Commit 9b725190 authored by Sebastien Moretti's avatar Sebastien Moretti
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......@@ -12,175 +12,175 @@ History of ProtoGene improvements:
Bug fixes: ...
3.4.2
Correct download for GeneID: 726214 / LOC726214
Enhance colored fasta CDS
Correct download for GeneID: 726214 / LOC726214
Enhance colored fasta CDS
3.4.1
Enhance colored fasta CDS
Enhance colored fasta CDS
3.4.0
Add html/css output
Add html/css output
3.2.6
Remove '>' sign in annotation line if any e.g.: NM_105729
Remove '>' sign in annotation line if any e.g.: NM_105729
3.2.5
The fasta file is too large, try with less than 60 sequences or
split your file
The fasta file is too large, try with less than 60 sequences or
split your file
3.2.4
Add a simple way to get chromosomic sequences info about gene
acc and positions via eSummary
Add a simple way to get chromosomic sequences info about gene
acc and positions via eSummary
3.2.3
Add more equivalent hits to ProtoGene
Add more equivalent hits to ProtoGene
3.2.2
Use more Perl Best Practices
NCBI links for NTUI has changed
Use more Perl Best Practices
NCBI links for NTUI has changed
3.2.1
Do not count N letters in (1st) sequence to avoid that nt seq with many N
(indetermined base) is considered as amino acid
Do not count N letters in (1st) sequence to avoid that nt seq with many N
(indetermined base) is considered as amino acid
3.2.0
Test if Gigablaster is reachable/available then use it else use NCBI blast
Test if Gigablaster is reachable/available then use it else use NCBI blast
3.0.4
Correct fasta headers in advance mode for CDS & CDSP: elements were
duplicated and a > was persistent.
Add exception for warnings when empty lines or non-fasta file were
used in ProtoGene advance mode
Correct fasta headers in advance mode for CDS & CDSP: elements were
duplicated and a > was persistent.
Add exception for warnings when empty lines or non-fasta file were
used in ProtoGene advance mode
3.0.3
Correct seq_name when starting with a blank
e.g.: > truc
Correct when first seq is revtrans and check for nt
Correct seq_name when starting with a blank
e.g.: > truc
Correct when first seq is revtrans and check for nt
3.0.2
Print an error message when input files are already nucleotides
Print an error message when input files are already nucleotides
2.2.5
Best management when only one gene match and alignment fails:
$intronStep==1 and $POS->{0} doesn't exist.
Best management of fake downloads:
- > without sequences
- sequences with Error: or <>
- ...
Best management when only one gene match and alignment fails:
$intronStep==1 and $POS->{0} doesn't exist.
Best management of fake downloads:
- > without sequences
- sequences with Error: or <>
- ...
2.2.4
Change intronless behavior if best nucleotide return
a GI number.
Change intronless behavior if best nucleotide return
a GI number.
2.2.3
Change gene locus coordinates to zero if they become
negative with +/- 5000 expansion.
Change gene locus coordinates to zero if they become
negative with +/- 5000 expansion.
2.2.2
Manage boj output when there are several intronless genes
for one query.
Manage boj output when there are several intronless genes
for one query.
2.2.1
Add a $lim variable to be able to fix max number of query
sequences as an input option.
Manage several geneIDs ?!?
Add a $lim variable to be able to fix max number of query
sequences as an input option.
Manage several geneIDs ?!?
2.2.0
New Release:
Better memory management
Code splits into more functions
Clean code
Write results when they are available, no more only at the exit
New Release:
Better memory management
Code splits into more functions
Clean code
Write results when they are available, no more only at the exit
1.2.8
Add an option to keep abnormal temporary files.
Increase size threshold for result file of exonerate, i.e.
no result or result.
Add an option to keep abnormal temporary files.
Increase size threshold for result file of exonerate, i.e.
no result or result.
1.2.6
Manage fake BLASTP acc when they have space, point or pipe
characters.
Check and correct perl POD text format.
Enhance fasta header for boj output like cds output.
Manage fake BLASTP acc when they have space, point or pipe
characters.
Check and correct perl POD text format.
Enhance fasta header for boj output like cds output.
1.2.4
Add an option to hide BOJ output for the IGS web server.
Output two CDS files: a standard one, and one with query prot
interleaved.
Add an option to hide BOJ output for the IGS web server.
Output two CDS files: a standard one, and one with query prot
interleaved.
1.2.2
Manage multiple runs of PACMAN and the co-occurance query name:
0.fas and 0.fas => now use temp name to limit this.
And temp names are mix of current date-time and a random nbr.
Manage multiple runs of PACMAN and the co-occurance query name:
0.fas and 0.fas => now use temp name to limit this.
And temp names are mix of current date-time and a random nbr.
1.2.0
Remove duplicated lines when a query, with multiple blastp hits
returns a single nucleotide for all hits. So, keeps only one.
Debug mode for BOJ, now available as a result file.
Enhance output for log files.
RefSeq -> 100% filters to avoid mis-species attribution
then NR -> 95%.
Remove duplicated lines when a query, with multiple blastp hits
returns a single nucleotide for all hits. So, keeps only one.
Debug mode for BOJ, now available as a result file.
Enhance output for log files.
RefSeq -> 100% filters to avoid mis-species attribution
then NR -> 95%.
1.0.4
Add a webblast step againt nr if refseq webblast returns no
hit: RefSeq, elsif nr, else NO HIT
Add a webblast step againt nr if refseq webblast returns no
hit: RefSeq, elsif nr, else NO HIT
1.0.3
Add an option to add the original peptide query beneath the
back-translated nt seq
Add the b,o,j identification in the Exonerate parser module
Add an option to add the original peptide query beneath the
back-translated nt seq
Add the b,o,j identification in the Exonerate parser module
1.0.2
New header format in the cds output
New header format in the cds output
1.0.1
Add standard log files for the web server
Manage multiple equal blast best hits
Mix PACMAN and Exoset, specially in the Exonerate parser
Add standard log files for the web server
Manage multiple equal blast best hits
Mix PACMAN and Exoset, specially in the Exonerate parser
0.99
Process the alignment between every nucleotide sequence found and use
the best one (transcript and genomic sequences)
Process the alignment between every nucleotide sequence found and use
the best one (transcript and genomic sequences)
0.98
Add a 'old' argument for the cache option to remove only 15 days
old files from the cache directory
Hide webblast parameters when it runs but the first one
Manage return lines from windows '^M'
Remove all the non-gap and non-alphabetic characters into the query
sequences
Add a 'old' argument for the cache option to remove only 15 days
old files from the cache directory
Hide webblast parameters when it runs but the first one
Manage return lines from windows '^M'
Remove all the non-gap and non-alphabetic characters into the query
sequences
0.97
Create a more robust 'cache directory' process
Add triplet to sure mismatches, i.e. Met and Trp
Create a more robust 'cache directory' process
Add triplet to sure mismatches, i.e. Met and Trp
0.96
Add a second result file, as library, with storage of accession
numbers resulting from blast query and prot-nt correspondances.
Add a second result file, as library, with storage of accession
numbers resulting from blast query and prot-nt correspondances.
0.95 - 24 oct 2005
Correct hash table variable define as semi-local, and not strictly as
local, in Exonerate.pm because some value were kept between
module executions due to misplaced brackets.
Clean Exonerate.pm file and remove usage of strand, exonup
list and genomic length because they are unnecessary here.
Correct hash table variable define as semi-local, and not strictly as
local, in Exonerate.pm because some value were kept between
module executions due to misplaced brackets.
Clean Exonerate.pm file and remove usage of strand, exonup
list and genomic length because they are unnecessary here.
0.9 - 20 oct 2005
Perldoc
Perldoc
19 oct 2005
Addition of a test to avoid to download the same file if
it has ever been downloaded in the past half day.
Addition of stop codon triplet management
Addition of a process to select the best alignment if there
are several nt sequences of the same category for a query
Addition of a test to avoid to download the same file if
it has ever been downloaded in the past half day.
Addition of stop codon triplet management
Addition of a process to select the best alignment if there
are several nt sequences of the same category for a query
18 oct 2005
Get genomic and transcript acc, sort them to get only the
best category of sequences:
transcripts > chromosomes > contigs > bac,cosmid,... for RefSeqN
sort by size for other acc
Get genomic and transcript acc, sort them to get only the
best category of sequences:
transcripts > chromosomes > contigs > bac,cosmid,... for RefSeqN
sort by size for other acc
17 oct 2005
Addition of a version option and variable
Addition of a version option and variable
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