Commit bb513d52 authored by Tizian Schulz's avatar Tizian Schulz
Browse files

Minor bug fixes in comparison workflow

parent b5020113
......@@ -8,7 +8,7 @@ rule all:
input:
expand("{msr}{lv}.pdf", msr=config['measure'], lv=["_" + i if i != "" else i for i in config['level']])
shell:
"rm %s/merged_c* BLAST/dbs/*" %config['dataDir']
"rm -rf %s/merged_c* BLAST/dbs/* MMseqs2/dbs" %config['dataDir']
###Common rules###
......@@ -192,7 +192,7 @@ rule runMMseqs2:
qryFls = expand("MMseqs2/dbs/query/randQrys_n%s_l%s{flnd}" %(config['numberOfQueries'],config['queryLength']), flnd=config['databaseFileEndings']),
target = "MMseqs2/dbs/target/db_{describtion}",
trgtFls = expand("MMseqs2/dbs/target/db_{describtion}{flnd}", describtion="{describtion}", flnd=config['databaseFileEndings']),
index = "MMseqs2/dbs/target/db_{describtion}.idx",
index = "MMseqs2/dbs/target/db_{describtion}.idx.index",
dirct = "MMseqs2/tmpdir_{describtion}",
subMat = config['subMatrix']
params:
......@@ -207,6 +207,7 @@ rule runMMseqs2:
result = temp("MMseqs2/results/results_{describtion, c[0-9a-z_]+}.txt"),
resFls = temp(expand("MMseqs2/results/results_{describtion}.txt{flnd}", describtion="{describtion, c[0-9a-z_]+}", flnd=config['MMseqs2ResultFileEndings'])),
runtime = "MMseqs2/runtimes/runtimesMMseqs2_{describtion, c[0-9a-z_]+}.txt"
threads: workflow.cores * 1.0
shell:
"mkdir -p MMseqs2/{{runtimes,results}}; /usr/bin/time -v %s search {input.query} {input.target} {output.result} {input.dirct} --search-type 3 --max-seqs {params.maxSeqs} -a -e {params.eThres} --threads {params.thrds} --seed-sub-mat {input.subMat} --gap-open {params.d} --gap-extend {params.e} --strand {params.strnd} -s {params.sens} 2> {output.runtime}" %config['mmseqs2Bin']
......
......@@ -31,7 +31,6 @@ measure: ["runtime", "memory"]
level: ["", "small"]
#Tools to compare
tool: ["PLAST", "BLAST", "MMseqs2", "UBLAST", "BLAT"]
# tool: []
#Pangenome sizes to test
pangenomeSizes: [25, 100, 200, 300, 400, 500, 1250, 2500, 3750, 5000]
#Largest size we want to have averaged measures for
......@@ -88,6 +87,6 @@ databaseFileEndings: ["", ".dbtype", ".index", ".lookup", ".source", "_h", "_h.d
#File endings of MMseq2's result files
MMseqs2ResultFileEndings: ["", ".dbtype", ".index"]
#File endings of MMseqs2's index files
MMseqs2IndexFileEndings: ["", ".dbtype", ".index"]
MMseqs2IndexFileEndings: [.dbtype", ".index"]
# #File endings of MMseqs2's query dbs
# queryDatabaseFileEndings: ["", ".dbtype", ".index", ".lookup", ".source", "_h", "_h.dbtype", "_h.index"]
\ No newline at end of file
......@@ -15,7 +15,7 @@ for n in rtfilenames:
for l in rtfile:
if l.find("User") >= 0:
compRt += float(l.split(' ')[3])
elif l.find("Max") >= 0:
elif l.find("Maximum") >= 0:
maxMem = max(maxMem, int(l.split(' ')[5]))
rtfile.close()
......
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