{"action":"created","issue":{"url":"https://api.github.com/repos/msettles/expHTS/issues/37","labels_url":"https://api.github.com/repos/msettles/expHTS/issues/37/labels{/name}","comments_url":"https://api.github.com/repos/msettles/expHTS/issues/37/comments","events_url":"https://api.github.com/repos/msettles/expHTS/issues/37/events","html_url":"https://github.com/msettles/expHTS/issues/37","id":113698858,"number":37,"title":"develop_new version does not identify gzipped fastqs","user":{"login":"bricesarver","id":6654412,"avatar_url":"https://avatars.githubusercontent.com/u/6654412?v=3","gravatar_id":"","url":"https://api.github.com/users/bricesarver","html_url":"https://github.com/bricesarver","followers_url":"https://api.github.com/users/bricesarver/followers","following_url":"https://api.github.com/users/bricesarver/following{/other_user}","gists_url":"https://api.github.com/users/bricesarver/gists{/gist_id}","starred_url":"https://api.github.com/users/bricesarver/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/bricesarver/subscriptions","organizations_url":"https://api.github.com/users/bricesarver/orgs","repos_url":"https://api.github.com/users/bricesarver/repos","events_url":"https://api.github.com/users/bricesarver/events{/privacy}","received_events_url":"https://api.github.com/users/bricesarver/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-10-27T21:57:56Z","updated_at":"2015-10-27T22:06:26Z","closed_at":null,"body":"/mnt/storage2/scratch2/projects/mouse_references$ expHTS preprocess -t 16\r\nsuper_deduper found\r\nsickle found\r\nflash2 found\r\nbowtie2 found\r\nscythe found\r\nNo fastq files were found under this directory - 00-RawData/cast\r\nFailure in Validation - exiting process\r\n\r\n/mnt/storage2/scratch2/projects/mouse_references/00-RawData/cast$ ls\r\nH12_88996_ERR019144_1.fastq.gz  H12_88996_ERR019144_2.fastq.gz\r\n/mnt/storage2/scratch2/projects/mouse_references/00-RawData/cast$ zcat H12_88996_ERR019144_1.fastq.gz | head\r\n@ERR019144.1 IL19_4344:5:1:1016:2407/1\r\nNTACCTACAAATTTAATATTTTCTAAGAGCAGAATGAAACTTCATAGTGTATGTATAAAACATTCCACTATTCTTTCCTGTTCATCAGTTGTTCGATACACAGACTGA\r\n+\r\n!+''+)(*'%556668:87977577565208855588666+.1-40-544566626525+/-/03+0//11././,,/13(((),60-//(&(&),,)+'(&($$/++\r\n@ERR019144.2 IL19_4344:5:1:1016:13842/1\r\nNGATCTGCACGCCAGACTCACCTTGTGACCTGCCTCTAGTCGGGGGTGTGCTCTCCTGAGGAGAGAGAGGATAGCTACAGAGAGAAGATCACAGCATCGACGTCCTGT\r\n+\r\n!)(,(1/2//023077:;994,3540/+1'01,,-1113388'6%(&%$-/-,.-$#'&$#%(%'&$#%#$%$#'%%&#%#$$%$#$#$)%%%$%&*'('%'%)&'+'\r\n@ERR019144.3 IL19_4344:5:1:1016:7439/1\r\nNTTGTTTTACTCAGGTTCCACACATGTGCCTTCAAATTTCATATCATTGTTTTTAATATCTGAGTAATAATCTACTGTGTAAATGTATCAAATTTTATTTATCTATCT\r\n\r\nThe bug is in this function:\r\n\r\n    def directoryFiles(self, sampleSeq):\r\n        sampleSeq = tuple(sampleSeq)\r\n        #print sampleSeq\r\n        directoryTest = sampleSeq[0].rstrip();\r\n        #fastqCount insures at least one fastq files is under the directory\r\n        fastqCount = 0\r\n        if self.testDirectory(directoryTest):\r\n            for subdir, dir, files in os.walk(directoryTest):\r\n                for file in files:\r\n                    file = os.path.abspath(os.path.join(directoryTest, file))\r\n                    if \"_R1\" in file and \".fastq\" in file:\r\n                        fastqCount += 1\r\n                        if not sampleSeq in self.sampleFiles:\r\n                            self.sampleFiles[sampleSeq] = []\r\n                        \r\n                        self.sampleFiles[sampleSeq].append(self.isPairedEnd(file))\r\n\r\n\r\n            if (fastqCount == 0):\r\n                self.exitTime(\"No fastq files were found under this directory - \" + directoryTest)\r\n\r\n        else:\r\n            self.exitTime(\"Directory \" + directoryTest + \" does not exists\")\r\n\r\nYou set fastqCount to 0, then call self.exitTime() below. This is never updated because the reads are named (e.g.,) H12_88996_ERR0191444_1.fastq and the function looks for _R1. Little edge case action going on.\r\n\r\nEdit: new_devel branch too."},"comment":{"url":"https://api.github.com/repos/msettles/expHTS/issues/comments/151659414","html_url":"https://github.com/msettles/expHTS/issues/37#issuecomment-151659414","issue_url":"https://api.github.com/repos/msettles/expHTS/issues/37","id":151659414,"user":{"login":"dstreett","id":6163528,"avatar_url":"https://avatars.githubusercontent.com/u/6163528?v=3","gravatar_id":"","url":"https://api.github.com/users/dstreett","html_url":"https://github.com/dstreett","followers_url":"https://api.github.com/users/dstreett/followers","following_url":"https://api.github.com/users/dstreett/following{/other_user}","gists_url":"https://api.github.com/users/dstreett/gists{/gist_id}","starred_url":"https://api.github.com/users/dstreett/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dstreett/subscriptions","organizations_url":"https://api.github.com/users/dstreett/orgs","repos_url":"https://api.github.com/users/dstreett/repos","events_url":"https://api.github.com/users/dstreett/events{/privacy}","received_events_url":"https://api.github.com/users/dstreett/received_events","type":"User","site_admin":false},"created_at":"2015-10-27T22:06:26Z","updated_at":"2015-10-27T22:06:26Z","body":"Some might call it a feature :) That was by design, but I will add _1 in the function. @msettles  also said something about adding in a \"user specified\" search at one point. How should that be handled? User gives PE 1 key, PE 2 key, and SE key?"}}