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update_fasta.py
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import os
import sys
### Load new sequences
fastaFile = sys.argv[1]
pjson = fastaFile.split('.')[0] + ".pjson"
#os.system("perl faa2pjson.pl " + fastaFile + " >" + pjson + " || exit 1")
os.system("python3 loadAseqsJson.py " + pjson + " -id gi -col aseqs || exit 1")
import datetime
theDate = str(datetime.datetime.now()).split(' ')[0]
JOBNAME = "SDU" + theDate
print(JOBNAME)
col = "aseqs"
col = "testAseqs"
#os.system("./createSuperJob-v1.pl -C superjobs -t pfam27,segs,coils,agfam1,das,ecf,tigrfam14 " + JOBNAME + " ||exit 1")
###
#os.system("./createSuperJob-v1.pl -C superjobs -t segs,coils,agfam1,das,ecf,pfam28,tigrfam15 " + JOBNAME + " ||exit 1")
#os.system("./createSuperJob-v1.pl -C superjobs -t pfam27 " + JOBNAME + " ||exit 1")
###
#os.system("./tarSendAndStartSuperJob.sh superjobs/" + JOBNAME + " || exit 1")
code = "./watchNewtonUntilJobDone.pl " + JOBNAME + " && ./fetchSuperJobResults.sh superjobs " + JOBNAME + " && ./loadSuperJobData.pl superjobs/" + JOBNAME + "-results || exit 1"
#os.system(code)
def cleanupResults():
os.system("rm -rf superjobs/" + JOBNAME + "-results")
os.system("rm superjobs/" + JOBNAME + "-results.tar")
os.system("rm superjobs/" + JOBNAME + ".tar.gz")
os.system("rm superjobs/" + JOBNAME + ".tar.gz.md5")
os.system("rm -f superjobs/" + JOBNAME + ".log")
os.system("rm -f superjobs" + JOBNAME + ".err")
#cleanupResults()