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Move MAFFT and FastTree config into config.json #438

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Move MAFFT and FastTree config into config.json #438

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c8fc93d
Move config of MAFFT and FastTree in config.json
dilema Aug 6, 2020
6a90cf4
Typos in warning messages
dilema Aug 6, 2020
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22 changes: 17 additions & 5 deletions scripts_of/config.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,18 +7,30 @@
"__comment": "BASEOUTNAME : Just the filename without the directory path (of the output filename)",
"__comment": "IDENTIFIER : A name generated by OrthoFinder to uniquely identify the orthogroup (a number of methods use this to name the output file automatically, see RAxML command for an example). Not applicable for program_type search.",
"__comment": "DATABASE : For the search program_type, for use in the search_cmd. The full path of the database to search against",


"mafft":{
"program_type": "msa",
"cmd_line": "mafft --localpair --maxiterate 1000 --anysymbol INPUT > OUTPUT 2> /dev/null",
"cmd_line_fast": "mafft --anysymbol INPUT > OUTPUT 2> /dev/null",
"n_seqs_use_fast" : "500"
},

"muscle":{
"program_type": "msa",
"cmd_line": "muscle -in INPUT -out OUTPUT"
},


"fasttree":{
"program_type": "tree",
"cmd_line": "FastTree INPUT > OUTPUT 2> /dev/null"
},

"raxml":{
"program_type": "tree",
"cmd_line": "raxmlHPC-AVX -m PROTGAMMALG -p 12345 -s INPUT -n IDENTIFIER -w PATH > /dev/null",
"ouput_filename": "PATH/RAxML_bestTree.IDENTIFIER"
},

"raxml-ng":{
"program_type": "tree",
"cmd_line": "raxml-ng --msa INPUT --model LG+G4 --seed 12345 --threads 1",
Expand All @@ -36,13 +48,13 @@
"db_cmd": "diamond makedb --in INPUT -d OUTPUT",
"search_cmd": "diamond blastp -d DATABASE -q INPUT -o OUTPUT --more-sensitive -p 1 --quiet -e 0.001 --compress 1"
},

"blast_gz":{
"program_type": "search",
"db_cmd": "makeblastdb -dbtype prot -in INPUT -out OUTPUT",
"search_cmd": "blastp -outfmt 6 -evalue 0.001 -query INPUT -db DATABASE | gzip > OUTPUT.gz"
},

"mmseqs":{
"program_type": "search",
"db_cmd": "mmseqs createdb INPUT OUTPUT.fa ; mmseqs createindex OUTPUT.fa /tmp",
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11 changes: 4 additions & 7 deletions scripts_of/program_caller.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,6 @@ def __init__(self, configure_file):
self.tree = dict()
self.search_db = dict()
self.search_search = dict()
# Add default methods
self.msa['mafft'] = Method('mafft', {"cmd_line": "mafft --localpair --maxiterate 1000 --anysymbol INPUT > OUTPUT 2> /dev/null", "cmd_line_fast": "mafft --anysymbol INPUT > OUTPUT 2> /dev/null", "n_seqs_use_fast" : "500"})
self.tree['fasttree'] = Method('fasttree', {"cmd_line": "FastTree INPUT > OUTPUT 2> /dev/null"})
if configure_file == None:
return
if not os.path.exists(configure_file):
Expand All @@ -86,7 +83,7 @@ def __init__(self, configure_file):
continue

if 'program_type' not in v:
print(("WARNING: Incorrecty formatted configuration file entry: %s" % name))
print(("WARNING: Incorrectly formatted configuration file entry: %s" % name))
print("'program_type' entry is missing")
try:
if v['program_type'] == 'msa':
Expand All @@ -101,7 +98,7 @@ def __init__(self, configure_file):
self.tree[name] = Method(name, v)
elif v['program_type'] == 'search':
if ('db_cmd' not in v) or ('search_cmd' not in v):
print(("WARNING: Incorrecty formatted configuration file entry: %s" % name))
print(("WARNING: Incorrectly formatted configuration file entry: %s" % name))
print("'cmd_line' entry is missing")
raise InvalidEntryException
if name in self.search_db:
Expand All @@ -110,10 +107,10 @@ def __init__(self, configure_file):
self.search_db[name] = Method(name, {'cmd_line':v['db_cmd']})
self.search_search[name] = Method(name, {'cmd_line':v['search_cmd']})
if 'ouput_filename' in v:
print(("WARNING: Incorrecty formatted configuration file entry: %s" % name))
print(("WARNING: Incorrectly formatted configuration file entry: %s" % name))
print("'ouput_filename' option is not supported for 'program_type' 'search'")
else:
print(("WARNING: Incorrecty formatted configuration file entry: %s" % name))
print(("WARNING: Incorrectly formatted configuration file entry: %s" % name))
print(("'program_type' should be 'msa' or 'tree', got '%s'" % v['program_type']))
except InvalidEntryException:
pass
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