Commit 0aa697dd authored by Laros's avatar Laros
Browse files

Started on the TRM, therefore the separate files Db.txt and errorcodes.txt have

vanished. Fixed a large number of bugs.

Db.txt, errorcodes.txt:
- Renamed and converted to LaTeX.

bibliography.bib:
- Added references for the TRM.

TechnicalReference.tex:
- Documented a large part of the modules.

Mutalyzer.py:
- Added a __formatRange() function for better output of a range.
- Added a __checkIntronPosition() function that checks the validity of an 
  intronic notation.
- Fixed a bug that made a change in the first 9 nucleotides result in an
  unknown protein description.
- Modified the error- and warning messages for large strings (see Mutator.py)
  and ranges.
- Added a filter for indexing by protein isoform.

Mutator.py:
- Replaced the calculation of restriction sites using sets with code that does
  so using multisets. This allows the deletion of a site while an other site
  with the same name remains to be detected. Restriction sites are also
  reported in a more compact way.
- Extracted the part of the visualisation where large strings are represented
  by their pre- and suffix and a number of omitted nucleotides. This is now
  available as a function visualiseLargeString().

Parser.py:
- Separated the visualisation of a parse error from the error message. The 
  visualisation is now put in the output object as "parseError".

Output.py:
- Added documentation.

GBparser.py:
- Moved the reverse-complement logic for the __findMismatch() function to the
  function itself.
- Added an extra check for retrieving slicing information.
- Added a filter for poorly annotated exons.
- Added documentation.

Retriever.py:
- Added file type information (for lrg and gb files).
- Added sanity checks for the snpConvert() function.
- Added documentation.

GenRecord.py:
- Added a new type "construction" to the linking methods, meaning that the
  mRNA is generated from the CDS.

Web.py:
- Added an email variable for output to the website.

index.py:
- Added error information, to hide parts of the output.
- Added file type information (see Retriever.py) to make download links more
  sensible.
- Modified the syntax checker to work with the new parser output (see
  Parser.py).
- Fixed a bug (selecting the human build) in the position converter.
- Renamed download() to webservices().
- Renamed ConversionChecker to PositionConverter.

disclaimer.html:
- Added.

check.html:
- Modified the template to work with the new restriction site format and the
  new parse error format.
- Made lots of things conditional.

skel.html:
- Added.

snp.html:
- Added an example.

menu.html:
- Modified the layout, added some links, etc.

Other templates:
- Mainly edited the layout and indentation.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@75 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
parent 63031896
-- hg19 & hg18 databases
--------
-- The initial mapping table was created using the following command
---
USE hg19;
\subsubsection{Creating the user}
\begin{verbatim}
CREATE USER mutalyzer;
\end{verbatim}
\subsubsection{Creating the mapping databases}
\paragraph{Human genome build 18}
The table definitions of \texttt{refLink}, \texttt{refGene} and
\texttt{gbStatus} and their content can be found at \\
\verb#http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/#.
\vbox{
\begin{verbatim}
CREATE DATABASE hg18;
GRANT ALL PRIVILEGES ON hg18.* TO mutalyzer;
FLUSH PRIVILEGES;
\end{verbatim}
}
\vbox{
\begin{verbatim}
USE hg18;
CREATE TABLE map
SELECT DISTINCT acc, version, txStart, txEnd, cdsStart, cdsEnd, exonStarts,
exonEnds, name2 AS geneName, chrom, strand, protAcc
SELECT DISTINCT acc, version, txStart, txEnd, cdsStart,
cdsEnd, exonStarts, exonEnds, name2
AS geneName, chrom, strand, protAcc
FROM gbStatus, refGene, refLink
WHERE type = "mRNA"
AND refGene.name = acc
AND acc = mrnaAcc;
---
\end{verbatim}
}
\vbox{
\begin{verbatim}
CREATE TABLE map_cdsBackup LIKE map;
\end{verbatim}
}
\vbox{
\begin{verbatim}
CREATE TABLE ChrName (
AccNo CHAR(20) PRIMARY KEY,
name CHAR(20) NOT NULL
);
\end{verbatim}
}
\vbox{
\begin{verbatim}
INSERT INTO ChrName (AccNo, name) VALUES
("NC_000001.9", "chr1"),
("NC_000002.10", "chr2"),
("NC_000003.10", "chr3"),
("NC_000004.10", "chr4"),
("NC_000005.8", "chr5"),
("NC_000006.10", "chr6"),
("NC_000007.12", "chr7"),
("NC_000008.9", "chr8"),
("NC_000009.10", "chr9"),
("NC_000010.9", "chr10"),
("NC_000011.8", "chr11"),
("NC_000012.10", "chr12"),
("NC_000013.9", "chr13"),
("NC_000014.7", "chr14"),
("NC_000015.8", "chr15"),
("NC_000016.8", "chr16"),
("NC_000017.9", "chr17"),
("NC_000018.8", "chr18"),
("NC_000019.8", "chr19"),
("NC_000020.9", "chr20"),
("NC_000021.7", "chr21"),
("NC_000022.9", "chr22"),
("NC_000023.9", "chrX"),
("NC_000024.8", "chrY"),
("NC_001807.4", "chrM"),
("NT_113891.1", "chr6_cox_hap1"),
("NT_113959.1", "chr22_h2_hap1");
\end{verbatim}
}
\paragraph{Human genome build 19}
The table definitions of \texttt{refLink}, \texttt{refGene} and
\texttt{gbStatus} and their content can be found at \\
\verb#http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/#.
\vbox{
\begin{verbatim}
CREATE DATABASE hg19;
GRANT ALL PRIVILEGES ON hg19.* TO mutalyzer;
FLUSH PRIVILEGES;
\end{verbatim}
}
-- We need an auxillary table for updated entries where the version numbers are
-- not increased.
\vbox{
\begin{verbatim}
USE hg19;
CREATE TABLE map
SELECT DISTINCT acc, version, txStart, txEnd, cdsStart,
cdsEnd, exonStarts, exonEnds, name2
AS geneName, chrom, strand, protAcc
FROM gbStatus, refGene, refLink
WHERE type = "mRNA"
AND refGene.name = acc
AND acc = mrnaAcc;
\end{verbatim}
}
---
\vbox{
\begin{verbatim}
CREATE TABLE map_cdsBackup LIKE map;
---
\end{verbatim}
}
\vbox{
\begin{verbatim}
CREATE TABLE ChrName (
AccNo CHAR(20) PRIMARY KEY,
name CHAR(20) NOT NULL
);
\end{verbatim}
}
-- hg19 specific Accession Numbers
\vbox{
\begin{verbatim}
INSERT INTO ChrName (AccNo, name) VALUES
("NC_000001.10", "chr1"),
("NC_000002.11", "chr2"),
......@@ -59,67 +160,21 @@ INSERT INTO ChrName (AccNo, name) VALUES
("NT_167250.1", "chr4_ctg9_hap1"),
("NT_167251.1", "chr17_ctg5_hap1")
;
\end{verbatim}
}
--- SAME THING for HG18
USE hg18;
CREATE TABLE map
SELECT DISTINCT acc, version, txStart, txEnd, cdsStart, cdsEnd, exonStarts,
exonEnds, name2 AS geneName, chrom, strand, protAcc
FROM gbStatus, refGene, refLink
WHERE type = "mRNA"
AND refGene.name = acc
AND acc = mrnaAcc;
---
-- We need an auxillary table for updated entries where the version numbers are
-- not increased.
---
CREATE TABLE map_cdsBackup LIKE map;
---
CREATE TABLE ChrName (
AccNo CHAR(20) PRIMARY KEY,
name CHAR(20) NOT NULL
);
# hg18:
INSERT INTO ChrName (AccNo, name) VALUES
("NC_000001.9", "chr1"),
("NC_000002.10", "chr2"),
("NC_000003.10", "chr3"),
("NC_000004.10", "chr4"),
("NC_000005.8", "chr5"),
("NC_000006.10", "chr6"),
("NC_000007.12", "chr7"),
("NC_000008.9", "chr8"),
("NC_000009.10", "chr9"),
("NC_000010.9", "chr10"),
("NC_000011.8", "chr11"),
("NC_000012.10", "chr12"),
("NC_000013.9", "chr13"),
("NC_000014.7", "chr14"),
("NC_000015.8", "chr15"),
("NC_000016.8", "chr16"),
("NC_000017.9", "chr17"),
("NC_000018.8", "chr18"),
("NC_000019.8", "chr19"),
("NC_000020.9", "chr20"),
("NC_000021.7", "chr21"),
("NC_000022.9", "chr22"),
("NC_000023.9", "chrX"),
("NC_000024.8", "chrY"),
("NC_001807.4", "chrM"),
("NT_113891.1", "chr6_cox_hap1"),
("NT_113959.1", "chr22_h2_hap1")
;
\subsubsection{The internal database}
---
\vbox{
\begin{verbatim}
CREATE DATABASE mutalyzer;
GRANT ALL PRIVILEGES ON mutalyzer.* TO mutalyzer;
FLUSH PRIVILEGES;
---
\end{verbatim}
}
---
\vbox{
\begin{verbatim}
USE mutalyzer;
CREATE TABLE GBInfo (
AccNo CHAR(20) PRIMARY KEY,
......@@ -131,14 +186,22 @@ CREATE TABLE GBInfo (
orientation INT(2),
url CHAR(255)
);
\end{verbatim}
}
\vbox{
\begin{verbatim}
CREATE TABLE BatchQueue (
QueueID INT(5) PRIMARY KEY AUTO_INCREMENT,
JobID CHAR(20) NOT NULL,
Input CHAR(255) NOT NULL,
Flags CHAR(20)
);
\end{verbatim}
}
\vbox{
\begin{verbatim}
CREATE TABLE BatchJob (
JobID CHAR(20) PRIMARY KEY,
Filter CHAR(20) NOT NULL,
......@@ -147,12 +210,20 @@ CREATE TABLE BatchJob (
JobType CHAR(20) NULL,
Arg1 char(20) DEFAULT NULL
);
\end{verbatim}
}
\vbox{
\begin{verbatim}
CREATE TABLE Link (
mrnaAcc CHAR(20) PRIMARY KEY,
protAcc CHAR(20) UNIQUE NOT NULL
);
\end{verbatim}
}
\vbox{
\begin{verbatim}
INSERT INTO Link
SELECT DISTINCT acc, protAcc
FROM hg18.map
......@@ -161,7 +232,5 @@ INSERT INTO Link
SELECT DISTINCT acc, protAcc
FROM hg19.map
WHERE protAcc != '';
---------
-- End of mutalyzer database
---------
\end{verbatim}
}
\begin{table}[H]
\begin{center}
\begin{tabular}{l|l|l}
Code & Class & Description \\
\hline
INFO & N & Information.
\end{tabular}
\end{center}
\caption{Informative messages} \label{tab:info}
\end{table}
\begin{table}[H]
\begin{center}
\begin{tabular}{l|l|p{7cm}}
Code & Class & Description \\
\hline
WSTART & E & Mutation in the start codon. \\
WTXSTART & E & Mutation hits transcription start. \\
WSPLDON & E & Mutation hits a splice donor site. \\
WSPLACC & E & Mutation hits a splice acceptor site. \\
WROLL & D & Variant position is ambiguous and not the last one was
given. \\
WINSDUP & D & Variant was described as an insertion, but it is a
duplication. \\
WNOMRNA & R & No mRNA field was found in the GenBank record. \\
WNOCDS & R & No CDS field was found in the GenBank record. \\
WNOCDSLIST & R & No CDS list was found in the GenBank record. \\
WNOVER & R & No accession version number was given. \\
WHASH & N & Hash of a GenBank record has changed. \\
WNOCHANGE & D & Variant equals reference sequence. \\
WNOTMINIMAL & D & A shorter description of a raw variant is possible. \\
WPEND & R & The LRG file is still pending \\
WDIFFFOUND & D &
\end{tabular}
\end{center}
\caption{Warnings} \label{tab:warnings}
\end{table}
\begin{table}[H]
\begin{center}
\begin{tabular}{l|l|p{7cm}}
Code & Class & Description \\
\hline
ENOVAR & D & No mutation given. \\
EARGLEN & D & There was a discrepancy between the range and the length of
the optional argument. \\
EREF & D & There was a discrepancy between the reference sequence and
the optional argument. \\
EINSRANGE & D & The positions of an insertion are not consecutive. \\
WNOCDS & R & No CDS field was found in the GenBank record and none could
be constructed. \\
ENOGENE & R & Gene not found. \\
ESTOP & R & In frame stop codon found. \\
EPOS & D & Invalid position.
\end{tabular}
\end{center}
\caption{Errors} \label{tab:errors}
\end{table}
\begin{table}[H]
\begin{center}
\begin{tabular}{l|l|p{6cm}}
Code & Class & Description \\
\hline
EPARSE & D & Nomenclature parse error. \\
EBPARSE & D & Parse error in the submitted batch file. \\
ERECPARSE & R & GenBank record parse error. \\
EFILESIZE & N & The filesize is either too large or too small. \\
ERETR & R & Could not retrieve a GenBank record. \\
EARG & N & Error in the arguments (of a webservice). \\
ERANGE & D & Position out of range (webservice). \\
EONLYGB & D & Conversion only supports GenBank Files \\
EACCNOTINDB & E & Accession Number Not in Database \\
ENOVERSION & D & Must supply a version number \\
EINVALIDGENE & D & Invalid gene name given. \\
EINVALIDTRANSCRIPT & D & Invalid gene name given.
\end{tabular}
\end{center}
\caption{Fatal errors} \label{tab:fatal}
\end{table}
\begin{table}[H]
\begin{center}
\begin{tabular}{l|l}
Class & Description \\
\hline
N & No Error \\
E & Unspecified \\
R & Record related \\
D & Description error
\end{tabular}
\end{center}
\caption{Legend} \label{tab:legend}
\end{table}
@misc{ UCSC,
title = "{UCSC Genome Bioinformatics}",
note = "\begin{small}\texttt{http://genome.ucsc.edu/}\end{small}"
}
@misc{ NCBI,
title = "{National Center for Biotechnology Information}",
note = "\begin{small}\texttt{http://www.ncbi.nlm.nih.gov/}\end{small}"
}
@misc{ BIOPYTHON,
title = "Biopython",
note = "\begin{small}\texttt{http://biopython.org/}\end{small}"
}
@misc{ TAL,
title = "{SimpleTAL}",
note = "\begin{small}\texttt{http://www.owlfish.com/software/simpleTAL/}
\end{small}"
}
@misc{ HGVS,
title = "{Human Genome Variation Society}",
note = "\begin{small}\texttt{http://www.hgvs.org/}\end{small}"
}
@misc{ PYPARSING,
title = "Pyparsing",
note = "\begin{small}\texttt{http://pyparsing.wikispaces.com/}\end{small}"
}
@article{ BNF,
author = "Blavier, A.",
title = "{BNF for the HGVS nomenclature.}",
journal = "Internal document",
}
@article{ API,
author = "Laros, J.F.J.",
title = "Mutalyzer 2.0 {API} documentation.",
journal = "Internal document",
year = 2010
}
@article{ LOVD,
author = "Fokkema, I.F.A.C and {den} Dunnen, J.T. and Taschner, P.E.M.",
title = "{LOVD}: easy creation of a locus-specific sequence variation
database using an ``{LSDB-in-a-Box}'' approach.",
journal = "Human Mutation",
volume = 26,
number = 2,
pages = "63--68",
year = 2005
}
@article{ NOM1,
author = "{den} Dunnen, J.T. and Antonarakis, S.E.",
title = "Mutation nomenclature extensions and suggestions to describe
complex mutations: {A} discussion.",
journal = "Human Mutation",
volume = 15,
pages = "7--12",
year = 2000
}
@article{ NOM2,
author = "Antonarakis, S.E. and {the Nomenclature Working Group}",
title = "Recommendations for a Nomenclature System for Human Gene
Mutations.",
journal = "Human Mutation",
volume = 11,
pages = "1--3",
year = 1998
}
@article{ NOM3,
author = "Beaudet, A.L. and {the Ad Hoc Committee on Mutation Nomenclature}",
title = "Update on nomenclature for human gene mutations.",
journal = "Human Mutation",
volume = 8,
pages = "197--202",
year = 1996
}
@article{ NOM4,
author = "Beutler, E. and McKusick, V.A. and Motulsky, A. and Scriver, C.R.
and Hutchinson, F.",
title = "Mutation nomenclature: nicknames, systematic names and unique
identifiers.",
journal = "Human Mutation",
volume = 8,
pages = "203--206",
year = 1996
}
@article{ NOM5,
author = "Antonarakis, S.E. and McKusick, V.A.",
title = "Discussion on mutation nomenclature.",
journal = "Human Mutation",
volume = 4,
pages = "166",
year = 1994
}
@article{ NOM6,
author = "Beaudet, A.L. and Tsui, L.C.",
title = "A suggested nomenclature for designating mutations.",
journal = "Human Mutation",
volume = 2,
pages = "245",
year = 1993
}
@article{ NOM7,
author = "Beutler, E.",
title = "The designation of mutations.",
journal = "American Journal of Human Genetics",
volume = 53,
pages = "783--785",
year = 1993
}
\begin{longtable}{llp{7cm}}
name & $\rightarrow$ & ([a--z][A--Z][0--9])$^+$\\
Nt & $\rightarrow$ & `a' $|$ `c' $|$ `g' $|$ `t' $|$ `u' $|$ `r' $|$
`y' $|$ `k' $|$ `m' $|$ `s' $|$ `w' $|$ `b' $|$
`d' $|$ `h' $|$ `v' $|$ `i' $|$ `n' $|$ `A' $|$
`C' $|$ `G' $|$ `T' $|$ `U'\\
NtString & $\rightarrow$ & (Nt)$^+$\\
Number & $\rightarrow$ & ([0--9])$^+$\\
TransVar & $\rightarrow$ & `\_v' Number\\
ProtIso & $\rightarrow$ & `\_i' Number\\
GeneSymbol & $\rightarrow$ & `(' name (TransVar $|$ ProtVar)? `)'\\
GI & $\rightarrow$ & (`GI' $|$ `GI:')? Number\\
Version & $\rightarrow$ & `.' Number\\
AccNo & $\rightarrow$ & `ish.'? ([a--Z] Number `\_')$^+$ Version? \\
RefSeqAcc & $\rightarrow$ & (GI $|$ AccNo) (`(' GeneSymbol `)')?\\
Chrom & $\rightarrow$ & name\\
Offset & $\rightarrow$ & (`+' $|$ `-') (`u' $|$ `d')? (Number $|$ `?')\\
PtLoc & $\rightarrow$ & ((`-' $|$ `*')? Number Offset?) $|$ `?'\\
RefType & $\rightarrow$ & (`c' $|$ `g' $|$ `m' $|$ `n' $|$ `r') `.'\\
Ref & $\rightarrow$ & ((RefSeqAcc $|$ GeneSymbol) `:')? RefType?\\
Extent & $\rightarrow$ & PtLoc `\_' (`o'? (RefSeqAcc $|$ GeneSymbol) `:')? PtLoc\\
RangeLoc & $\rightarrow$ & Extent $|$ `(` Extent `)'\\
Loc & $\rightarrow$ & PtLoc $|$ RangeLoc\\
FarLoc & $\rightarrow$ & (RefSeqAcc $|$ GeneSymbol) (`:' RefType? Extent)? \\
Subst & $\rightarrow$ & PtLoc Nt `$>$' Nt\\
Del & $\rightarrow$ & Loc `del' (Nt$^+$ $|$ Number)?\\
Dup & $\rightarrow$ & Loc `dup' (Nt$^+$ $|$ Number)? Nest?\\
AbrSSR & $\rightarrow$ & PtLoc Nt$^+$ `(' Number `\_' Number `)'\\
VarSSR & $\rightarrow$ & (PtLoc Nt$^+$ `[' Number `]') $|$ (RangeLoc `[' Number `]') \\
Ins & $\rightarrow$ & RangeLoc `ins' (Nt$^+$ $|$ Number $|$ RangeLoc $|$ FarLoc) Nest?\\
Indel & $\rightarrow$ & RangeLoc `del' (Nt$^+$ $|$ Number)? `ins' (Nt$^+$ $|$ Number $|$ RangeLoc $|$ FarLoc) Nest?\\
Inv & $\rightarrow$ & RangeLoc `inv' (Nt$^+$ $|$ Number)? Nest?\\
Conv & $\rightarrow$ & RangeLoc `con' FarLoc Nest?\\
ChromBand & $\rightarrow$ & (`p' $|$ `q') Number `.' Number\\
ChromCoords & $\rightarrow$ & `(' Chrom `;' Chrom `)' `(' ChromBand `;' ChromBand `)'\\
TransLoc & $\rightarrow$ & `t' ChromCoords `(' FarLoc `)'\\
RawVar & $\rightarrow$ & Subst $|$ Del $|$ Dup $|$ VarSSR $|$ Ins $|$ Indel $|$ Inv $|$ Conv\\
SingleVar & $\rightarrow$ & Ref RawVar $|$ TransLoc\\
ExtendedRawVar & $\rightarrow$ & RawVar $|$ `=' $|$ `?'\\
SimpleAlleleVarSet & $\rightarrow$ & (`[' ExtendedRawVar (`;' ExtendedRawVar)$^*$ `]') $|$ ExtendedRawVar\\
MosaicSet & $\rightarrow$ & (`[' SimpleAlleleVarSet (`/' SimpleAlleleVarSet)$^*$ `]') $|$ SimpleAlleleVarSet\\
ChimeronSet & $\rightarrow$ & (`[' MosaicSet (`//' MosaicSet)$^*$ `]') $|$ MosaicSet\\
SingleAlleleVarSet & $\rightarrow$ & (`[' ChimeronSet ((`;' $|$ `\verb#^#') ChimeronSet)$^*$ (`(;)' ChimeronSet)$^*$ `]') $|$ ChimeronSet\\
SingleAlleleVars & $\rightarrow$ & Ref SingleAlleleVarSet\\
MultiAlleleVars & $\rightarrow$ & Ref SingleAlleleVarSet (`;' Ref? SingleAlleleVarSet)$^+$\\
MultiVar & $\rightarrow$ & SingleAlleleVars $|$ MultiAlleleVars\\
MultiTranscriptVar & $\rightarrow$ & Ref `[` ExtendedRawVar (`;' ExtendedRawVar)$^*$ (`,' ExtendedRawVar (`;' ExtendedRawVar)$^*$)$^+$ `]'\\
UnkEffectVar & $\rightarrow$ & Ref (`(=)' $|$ `?')\\
SplicingVar & $\rightarrow$ & Ref (`spl?' $|$ `(spl?)')\\
NoRNAVar & $\rightarrow$ & Ref `0' `?'?\\
Var & $\rightarrow$ & SingleVar $|$ MultiVar $|$ MultiTranscriptVar $|$ UnkEffectVar $|$ NoRNAVar $|$ SplicingVar\\
Nest & $\rightarrow$ & `\{' SimpleAlleleVarSet `\}'
\end{longtable}
Information:
N : No Error
E : Unspecified
R : Record related
D : Description error
INFO | N | Information.
Warnings:
WSTART | E | Mutation in the start codon.
WTXSTART | E | Mutation hits transcription start.
WSPLDON | E | Mutation hits a splice donor site.
WSPLACC | E | Mutation hits a splice acceptor site.
WROLL | D | Variant position is ambiguous and not the last one was given.
WINSDUP | D | Variant was described as an insertion, but it is a
duplication.
WNOMRNA | R | No mRNA field was found in the GenBank record.
WNOCDS | R | No CDS field was found in the GenBank record.
WNOCDSLIST | R | No CDS list was found in the GenBank record.
WNOVER | R | No accession version number was given.
WHASH | N | Hash of a GenBank record has changed.
WNOCHANGE | D | Variant equals reference sequence.
WNOTMINIMAL | D | A shorter description of a raw variant is possible.
WPEND | R | The LRG file is still pending
WDIFFFOUND | D |
Errors:
ENOVAR | D | No mutation given.
EARGLEN | D | There was a discrepancy between the range and the length of
the optional argument.
EREF | D | There was a discrepancy between the reference sequence and the
optional argument.
EINSRANGE | D | The positions of an insertion are not consecutive.
WNOCDS | R | No CDS field was found in the GenBank record and none could
be constructed.
ENOGENE | R | Gene not found.
ESTOP | R | In frame stop codon found.
EPOS | D | Invalid position.
Fatal errors:
EPARSE | D | Nomenclature parse error.
EBPARSE | D | Parse error in the submitted batch file.
ERECPARSE | R | GenBank record parse error.
EFILESIZE | N | The filesize is either too large or too small.
ERETR | R | Could not retrieve a GenBank record.
EARG | N | Error in the arguments (of a webservice).
ERANGE | D | Position out of range (webservice).
EONLYGB | D | Conversion only supports GenBank Files
EACCNOTINDB | E | Accession Number Not in Database
ENOVERSION | D | Must supply a version number
EINVALIDGENE | D | Invalid gene name given.
EINVALIDTRANSCRIPT | D | Invalid gene name given.
......@@ -33,7 +33,7 @@ internalDb = "mutalyzer"
# MySQL mapping database names.
dbNames = "hg18", "hg19"
# MySQL username for the local databases (inernalDb and dnNames).
# MySQL username for the local databases (internalDb and dbNames).
LocalMySQLuser = "mutalyzer"
# Host name for the local databases.
......@@ -123,6 +123,7 @@ syntaxCheckOutHeader = "Input", "Status"
# The output header for NameChecking
positionConverterOutHeader = "Input Variant", "Errors", "Chromosomal Variant", "Coding Variant(s)"
#
# These settings are used by the File module.
#
......@@ -133,7 +134,6 @@ bufSize = 32768
# The obligatory header in batch request files.
header = "AccNo", "Genesymbol", "Mutation"
# Directory for temporary files.
tempDir = "./var"
......
......@@ -279,6 +279,7 @@ class Crossmap() :