[emboss-dev] exotic bug
Guy Bottu
Guy.Bottu at skynet.be
Fri May 16 15:04:49 UTC 2014
Dear developers,
I bumped on something that seems a bug (if it is not a feature), but one
that you would not easily detect because it involves an exotic action.
If the output directory has a name that contains a colon and you use the
environment variable EMBOSS_DIRECTORY it fails because the program
should write in xxx:yyy but instead tries to write in the nonexistant
directory yyy. This causes troubles under wEMBOSS with some programs. I
attach an ACD file and the debug file. Note the last lines in the debug
file.
Regards,
Guy Bottu
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-------------- next part --------------
application: psiblast [
documentation: "Iterative BLAST search with generation of profile of
protein sequence against protein sequence set"
groups: "Database Search:Sequence, Protein:Profiles"
embassy: "wrappers4emboss"
]
section: programchoice [
information: "blastall/blastpgp program option"
type: "page"
]
list: mode [
information: "Mode"
help: "Mode. It is possible to restart psiblast with a profile from a
previous run or search a profile against another protein
databank or against a translated nucleic acid databank. You
must together with the profile provide the protein sequence
that was used to obtain the profile."
values: "regular : regular PSI-BLAST run ; restart : restart
PSI-BLAST with profile from previous run ; psitblastn : do
instead search of profile against nucleic acid db"
default: "regular"
]
endsection: programchoice
section: input [
information: "Input section"
type: "page"
]
sequence: seq [
parameter: "Y"
information: "Query sequence"
type: "protein"
]
list: dbtype [
standard: "Y"
information: "Select search set type"
help: "Search set type : public databank or databank provided by
user"
values: "1 : standard set ; 2 : user defined set ; 3 : user provided
BLAST databank"
default: "1"
]
list: nucdb [
standard: "@(@($(dbtype) == 1) & @($(mode) == psitblastn))"
information: "Standard nucleic acid search set"
values: "phg : EMBL bacteriophage section ; vrl : EMBL other viruses section ; vec : Intelligenetics vector databank"
default: "phg"
]
list: protdb [
standard: "@(@($(dbtype) == 1) & @($(mode) != psitblastn))"
information: "Standard protein search set"
values: "sw : SwissProt (including splice variants)"
default: "sw"
]
seqall: userdb [
standard: "@($(dbtype) == 2)"
nullok: "@($(dbtype) != 2)"
information: "User defined search set"
type: "@(@($(mode) == psitblastn) ? nucleotide : protein)"
]
infile: userblastdb [
standard: "@($(dbtype) == 3)"
nullok: "@($(dbtype) != 3)"
information: "User provided BLAST format databank (you can make one
using makeblastdb)"
prompt: "User provided BLAST format databank"
knowntype: "@(@($(mode) == psitblastn) ? nucleotide blast databank :
protein blast databank)"
]
infile: checkin [
standard: "@($(mode) != regular)"
nullok: "@($(mode) == regular)"
information: "BLAST-readable profile"
knowntype: "psiblast checkpoint file"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
integer: wordsize [
standard: "Y"
information: "Word size"
default: "3"
minimum: "2"
maximum: "3"
]
float: expect [
standard: "Y"
information: "E() value cutoff for display"
help: "E() value = number of databank sequences with same or higher
bit score that you expect to find by chance. BLAST lists
sequences with an E() value lower than the cutoff."
default: "10.0"
minimum: "0.0"
]
integer: rounds [
standard: "@($(mode) != psitblastn)"
information: "Maximum number of rounds"
default: "10"
minimum: "1"
]
float: include [
standard: "@(@($(mode) != psitblastn) & @($(rounds) > 1))"
information: "E() value threshold for inclusion in model"
help: "PSI-BLAST uses sequences with an E() value lower than this
threshold for generating a profile."
default: "0.002"
minimum: "0.0"
]
endsection: required
section: additional [
information: "Additional section"
type: "page"
]
list: protalipars [
additional: "Y"
information: "Amino acid comparison matrix, gap penalty, gap length
penalty"
help: "Parameters for making protein alignment : amino acid
comparison matrix, gap penalty, gap length penalty. BLAST
subtracts from the similarity score for each gap a penalty of
type <Gap penalty> + <Gap length penalty> * n. Only certain
combinations of matrix and gap penalty are allowed."
values: "1 : BLOSUM90 6 2 ; 2 : BLOSUM90 7 2 ; 3 : BLOSUM90 8 2 ; 4 :
BLOSUM90 9 1 ; 5 : BLOSUM90 9 2 ; 6 : BLOSUM90 10 1 ; 7 :
BLOSUM90 11 1 ; 8 : BLOSUM80 6 2 ; 9 : BLOSUM80 7 2 ; 10 :
BLOSUM80 8 2 ; 11 : BLOSUM80 9 1 ; 12 : BLOSUM80 9 2 ; 13 :
BLOSUM80 10 1 ; 14 : BLOSUM80 11 1 ; 15 : BLOSUM80 13 2 ; 16
: BLOSUM80 25 2 ; 17 : BLOSUM62 6 2 ; 18 : BLOSUM62 7 2 ;
19 : BLOSUM62 8 2 ; 20 : BLOSUM62 9 1 ; 21 : BLOSUM62 9 2 ;
22 : BLOSUM62 10 1 ; 23 : BLOSUM62 10 2 ; 24 : BLOSUM62 11 1
; 25 : BLOSUM62 11 2 ; 26 : BLOSUM62 12 1 ; 27 : BLOSUM62
13 1 ; 28 : BLOSUM50 9 3 ; 29 : BLOSUM50 10 3 ; 30 :
BLOSUM50 11 3 ; 31 : BLOSUM50 12 2 ; 32 : BLOSUM50 12 3 ; 33
: BLOSUM50 13 2 ; 34 : BLOSUM50 13 3 ; 35 : BLOSUM50 14 2 ;
36 : BLOSUM50 15 1 ; 37 : BLOSUM50 15 2 ; 38 : BLOSUM50 16
1 ; 39 : BLOSUM50 16 2 ; 40 : BLOSUM50 17 1 ; 41 : BLOSUM50
18 1 ; 42 : BLOSUM45 10 3 ; 43 : BLOSUM45 11 3 ; 44 :
BLOSUM45 12 2 ; 45 : BLOSUM45 12 3 ; 46 : BLOSUM45 13 2 ; 47
: BLOSUM45 13 3 ; 48 : BLOSUM45 14 2 ; 49 : BLOSUM45 15 2 ;
50 : BLOSUM45 16 1 ; 51 : BLOSUM45 16 2 ; 52 : BLOSUM45 17
1 ; 53 : BLOSUM45 18 1 ; 54 : BLOSUM45 19 1 ; 55 : PAM30 5 2
; 56 : PAM30 6 2 ; 57 : PAM30 7 2 ; 58 : PAM30 8 1 ; 59 :
PAM30 9 1 ; 60 : PAM30 10 1 ; 61 : PAM70 6 2 ; 62 : PAM70 7
2 ; 63 : PAM70 8 2 ; 64 : PAM70 9 1 ; 65 : PAM70 10 1 ; 66 :
PAM70 11 1 ; 67 : PAM250 11 3 ; 68 : PAM250 12 3 ; 69 :
PAM250 13 2 ; 70 : PAM250 13 3 ; 71 : PAM250 14 2 ; 72 :
PAM250 14 3 ; 73 : PAM250 15 2 ; 74 : PAM250 15 3 ; 75 :
PAM250 16 2 ; 76 : PAM250 17 1 ; 77 : PAM250 17 2 ; 78 :
PAM250 18 1 ; 79 : PAM250 19 1 ; 80 : PAM250 20 1 ; 81 :
PAM250 21 1 ;"
default: "24"
]
list: dbgencode [
additional: "@($(mode) == psitblastn)"
information: "Genetic code for translating databank sequences"
values: "1 : Standard ; 2 : Vertebrate Mitochondrial ; 3 : Yeast
Mitochondrial ; 4 : Mold, Protozoan, Coelenterate
Mitochondrial and Mycoplasma/Spiroplasma ; 5 : Invertebrate
Mitochondrial ; 6 : Ciliate, Dasycladacean and Hexamita ; 9
: Echinoderm Mitochondrial ; 10 : Euplotid ; 11 : Bacterial
; 12 : Alternative Yeast ; 13 : Ascidian Mitochondrial ; 14
: Flatworm Mitochondrial ; 15 : Blepharisma ; 16 :
Chlorophycean Mitochondrial ; 21 : Trematode Mitochondrial ;
22 : Scenedesmus obliquus mitochondrial ; 23 :
Thraustochytrium mitochondrial"
default: "1"
]
list: compstats [
additional: "@($(mode) != psitblastn)"
information: "Adjustment of scoring scheme according to composition"
help: "The E() value can be computed more accurately if the
composition of the sequences being compared is taken into
account. By default the scoring scheme is adjusted as
explained in Bioinformatics 21:902 when an empiric test
suggests this to be beneficial, otherwise the scoring scheme
is rescaled as explained in NAR 29:2994. You can force
psiblast to always use any of both methods or none."
values: "0 : none ; 1 : scale ; 2 : adjust conditionally, otherwise
scale ; 3 : adjust"
default: "2"
]
endsection: additional
section: advanced [
information: "Advanced section"
type: "page"
]
boolean: compfilter [
information: "Filter low complexity segments out of query sequence"
]
boolean: coilfilter [
information: "Filter coiled coils out of query sequence"
]
boolean: softfilter [
needed: "@($(compfilter) | $(coilfilter))"
information: "Use soft filtering"
help: "Use soft filtering, that is, filter only at initial hit
searching, not at hit extension"
]
boolean: doublehit [
information: "Double hit algorithm"
help: "Try to extend hit only if there is a second hit (is default)"
default: "Y"
]
integer: window [
needed: "$(doublehit)"
information: "Multiple hits window size"
default: "40"
minimum: "0"
]
float: effdbsize [
information: "Effective databank size for statistical calculations"
minimum: "0.0"
]
endsection: advanced
section: output [
information: "Output section"
type: "page"
]
integer: keep [
information: "Keep only n best hits from same region"
help: "Keep only n best hits from same region. Default is to show
them all. If you use this option, a value of 100 is
recommended."
minimum: "0"
]
integer: listsize [
information: "Show only the n best scoring sequences that satisfy E()
cutoff"
default: "500"
minimum: "0"
]
integer: align [
information: "Show only alignments for the n first sequences"
default: "@(@($(listsize) < 250 ) ? $(listsize) : 250)"
expected: "250"
minimum: "0"
maximum: "$(listsize)"
failrange: "N"
trueminimum: "Y"
valid: "Integer 0 or more, but not < listsize"
]
list: format [
information: "Alignment format"
additional: "Y"
values: "0 : pairwise ; 1 : query-anchored, showing identities ; 2 :
query-anchored, no identities ; 3 : flat query-anchored,
show identities ; 4 : flat query-anchored, no identities ; 5
: query-anchored, no identities and blunt ends ; 6 : flat
query-anchored, no identities and blunt ends ; 7 : XML Blast
output ; 8 : tabular ; 9 : tabular, with comment lines ; 10
: ASN.1"
default: "0"
]
boolean: fulloutput [
needed: "@(@($(mode) != psitblastn) & @($(rounds) > 1))"
information: "Show output of all rounds"
]
outfile: outfile [
parameter: "Y"
extension: "@(@($(mode) == psitblastn) ? psitblastn : psiblast)"
knowntype: "blast output"
]
toggle: makeasciiout [
needed: "@($(mode) != psitblastn)"
information: "Make output file with profile in ASCII format"
help: "Make output file with profile in ASCII format (can only be
done if number of rounds is 2 or more)"
]
outfile: asciiout [
standard: "$(makeasciiout)"
nullok: "@(!$(makeasciiout))"
nulldefault: "@(!$(makeasciiout))"
information: "Name output file with profile in ASCII format"
prompt: "Output file with profile"
name: "$(outfile)"
extension: "profile"
]
toggle: makecheckout [
needed: "@($(mode) != psitblastn)"
information: "Make output file with profile in BLAST-readable format
for restarting search"
help: "Make output file with profile in BLAST-readable format for
restarting search (can only be done if number of rounds is 2
or more)"
]
outfile: checkout [
standard: "$(makecheckout)"
nullok: "@(!$(makecheckout))"
nulldefault: "@(!$(makecheckout))"
information: "Name output file with profile in BLAST-readable format"
prompt: "BLAST-readable output file with profile"
name: "$(outfile)"
extension: "check"
knowntype: "psiblast checkpoint file"
]
endsection: output
-------------- next part --------------
ajNamGetValueC 'debugbuffer'
ajNamGetValueC search for 'EMBOSS_DEBUGBUFFER': EMBOSS_DEBUGBUFFER not found
Debug file psiblast.dbg buffered:No
ajAcdInitPV pgm 'psiblast' package ''
version '6.6.0.0' system 'Linux'
ajNamGetValueC 'acdroot'
ajNamGetValueC search for 'EMBOSS_ACDROOT': EMBOSS_ACDROOT not found
ajFileNewInNameS '/OPT/emboss66/share/EMBOSS/acd/psiblast.acd'
EOF ajFileGetsL file /OPT/emboss66/share/EMBOSS/acd/psiblast.acd
ajNamGetValueC 'language'
ajNamGetValueC search for 'EMBOSS_LANGUAGE': EMBOSS_LANGUAGE not found
ajNamGetValueC 'acdroot'
ajNamGetValueC search for 'EMBOSS_ACDROOT': EMBOSS_ACDROOT not found
ajFileNewInNameS '/OPT/emboss66/share/EMBOSS/acd/codes.english'
EOF ajFileGetsL file /OPT/emboss66/share/EMBOSS/acd/codes.english
ajNamGetValueC 'acdroot'
ajNamGetValueC search for 'EMBOSS_ACDROOT': EMBOSS_ACDROOT not found
ajFileNewInNameS '/OPT/emboss66/share/EMBOSS/acd/knowntypes.standard'
EOF ajFileGetsL file /OPT/emboss66/share/EMBOSS/acd/knowntypes.standard
ajNamGetValueC 'timetoday'
ajNamGetValueC search for 'EMBOSS_TIMETODAY': EMBOSS_TIMETODAY not found
Set acdprotein value '$(seq.protein)'
ajNamGetValueC 'stdout'
ajNamGetValueC search for 'EMBOSS_STDOUT': EMBOSS_STDOUT not found
ajNamGetValueC 'filter'
ajNamGetValueC search for 'EMBOSS_FILTER': EMBOSS_FILTER not found
ajNamGetValueC 'options'
ajNamGetValueC search for 'EMBOSS_OPTIONS': EMBOSS_OPTIONS not found
ajNamGetValueC 'debugbuffer'
ajNamGetValueC search for 'EMBOSS_DEBUGBUFFER': EMBOSS_DEBUGBUFFER not found
ajNamGetValueC 'verbose'
ajNamGetValueC search for 'EMBOSS_VERBOSE': EMBOSS_VERBOSE not found
ajNamGetValueC 'help'
ajNamGetValueC search for 'EMBOSS_HELP': EMBOSS_HELP not found
ajNamGetValueC 'warning'
ajNamGetValueC search for 'EMBOSS_WARNING': EMBOSS_WARNING not found
ajNamGetValueC 'error'
ajNamGetValueC search for 'EMBOSS_ERROR': EMBOSS_ERROR not found
ajNamGetValueC 'fatal'
ajNamGetValueC search for 'EMBOSS_FATAL': EMBOSS_FATAL not found
ajNamGetValueC 'die'
ajNamGetValueC search for 'EMBOSS_DIE': EMBOSS_DIE not found
ajNamGetValueC 'version'
ajNamGetValueC search for 'EMBOSS_VERSION': EMBOSS_VERSION not found
ajSeqinClear called
ajTextinClear called
ajFeattabinClear called Local:No
ajTextinClear called
ajNamGetValueC 'format'
ajNamGetValueC search for 'EMBOSS_FORMAT': EMBOSS_FORMAT not found
ajSeqRead: no file yet - test USA 'sw:papa1_carpa'
seqinUsaProcess 'sw:papa1_carpa'
++ajQuerystrParseFormat 'sw:papa1_carpa'
seqinUsaProcess ... fmtstr '<null>' 'sw:papa1_carpa'
ajQuerystrParseRange: 'sw:papa1_carpa'
seqinUsaProcess ... range 0..0 rev:No 'sw:papa1_carpa'
++ajQuerystrParseListfile 'sw:papa1_carpa'
seqinUsaProcess ... no listfile 'sw:papa1_carpa'
ajQuerystrParseRead qry 'sw:papa1_carpa' iquery '' ioffset '0' format: '' (0)
query to test: 'sw:papa1_carpa'
server dbexp: Yes 'sw:papa1_carpa'
unknown server sw, try dbname
entry-id regexp: No
filetest regexp queryRegFieldId: No 'sw:papa1_carpa'
entry-id regexp: Yes
filetest regexp queryRegId: Yes 'sw:papa1_carpa'
queryRegId 'sw'
queryDbfind db: 'sw' svr: '<null>'
regstat: Yes qry 'sw:papa1_carpa' iquery '' queryDB: 'sw' dbstat: Yes open: '' close: '' field: '<null>' qryfields: 'papa1_carpa'
found dbname 'sw' level: '<null>' qryfields: 'papa1_carpa'
namInformatTest format 'swiss' dbtype 'Protein' namtype 'Protein'
seqinFormatFind 'swiss'
Query qryfields: 'papa1_carpa' open: '' close: '' inbraces: No
database type: 'Protein' format 'swiss' 5 textformat 0
file Qry 'papa1_carpa' Field '<null>' hasAcc:Yes queryChr ':'
query processing: simple id 'papa1_carpa'
ajNamDbQuery SetQuery:No QueryType:1
ajQuerySetWild fields: 0
wildcard in stored query: No
namMethod2Qlinks method: 'emboss' datatype: 1 text: '|&!^='
ajQueryfieldNewC 'id' 'papa1_carpa'
ajQueryAddFieldOrC.d 'id' 'papa1_carpa'
ajQueryKnownFieldC qry 'acc' fields 'id acc key des org'
ajQueryKnownFieldC match 'acc'
ajQueryfieldNewC 'acc' 'papa1_carpa'
ajQueryAddFieldElseC.d 'acc' 'papa1_carpa'
ajQueryKnownFieldC qry 'sv' fields 'id acc key des org'
ajQuerySetWild fields: 2
test1 query id 'papa1_carpa' 0
test2 query id 'papa1_carpa'
test2 query acc 'papa1_carpa'
wildcard in stored query: No
Query Trace
DbName: 'sw'
DbType: 'Protein' (1)
id: 'papa1_carpa' 0 (init)
acc: 'papa1_carpa' 5 (ELSE)
Case-sensitive Id: 'No'
Has accession: Yes
Method: 'emboss'
Formatstr: 'swiss'
IndexDir: '/OPT/sequences/swissprot'
Directory: '/OPT/sequences/swissprot'
DbFields: 'id acc key des org'
QryString: 'sw:papa1_carpa'
QryFields: 'papa1_carpa'
Fpos: 0
QryDone: No
Wildcard in query: No
try TEXT access by method 'emboss'
textAccessEmboss type 1 Single:No Count:0 Multi:No QryData:0
ajFileNewInNameS '/OPT/sequences/swissprot/sw.pxid'
EOF ajFileGetsL file /OPT/sequences/swissprot/sw.pxid
ajFileNewInNameS '/OPT/sequences/swissprot/sw.ent'
EOF ajFileGetsL file /OPT/sequences/swissprot/sw.ent
ajFileNewInNameS '/OPT/sequences/swissprot/sw.pxid'
EOF ajFileGetsL file /OPT/sequences/swissprot/sw.pxid
ajFileNewInNameS '/OPT/sequences/swissprot/sw.pxac'
EOF ajFileGetsL file /OPT/sequences/swissprot/sw.pxac
directory '/OPT/sequences/swissprot' query: 'id:papa1_carpa ELSE acc:papa1_carpa'
textEmbossQryEntry fields: 2 hasacc:Yes
link: 0 list: 0
link: 5 list: 1
B+tree Entry success list:1
textEmbossQryNext list 1 skip:No
ajFileNewInNameS '/OPT/sequences/swissprot/uniprot_sprot.dat'
textEmbossQryNext returned Yes list 0 samefile No
textEmbossQryClose clean up qryd
textAccessEmboss db: 'sw' returns: Yes
... input format value 'swiss'
seqinFormatFind 'swiss'
...format OK 'swiss' = 5
seqinUsaProcess ... read nontext: No 'sw:papa1_carpa'
seqinUsaProcess text method 'emboss' success
ajTextinClearNewfile called
seqRead: cleared Single:Yes Count:0 SeqData:0 TextData:0
seqRead: seqin format 5 'swiss'
ajFilebuffClear (1) Nobuff: No size: 1
seqRead: one format specified
ajFilebuffSetUnbuffered '/OPT/sequences/swissprot/uniprot_sprot.dat' fsize: 1
++seqRead known format 5
++seqReadFmt format 5 (swiss) 'sw:papa1_carpa' feat No
ajTextinClearNewinput called
seqReadSwiss first line 'ID PAPA1_CARPA Reviewed; 345 AA.
'
seqSetName word 'PAPA1_CARPA'
seqSetName 'PAPA1_CARPA' result: 'PAPA1_CARPA'
ajNamGetValueC 'timetoday'
ajNamGetValueC search for 'EMBOSS_TIMETODAY': EMBOSS_TIMETODAY not found
ajNamGetValueC 'timetoday'
ajNamGetValueC search for 'EMBOSS_TIMETODAY': EMBOSS_TIMETODAY not found
ajNamGetValueC 'timetoday'
ajNamGetValueC search for 'EMBOSS_TIMETODAY': EMBOSS_TIMETODAY not found
ajFilebuffClear (0) Nobuff: Yes size: 1
seqReadFmt success with format 5 (swiss)
id: 'PAPA1_CARPA' len: 345
seqQueryMatch 'PAPA1_CARPA' fields: 2 Case No Done Yes
seqQueryMatch Features:No FtTable: 0 (0)
testing sequence 'PAPA1_CARPA' 'MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFES' type 'protein' IsNuc No IsProt No
seqTypeSet 'Protein'
ajSeqTypeCheckIn type 'protein' found (protein sequence)
Remove all gaps
ajSeqIsProt Type 'P'
ajSeqTypeCheckIn: bad characters test passed, convert
Convert '?*' to 'XX'
ajSeqTypeCheckIn: OK - no badchars
++seqRead OK (2), set format 5
ajSeqRead: new usa: 'sw:papa1_carpa' returns: Yes
ajNamGetValueC 'acdfilename'
ajNamGetValueC search for 'EMBOSS_ACDFILENAME': EMBOSS_ACDFILENAME not found
ajSeqIsNuc Type 'P'
ajSeqIsNuc Type 'P'
ajSeqIsProt Type 'P'
ajSeqGetUsa '<null>'
seqMakeUsa (Name <PAPA1_CARPA> Formatstr <swiss> Db <sw> Entryname <PAPA1_CARPA> Filename <>)
Begin:0 End:0 Rev:No Reversed:No
result: <sw-id:PAPA1_CARPA>
ajSeqinDel called usa:'sw:papa1_carpa'
ajTextinDel called qry:'sw:papa1_carpa' filebuff: 23cdc80
ajQueryDel db:'sw' svr: '' fields:2
textAccessFreeEmboss
textEmbossQryClose clean up qryd
ajFilebuffDel '/OPT/sequences/swissprot/uniprot_sprot.dat' fp: 24b1480 size:0
ajFilebuffClear (-1) Nobuff: Yes size: 0
ajTextinDel called qry:'' filebuff: 0
ajQueryDel db:'' svr: '' fields:0
ajSeqallDel
ajSeqinDel called usa:''
ajTextinDel called qry:'' filebuff: 0
ajQueryDel db:'' svr: '' fields:0
ajTextinDel called qry:'' filebuff: 0
ajQueryDel db:'' svr: '' fields:0
ajNamGetValueC 'outdirectory'
ajNamGetValueC search for 'EMBOSS_OUTDIRECTORY': Found environment variable value 'xxx:yyy'
ajWarn: Warning: Failed to open output file 'yyy/papa1_carpa.psiblast.profile' error:2 'No such file or directory'
ajVErr: Error: Unable to open file 'yyy/papa1_carpa.psiblast.profile' for output
ajDie: Died: psiblast terminated: Bad value for '-asciiout' with -auto defined
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