILLETVSKSPFKITEVEPIDGRSYSTLSEKCHEAGYDAYITGICFIALSNYLGSLQKPEVPIVLSDSPLLNPFLNKLLIARLKDVPYINLVGDDPNPSRDHVFHLTFPKEWKFNDISHLFSPFGSVHVSWLSDISAYIELHRRDQVNEVMKVLAKTSTYKLQRYADYQASLENFNTGERKRKLSSSEETTPEAEELCGCRECAKIETETLCRA

Length for the following one is only 70. 

>test2
MLPQTPDIIPTTLNQQKCVKARALYDNIAEAPDELAFRKGDVLTVLEQNTAGLEGWWLCALRGRQGICPG
NRLRLLVGQYDTGGCLVGSRPDLTISEDGIQRHGKRRSWHVQPNRVVTPQKCGDVYLYDLPASRGSPAPP
SRHDSPLNSNNEHLHNSGRYTTSSRNSVDNGGDVSDCYDVPPRAIPVIPSPASSPSPAPSCYDIPRPPTS
CTPISNCSGGSGVTPLDCYDVPRPLQPLTPSSSASSLTNDGSLSGSNRSSLAAPDYDVPRSRLPASSLPS
RHNTPVPKTPTPPPPPQTQQIYDVPVSKELPLELDSALEGLQRLQSEASAAIARLLGFVSPVWRTPQRLD
ATLMDLRLAALRLRTSLHDLAEFAEGTLGNAGKAPDKGLATKLRPLVKALRDSDKLVQEAATELDAMEWD
AGKLCRGGGDTPTPTNGPPSTILPPAQPDPLDQLIACARALTEDVRQVASFIQGNSTLLFKRSSIISTGS
SNNSGAGEDYDYVNLDSREVVAKQREEVRASLPQELRSNYDLLVSESDNATIQMPPTTPTPMDPNDKQLL
AFYAAQVITHGNHLTHAIDAFMQTVEHNQPPKVFLAHGKFVVLSAHRLVHIGDTVHRNVIRNDVKTRVLE
CANALNEALKQTVSKTKQAAQFFPSVSAVQEMVDSVVDVSHLAKDLKVAIINGAQQP
MEVTSSNFQEVLVELDEILKNATFLCIDGEFTGLNSGPDGGVFDTPAQYYAKLRTGSMDFLLIQFGLSVF
TFNKEMQKYNQRSYNFYVFPRPLNRMAPDCRFMCQTSSISFLASQGFDFNKLFKLGIPYLTTNEEEKLMK
RLEEKQRIRDEGTEILPISDVERPQIEEICSRIDEFVTSETEELLIEKCNAFIRRLVYQEVKLRWPNKLK
VESKMNNFGCILVVQRLGTKEEEEQREIEKREREKTEIQQAVGLSILMRKIADSGKLIVGHNMLLDLCHI
VHQFFGQLPESYFEFKSLVHSLFPRILDTKIICHSQQFKENIPSSNLGILLETVSKSPFKITEVEPIDGR
SYSTLSEKCHEAGYDAYITGICFIALSNYLGSLQKPEVPIVLSDSPLLNPFLNKLLIARLKDVPYINLVG
DDPNPSRDHVFHLTFPKEWKFNDISHLFSPFGSVHVSWLSDISAYIELHRRDQVNEVMKVLAKTSTYKLQ
RYADYQASLENFNTGERKRKLSSSEETTPEAEELCGCRECAKIETETLCRA
yannickwurm commented 9 years ago

(@ismailm this is a major bug because most fastas are multiline)

yannickwurm commented 9 years ago

@yeban @IsmailM

IsmailM commented 9 years ago

Fixed - 5725c7483a9d8bc6b6c5487ff82e701ff25b1c4b

I'll release an updated gem shortly.