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1 MODULE flat2asn
2 $$ FORMAT, 1
3 $^ NonAsciiChar, 1, SEV_ERROR
4 # This is a comment REJECT(LANL,EMBL,DDBJ,PIR,SP)
5 No column of any block of the flat file in any of the formats
6 is allowed to have a nonASCII character. NonASCII is defined
7 as anything greater than decimal value 126 (`~`) or less than
8 decimal 32 (space) except decimal 10, which is a newline.
9 $^ MissingEnd, 2, SEV_ERROR
10 The // line was not found after sequence was found before a line
11 with an letter was found. Likely to be a truncated entry.
12 $^ MissingField, 3, SEV_ERROR
13 Required field was not found in the flat file
14 $^ LocusLinePosition, 4, SEV_ERROR
15 The GenBank flat file format requires fixed column positions
16 for a variety of fields. The following are the fields and
17 the columns that are expected:
18 bp 31-32 literally, "bp"
19 Strand 34-36
20 This must be blank or ss-, ds-, ms-};
21 Molecule type 37-40
22 This must be blank or DNA , RNA , pre-mRNA, mRNA,
23 rRNA, tRNA, uRNA, or scRNA.
24 Topology 43-52
25 Circular, may be specified or it may be blank
26 ("Tandem???")
27 Division 53-55
28 Legal division codes are: PRI, ROD, MAM, VRT, INV, PLN,
29 BCT, RNA, VRL, PHG, SYN, UNA, or EST.
30 (blank???)
31 New or mispelled Embl divisions will be reported with a
32 DIVISION_NewDivCode error code. Note that EMBL uses FUN.
33 Date 63-73, and be in dd-mmm-yyyy format.
34 $^ DirSubMode, 5, SEV_WARNING
35 Not standard EMBL format, used in DirSubMode only
36 $^ LineTypeOrder, 6, SEV_WARNING
37 $^ MissingSequenceData, 7, SEV_ERROR
38 $^ ContigWithSequenceData, 8, SEV_ERROR
39 $^ MissingContigFeature, 9, SEV_ERROR
40 $^ MissingSourceFeature, 10, SEV_ERROR
41 $^ MultipleCopyright, 11, SEV_WARNING
42 $^ MissingCopyright, 12, SEV_ERROR
43 $^ MultiplePatRefs, 13, SEV_ERROR
44 $$ DATACLASS, 2
45 $^ UnKnownClass, 1, SEV_WARNING
46 Swissprot error, only standard and preliminary are allowed.
47 $$ ENTRY, 3
48 $^ ParsingComplete, 2, SEV_INFO
49 $^ Begin, 3, SEV_ERROR
50 Looking for valid begining according to -f arguement in command line:
51 LOCUS for GenBank; ID for EMBL; ENTRY for PIR;
52 $^ Skipped, 6, SEV_ERROR
53 $^ Repeated, 7, SEV_WARNING
54 $^ LongSequence, 8, SEV_ERROR
55 $^ THC_Sequence, 9, SEV_WARNING
56 $^ Parsed, 10, SEV_INFO
57 $^ ParsingSetup, 11, SEV_INFO
58 $^ GBBlock_not_Empty, 12, SEV_WARNING
59 $^ LongHTGSSequence, 13, SEV_WARNING
60 $$ DATE, 5
61 $^ IllegalDate, 2, SEV_WARNING
62 Date not in dd-mmm-yyy format
63 $$ SEQUENCE, 7
64 $^ UnknownBaseHTG3, 1, SEV_WARNING
65 $^ SeqLenNotEq, 2, SEV_WARNING
66 The declared length of the sequence in the record was not
67 equal to the acutal number of residues found.
68 $^ BadResidue, 3, SEV_ERROR
69 Depending upon whether nucleic acid or protein, there are
70 different single letter legal codes.
71 $^ BadData, 4, SEV_WARNING
72 Can't parse the entry because of bad sequence data.
73 $$ SEGMENT, 8
74 $^ MissSegEntry, 1, SEV_ERROR
75 The Segmented set (GenBank) that is declared has some
76 missing members. That is, if there 6 members declared,
77 The set might only have:
78 1 of 6,
79 2 of 6,
80 4 of 6,
81 5 of 6 and
82 6 of 6, and thus be missing 3 of 6.
83 Another possible problem is there could be a line:
84 "3 of 5", instad of "3 of 6"
85 $^ DiffMolType, 2, SEV_WARNING
86 A segmented set is supposed to be from the same molecule,
87 but with some unknown regions. It should therefore all be
88 of the same type of molecule. For this error to occur, there
89 have to be different molecule types for different segments
90 within the set.
91 $^ BadLocusName, 3, SEV_ERROR
92 For GenBank in a segmented set, it is an error if the segment number
93 can not be found at the end of the LOCUS name. So a LOCUS name
94 in SEGMENT 2 of 10 must end in 02, as ABCD02.
95 $^ IncompSeg, 4, SEV_ERROR
96 There were not three blank-separated token on the SEGMENT line, in
97 GenBank Flat File format, the segment line has to look like:
98 SEGMENT 4 of 14
99 for example.
100 $^ PubMatch, 5, SEV_WARNING
101 There were matching reference with different serial numbers in
102 segments.
103 $^ OnlyOneMember, 6, SEV_WARNING
104 $^ Rejected, 7, SEV_WARNING
105 $$ ACCESSION, 9
106 $^ BadAccessNum, 2, SEV_ERROR
107 Accession must be upper case letter followed by 5 digits.
108 $^ NoAccessNum, 3, SEV_ERROR
109 No accession number could be found for this entry. The line number
110 given is only approximate.
111 $^ MoreAccessLine, 4, SEV_INFO
112 More than one accession block was found. Continuation lines with
113 the wrong format can cause this in GenBank format.
114 $^ ForeignAccessNum, 5, SEV_WARNING
115 $$ LOCUS, 10
116 $^ WrongTopology, 2, SEV_WARNING
117 This message occurs when looking for either Circular or 'RNA' or 'DNA' in
118 embl mode. Anything other than this will cause this warning.
119 $^ NoGIBBModMolType, 3, SEV_WARNING
120 In the flat files, the only legal values are blank, RNA, pre-mRNA, mRNA,
121 rRNA, tRNA, uRNA, ss-RNA, ds-RNA, ms-RNA, scRNA, DNA, ds-DNA, and ss-DNA
122 $^ MayBeNewSpeciesCode, 4, SEV_WARNING
123 Swiss-Prot specific error. The species is not in the list of
124 LOCUS name prefix-species pairs.
125 $^ NoSpeciesCode, 5, SEV_WARNING
126 Swiss-Prot error when no species can be found.
127 $^ NoMolType, 6, SEV_WARNING
128 Can't find Molecule type
129 $^ BadLocusName, 7, SEV_ERROR
130 There are multiple possible ways to get this error message.
131 In all formats, this identifier must have either digits or
132 uppercase letters.
133 For Swiss-Prot, the rules are more complicated:
134 Locus name consists of up to 10 uppercase alphanumeric characters
135 rule: X_Y format
136 X is a mnemonic code, up to 4 alphanumeric characters to represent
137 the protein name.
138 Y is a mnemonic species identification code of at most 5
139 alphanumeric characters to representing the biological source of
140 the protein
141 $^ NoLocusName, 8, SEV_ERROR
142 No token after 'LOCUS' found in GenBank format.
143 $^ NonViralRNAMoltype, 9, SEV_ERROR
144 $$ ORGANISM, 11
145 $^ NoOrganism, 1, SEV_WARNING
146 EMBL: no OS line found
147 GenBank: No ORGANISM line in the SOURCE block.
148 This message might repeat which trying to guess genetic code.
149 $^ HybridOrganism, 2, SEV_WARNING
150 In EMBL format only, can have multiple organisms (OS blocks).
151 If the taxonomy changes (OC block), this warning is produced.
152 $^ Unclassified, 3, SEV_WARNING
153 $^ MissParen, 4, SEV_WARNING
154 In EMBL format missing parenthesis after common name
155 $^ UnknownReplace, 5, SEV_INFO
156 $^ DoesntMatchFeats, 6, SEV_ERROR
157 $$ KEYWORD, 12
158 $^ MultipleHTGPhases, 1, SEV_ERROR
159 $^ ESTSubstring, 2, SEV_WARNING
160 $^ STSSubstring, 3, SEV_WARNING
161 $^ GSSSubstring, 4, SEV_WARNING
162 $$ DIVISION, 13
163 $^ NewDivCode, 1, SEV_WARNING
164 EMBL only (GenBank format related error is a FORMAT.LocusLinePosition
165 error), and the legal codes are:
166 FUN, INV, MAM, ORG, PHG, PLN, PRI, PRO, ROD, SYN,
167 UNA, VRL, VRT, and UNC (UNA == UNC)
168 $^ MappedtoEST, 2, SEV_INFO
169 KW line maps one of these words:
170 "EST", "EST PROTO((expressed sequence tag)", "expressed sequence tag",
171 "partial cDNA sequence", "transcribed sequence fragment", "TSR",
172 "putatively transcribed partial sequence", "UK putts" };
173 GB-block.div becomes "EST"
174 $^ MappedtoPAT, 3, SEV_WARNING
175 $^ MappedtoSTS, 4, SEV_WARNING
176 $^ Mismatch, 5, SEV_WARNING
177 $^ MissingESTKeywords, 6, SEV_WARNING
178 $^ MissingSTSKeywords, 7, SEV_WARNING
179 $^ MissingPatentRef, 8, SEV_WARNING
180 $^ PATHasESTKeywords, 9, SEV_WARNING
181 $^ PATHasSTSKeywords, 10, SEV_WARNING
182 $^ PATHasCDSFeature, 11, SEV_INFO
183 $^ STSHasCDSFeature, 12, SEV_WARNING
184 $^ NotMappedtoSTS, 13, SEV_WARNING
185 $^ ESTHasSTSKeywords, 14, SEV_INFO
186 $^ ESTHasCDSFeature, 15, SEV_WARNING
187 $^ NotMappedtoEST, 16, SEV_WARNING
188 $^ ShouldBeHTG, 17, SEV_ERROR
189 $^ MissingGSSKeywords, 18, SEV_INFO
190 $^ GSSHasCDSFeature, 19, SEV_WARNING
191 $^ NotMappedtoGSS, 20, SEV_WARNING
192 $^ MappedtoGSS, 21, SEV_WARNING
193 $^ PATHasGSSKeywords, 22, SEV_WARNING
194 $^ LongESTSequence, 23, SEV_WARNING
195 $^ LongSTSSequence, 24, SEV_WARNING
196 $^ LongGSSSequence, 25, SEV_WARNING
197 $^ GBBlockDivision, 26, SEV_WARNING
198 $^ MappedtoCON, 27, SEV_WARNING
199 $^ MissingHTGKeywords, 28, SEV_WARNING
200 $^ ShouldNotBeHTG, 29, SEV_ERROR
201 $^ ConDivInSegset, 30, SEV_ERROR
202 $^ ConDivLacksContig, 31, SEV_WARNING
203 $^ WrongHTGKeyword, 32, SEV_ERROR
204 $$ DEFINITION, 15
205 $^ HTGNotInProgress, 1, SEV_WARNING
206 $^ DifferingRnaTokens, 2, SEV_WARNING
207 $^ HTGShouldBeComplete, 3, SEV_ERROR
208 $$ REFERENCE, 16
209 $^ IllegPageRange, 3, SEV_WARNING
210 There are many classes of problems that can give this error message, some
211 of which are really warnings to have a human take a closer look.
212 $^ UnkRefRcToken, 4, SEV_WARNING
213 There are a limited number of valid Swiss-Prot Reference Comment
214 (RC line) tokens. This one is not one.
215 $^ UnkRefSubType, 5, SEV_WARNING
216 Illegal Swiss-prot Reference SubType.
217 $^ IllegalFormat, 6, SEV_WARNING
218 $^ IllegalAuthorName, 7, SEV_WARNING
219 $^ YearEquZero, 8, SEV_WARNING
220 $^ IllegalDate, 9, SEV_WARNING
221 $^ Patent, 10, SEV_WARNING
222 $^ Thesis, 12, SEV_WARNING
223 $^ Book, 14, SEV_WARNING
224 $^ DirectSubmission, 15, SEV_WARNING
225 $^ Illegalreference, 16, SEV_ERROR
226 $^ Fail_to_parse, 17
227 $^ No_references, 18, SEV_ERROR
228 $^ Xtratext, 19, SEV_WARNING
229 $^ InvalidInPress, 22, SEV_WARNING
230 $^ EtAlInAuthors, 24, SEV_WARNING
231 $^ NonDigitInPages, 25, SEV_WARNING
232 $^ LargePageRange, 26, SEV_WARNING
233 Total pages more than .... means that the total number in the
234 article is greater than normal. This
235 is usually caused by a typographical error.
236 $^ InvertPageRange, 27, SEV_WARNING
237 Page number may invert . . . it looks like the first page is greater
238 that the last page.
239 $^ SingleTokenPageRange, 28, SEV_WARNING
240 $^ MissingBookPages, 29, SEV_WARNING
241 $^ MissingBookAuthors, 30, SEV_WARNING
242 $^ DateCheck, 31, SEV_WARNING
243 $^ GsdbRefDropped, 32, SEV_WARNING
244 $^ UnusualBookFormat, 33, SEV_WARNING
245 $$ FEATURE, 17
246 $^ MultFocusedFeats, 1, SEV_ERROR
247 $^ ExpectEmptyComment, 6, SEV_WARNING
248 specific Swiss-Prot message for INIT_MET feature
249 $^ DiscardData, 7, SEV_WARNING
250 includes unbalance double quote
251 $^ InValidEndPoint, 9, SEV_WARNING
252 $^ MissManQual, 10, SEV_WARNING
253 $^ NoFeatData, 11, SEV_WARNING
254 $^ NoFragment, 12, SEV_WARNING
255 $^ NotSeqEndPoint, 13, SEV_WARNING
256 $^ OldNonExp, 15, SEV_WARNING
257 $^ PartialNoNonTer, 16, SEV_WARNING
258 $^ Pos, 17, SEV_WARNING
259 $^ TooManyInitMet, 20, SEV_WARNING
260 specific Swiss-Prot error message
261 $^ UnEqualEndPoint, 22, SEV_WARNING
262 $^ UnknownFeatKey, 23, SEV_WARNING
263 $^ UnknownQualSpelling, 24, SEV_WARNING
264 $^ LocationParsing, 30, SEV_ERROR
265 $^ FeatureKeyReplaced, 32, SEV_WARNING
266 $^ Dropped, 33, SEV_ERROR
267 $^ UnknownDBName, 36, SEV_WARNING
268 $^ Duplicated, 37, SEV_WARNING
269 $^ NoSource, 38, SEV_WARNING
270 $^ MultipleSource, 39, SEV_WARNING
271 $$ LOCATION, 18
272 $^ FailedCheck, 1, SEV_WARNING
273 $^ MixedStrand, 2, SEV_WARNING
274 $$ GENENAME, 19
275 $^ IllegalGeneName, 1, SEV_WARNING
276 $^ DELineGeneName, 2, SEV_WARNING
277 $$ BIOSEQSETCLASS, 20
278 $^ NewClass, 1, SEV_INFO
279 $$ CDREGION, 21
280 $^ FrameNotSet, 1, SEV_WARNING
281 $^ InternalStopCodonFound, 2, SEV_WARNING
282 $^ NoProteinSeq, 6, SEV_WARNING
283 $^ TerminalStopCodonMissing, 7, SEV_WARNING
284 $^ TranslationDiff, 8, SEV_WARNING
285 $^ TranslationsAgree, 9, SEV_INFO
286 $^ IllegalStart, 10, SEV_WARNING
287 This error is caused by the start of translation being an unrecognized
288 initiation codon when the CDS is not recognized as partial. Usually,
289 one adds '<' or '>' on the locations to accurately reflect the biology
290 and remove this error. On rare occasions, a /partial should be added.
291 $^ GeneticCodeDiff, 11, SEV_WARNING
292 Genetic code returned by Taxonomy server is different from /transl_table
293 $^ UnevenLocation, 12, SEV_WARNING
294 $^ ShortProtein, 13, SEV_WARNING
295 $^ GeneticCodeAssumed, 14, SEV_WARNING
296 $^ NoTranslationCompare, 15, SEV_WARNING
297 $^ TranslationAdded, 16, SEV_INFO
298 $^ InvalidGcodeTable, 17, SEV_WARNING
299 $^ ConvertToImpFeat, 18, SEV_ERROR
300 $^ BadLocForTranslation, 19, SEV_ERROR
301 $^ LocationLength, 20, SEV_WARNING
302 $^ TranslationOverride, 21, SEV_WARNING
303 $^ FoundBadPIDType, 22, SEV_ERROR
304 $^ FoundBadPIDNumber, 23, SEV_RROR
305 $^ InvalidDb_xref, 24, SEV_ERROR
306 $^ TooManyDbxref, 25, SEV_ERROR
307 $^ Multiple_PID, 28, SEV_WARNING
308 $$ GENEREF, 22
309 $^ GeneIntervalOverlap, 1, SEV_WARNING
310 $^ NoUniqMaploc, 2, SEV_WARNING
311 $$ PROTREF, 23
312 $^ NoNameForProtein, 1, SEV_WARNING
313 $$ SEQID, 24
314 $^ NoSeqId, 1, SEV_ERROR
315 $$ SERVER, 26
316 $^ NotUsed, 1, SEV_WARNING
317 No protein translation sequence or organism name has been checked;
318 Could not guess the genetic code, standard code used.
319 $^ Failed, 2, SEV_ERROR
320 Call for Taxonomy or/and Medline service failed.
321 $^ GcFromSuppliedLineage, 6, SEV_WARNING
322 $^ TaxNameWasFound, 7, SEV_INFO
323 $$ NCBI_GI, 27
324 $^ BadDataFormat, 1, SEV_ERROR
325 $$ SPROT, 28
326 $^ DRLine, 1, SEV_WARNING
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