| Links to HEAD: | (view) (download) (as text) (annotate) |
| Links to rast_rel_2010_1206: | (view) (download) (as text) (annotate) |
| Sticky Tag: |
FIGFAM 6 digit problem
add missing use
If we don't have sims for an org, see if we have RAST-generated sims file. If so use FIGV::retrieve_sims to fill them in.
correcting join attributes for non-pegs
don't do annotation/assigned_functions renaming when installing from PSEED to SEED.
add pegs_to_usable_subsystems()
Paranoia fixes for assign_function.
turn off recognition of locks
memcached support
fixes to active subsystem
adding load_dlits to load_all
adding by_all_aliases, and fixing featre aliases
added quotemeta for title variable in add_title and update_title
Fix comment
1. Removing md5 ids from raw sims. 2. fixing a distinct SQL query that very occassionaly reported duplicate entries
add FIG::assess_completeness
Add rewrite-loop breaking to the role rewrite process.
minor change to ignore blank lines while parsing transaction records
Support for Seedviewer Subsystems.pm speedups.
Optimize subsystems_for_peg for the case where we don't want non-active variants.
Fix missing quotes in query
Make wikipedia_link in the SEED case use the local SEED wikipedia cache.
*** empty log message ***
add co-occurs stuff
Added "sapling" method for accessing a Sapling database from the FIG object.
minor documentation fix
fixed protein_subsystem_to_roles
Adding a replace method to tell if one genome replaced an older version
fix bad calls to possibly_truncated
Make function_of() use sql parameters Sorted returns from keep a sort on the id1.
return hope_reactions with scenario information
Fixed attribute server documentation.
put in ext_bin
return distinct values on pros_for_role
change active_subsystems to use opendir/open instead of a backtick grep.
fixes to blastit
make is_aux_role_in_subsystem use the database instead of instantiating Subsystem objs
add variant to returned data on get_genome_subsystem_data
clean up warnings
suppress variant check in accessing subsystem data, if desired
fix operator in SQL
fix operator in SQL
fix operator in SQL
fix typo bug
On genome installation, rename any roles that were changed in the role rename log. Don't perform subsystem salvage.
fix blast to add ln2
remove warning
add blastx and get rid of warnings
Added all_subsystems_with_roles
minor fix
add variant_code
fix nonumeric comparisons
make comparison of -1 nonnumeric compare
Fixed initialization error in fid_from_clearinghouse().
Fixed unitialized variable warning in add_annotation().
Fix bug in location_overlap().
add function FIG::location_overlap( loc1, loc2 )
Base $fig->is_plasmid() on TAXONOMY, not PLASMID file. (The PLASMID file is now obsolete.)
fix dumb mistake
Fixes for prots_with_md5/pegs_with_md5 to use the peg.synonyms where possible.
modified pegs_with_md5 to return only fig ids matching an md5 hash added prots_with_md5 to return all ids matching an md5 hash
Added a method to clear the subsystem cache.
Added "is_plasmid()" function.
added searching of alias column to search database function
minor correction in documentation
Fixed the compiler warnings caused by use recursion.
Updated get_representative_genome
Added get_representative_genome
Fixed several methods so that they work for rna and other non-peg features.
Restored lost fix of TAXONOMY whitespace and "Candidatus" bugs
added function subsystems_for_pegs_complete commented out warning for 'no taxonomy found' since it is triggered for every private organism
fix is_cluster_based_subsystem
bugfix
added function subsystems_for_pegs_complete
Fixed (hopefully) a TAXONOMY-sorting bug, and remaining instances of "Candidatus."
make ex_assertions.cgi ignore inactive variants
put ext_bin on invocations of formatdb and blastall
add is_cluster_based_subsystem
Fixed subsystems_for_peg so it works for non-pegs.
LRU cache used for get_subsystem(). Add clearinghouse_ping()
Strip any leading whitespace off the TAXONOMY string.
Automatically strip "Candidatus" off genus/species.
*** empty log message ***
Added get_scenario_info to speed up reading scenario info for a list of subsystems
fix scenario_directory to work for All
switch to scenario_directory
added a function for getting dlits
add routine to get close pegs in the same subsystem
fixed the case where function_of_bulk would break if there were no ids passed
Set to use old attributes if the attrHost variable is empty.
Add FIG.pm caching of all-subsystem data, and use that for subsystem-classification calls made after a call to all_subsystem_classifications.
Heh. return inside eval returns from the eval, not the enclosing sub.
updated function 'search_database' now excepts limit for protein searches protein searches also return organism name and domain
Fixed a comment.
Add support for subsystem_metadata table. Updates via Subsystem::db_sync.
Added a new method for getting subsystem data of a genome's features. This is used by the Sprout loader.
get rid of warning and update conditionally_assign
fixes to FIGV.pm, CompareMR.pm and FIG.pm to support comparison of metabolic reconstructions
Remove load_attributes from load script, add load_id_correspondence.
Fixed typo in &possibly_truncated_stop(), and added POD for the mods to &possibly_truncated(). -- /gdp
Modified &possibly_truncated() to return whether STOP or START is truncated; added &possibly_truncated_stop(), and &possibly_truncated_start(). -- /gdp
changed function change_funcrole so that it keeps the comments
Add support for $fig->change_funcrole()
changed publish_subsystem_to_clearinghouse so that it can be used by a webpage
Fixed to recover from an inability to reach the attribute server.
Move writing of assignment annotation from a case-by-case basis (and it was missing in several key places) to the FIG::assign_function. Modify the code in each of the calling locations to not make duplicate annotations. At the same time, remove (most) of the instances of making different calls to assign_function depending on the user name. assign_function treats everyone as master (but writes an annotation with the real user name).
fix clearinghouse urls.
Fixed for sprout compatability.
Moved to_structured_english to FIGRules.
added functions is_experimental_subsystem and is_private_subsystem
Added uniprot_aliases. Most organisms do not have uniprot ids in their tbl files, and so the regular alias routines are missing them. The new routine gets the uiprot ids from other sources.
Many code clean-ups in the dlits routines, and associated literature. Add support for indexing the translations in Global/nr.
Remove warning from dispaly_id_and_seq Add mechanism in get_trnaslation to pull xxx id translations directly from NR.
A bug fix in an SQL statement in get_dlits (I still don't fully understand the nature, but it left a query 'SELECT DISTINCT hash_role.role ...' hung). Add code for an index of the dlits table by pubmed id.
Minor changes including: Display literature curator in literature curation table Do not display master: on literature curator Do not record msster: on literature curator Filter for real features before picking representative peg with md5
Add update of curator on propagation of 'G' status code. Add logging of delete and insert events (but not that due to propagation of 'G' status codes).
Improving navigation in the dlits scripts, and improving behavior in the FIG.pm support for it.
added a function to read the curation log
Changed text for ilit, dlit
code relating to dlit/ilit maintenance
Fixed up ILIT text
Added escape arg to structured english
Support for MD5 indexing of SEED translations.
Removed test code accidentally left in
Added Structured English to Seed Viewer pages
Add lookup_subsystem_by_id
remove the debugging url
Add clearinghouse_register_subsystem_id
add metagenome register taxon method in salvage, always add a * to the variant even if all roles were fulfilled.
Changed display_id_and_seq to work in Sprout. Changed boundaries_of to be more tolerant of spaces in the location string.
Fix the code for adding links to a fid page so that the code to write the new link to a file works (all old links were put in DBMS, but not written to the disk), and add HTML escaping to the use-supplied link name.
Fixed syntax error in definition of %named_hash. -- /gdp
fix up add_feature
don't die in perorm_subsystem_salvage() if a ss is missing.
added function subsystems_for_peg_complete which returns subsystem, role, variant, is_auxiliary tuples for all subsystems of a peg
minor fixes to lengths on blast
Changed a warning to a cluck to give us better information about how invalid locations get into the data.
Introduce get_figfam_data().
fixes to the ACH_resolution stuff
updates to FIGfam quality control
updated get_organism_info_from_ncbi, using Gary Olsens function decode_html_chars to extract the correct string from the xml
allow suppression of cluster-based subsystems
fixed feature_aliases_bulk to not break on deleted ids
changes to dsims
added get_all_assertions which queries all annotations from the aclh for a set of pegs
Fix query for get_id_correspondence.
updates to the load_id_correspondence loader and searching code.
add get_assertions to access clearinghouse expert assertions
added a method for getting the number of NEW diagrams
Finish load_id_correspondence; add get_corresponding_ids();
added two functions get_taxonomy_id_of and set_taxonomy_for
added taxonomy to genome_info
fix stripping comments in roles_of_function
reverted to 1.665, readded corrected change from 1.666
added method genome_info
make the parse test in boundaries_of also check for beginning & end > 0.
Fix boundaries_of bug leading ot incorrect parse failures where $end == 0.
add delete_subsystem and rename_subsystem to FIG.pm
add routines to delete and rename subsusyems to FIG.pm
add routines to delete and rename subsusyems to FIG.pm
added method taxonomy_list for bulk retrieval of organism taxonomies
screen out bad genomes from genome list in FIG.pm
Appended the strand to the results returned by &boundaries_of(), -- /gdp
Removed a redundant "my %hits;" from "&dsims()", and added a "defined()" around a "$_ = <PARTITION>" that perl was kvetching about. -- /gdp
close a file left open in dsims
minor fixes to dsims
fixes to dsims in FIG.pl
make dsims handle min_nbsc properly
implemented new version of dsims based on partitions
Fixed some headings.
Fixed &FIG::flatten_dumper() to support OOP calling syntax. -- /gdp
Added search-interval constraint to &pick_gene_boundaries(). -- /gdp
Revised &pick_gene_boundaries() to use new code in "Location.pm". -- /gdp
Add next_feature and previous_feature functions, and some more general functions for handling complex location descriptions: filtered_location and boundaries_of_2.
get_organism_info_from_ncbi For a given taxonomy ID returns a hash containing scientific name , genetic code , synonyms and lineage
Changed POD format for better compatability with Wiki.
Added sort function &by_locus(). -- /gdp
minor modifications
add possible_frameshift to FIG.pm (and, hence, FIGV.pm)
Added support for FIGV calls of &FIG::pick_gene_boundaries() and &FIG::call_start(). -- /gdp
updated perldoc for method wikipedia link added method organism_directory
I added a method 'feature_aliases_in_tbl', which gives back only the aliases in the tbl file and not external aliases.
Fix no-results return from in_pch_pin_with_and_evidence.
some fixes for RAST genome installation.
If a genome is not marked COMPLETE, but it is marked NMPDR, mark it complete anyway. This until Bruce makes the changes that always import NMPDR orgs even if not complete.
fix get_genome_assignment_data & get_genome_stats to account for deleted genomes and pegs
added function md5sum_to_contig_genome
Add sub interpret_error_code.
fix coupled_to_batch in non-server ccase
add batch coupling_and_evidence calls
Add subsystem-at-a-time coupling lookup in get_ev_codes that goes iwth the new coupled_to_batch interface.
Register new genomes' features with the clearinghouse in add_genome. Allow missing peg stop truncations as reported by verify_genome_directory to not abort an add genome, if they are the only error reported.
add check_variants.cgi, a program to automatically validate variant codes
add in_pch_pin_with and in_pch_pin_with_and_evidence
Add support for $fig->sims([list of ids]) in the non-sim-server case.
Minor fix to POD of &taxonomy_of(). -- /gdp
add a routine in FIG.pm giving who set the function of a peg
fix vc * bug
add index_annotations to add_genome_body
add perform_subsystem_salvage and its invocation in add_genome_body.
fix typoe
Fix a corner case in all_features_detailed_fast that made a contig with exactly two pegs show nothing at all in the context view.
minor fix to rast install code
Mods for RAST org installation
Removed some "my"s to prevent compiler warnings.
add_genome mods for rast import
changed model_directory to default to Data/Organisms
add support for asserting presence of genomes (for use in the RAST import environment).
commented out warn statements in all_subsystems
add strip comments argument on function_of
Make NMPDR-generated GFF files validate cleanly.
made additions to FIG.pm - added batch method to get subsystem data
Added some POD documentation.
removed addition of subsystems in all_features_detailed_fast, as it introduced an unforeseen error
Moved coupling code to FIGRules. Added support for the Subsystem List Editor.
added subsystem information to function all_features_detailed_fast
fix bug in undeleting features
add get_basic_statistics() and get_peg_statistics(); both use caching.
Fixed duplicate declaration of $cache_dir in &get_cache_directory(). -- /gdp
add caching support for $fig->all_usable_subsystems() - new routine.
Added boolean test "&is_viral()". -- /gdp
introduced a method called 'genome_list' which returns a list of all complete genomes, every entry composed of genome_id, genome_name, maindomain
add ability to filter aux roles on peg_to_subsystems
fix to auto_assign
changed scenario_directory to model_directory
Changes for using $fig->scenario_directory() instead of constructed paths.
added the function scenario_directory, which returns the scenario directory
Add $fig->compute_genome_similarity and supporting routines.
Not using URI now.
FIG.pm support for installing subsystme dir
added the option of getting all non -1 variant subsystems in subsystems_for_genome
Hope college modifications.
added the function get_genome_subsystem_count
Added a method to download attribute keys and their definitions.
add computation of alignments to building FIGFAMS
Added initial support for alternate genetic codes. -- /gdp
Added initial support for alternate genetic codes. -- /gdp
Added initial support for alternate genetic codes. -- /gdp
Added support for the new QueryAttributes feature.
add recast_ids
Moved the guts of wikipedia_link to FIGRules so that SFXlate can use it. Added POD documentation to some more methods.
updating db_xref
problem using subsystem that does not exist
caching fix for taxonomy_of, support non-pegs in translate_pegs
changes to gff3 file to be in line with BRC requirements
add function_of_quick that uses a cached prepared statement
add caching to build_tree_of_all
moved the method rewrite_db_xrefs here, because it's used in more than one place now
add PHOB.pm to support some phylogeny stuff
added quoting to catalyzes
Added a user name to the custom attributes constructor and fixed some comments.
Added &get_dna_seq($fid). -- /gdp
Changed call signature for the Custom Attributes constructor to pass in a user name.
strip trailing spaces off roles
initial, undebugged version of edit_feature.cgi
beef up error messages from the clearinghouse mon add_feature failure
fixes to add_features and display of non-peg features
Added tracing for attributes.
Removed support for full-text attribute search.
Fixed a bug in the erase_attribute_entirely method.
Added a find_attributes method for word-searching the attribute data base and converted search_index to use Glimpse for attribute searches.
fix on assignments with user of master
add comments to functions
add support for # as a comment initiator in gene functions
make assignments without user fail
Parent DirectoryChange the key used in caching peg keys in get_peg_keys so that it
extends naturally to any feature type: _attribute_keys->{ type }
Add caching for get_peg_keys(). This speeds scripts that use it more than once (e.g., subsys.cgi).
lock/unlock should annotate only on real change
add lock_subsys.cgi
fixes to add_feature, delete_feature, and replace_feature_with
Enhanced "get_attributes" so that you can specify a list of object IDs.
add GO attribute genertation
put in the fr2go stuff
added subroutine fr_to_go. Give the routine a peg, and it returns the GO values
new go_number_to_term method
remove warning from boundaries_of and add genes_in_region to FIGV
add initial version of FIGO.pm - OO services
Added support for more attribute methods.
Added an override available from the FIG_Config.pm so that the attribute migration can work properly.
Added support for the EraseAttribute method.
Made CustomAttributes a conditional import.
Converted to new attribute system.
Converted to use the new attribute system if it is available (which it isn't on most machines.
Removed redundant copy of essentiality_data. Fixed an extraneous "my". Added some tracing.
Fix leftover <<<<< from a cvs update conflict marker.
exchanged DISTINCTROW for equivalent DISTINCT which is supported by Postgress
Removed a multiply-defined method. Fixed an extraneous "my".
added methods for feature retrieval, neccessary for the genome browser
Added "virulent" and "essential" methods.
Adding tools to handle essentiality data for Sveta
readonly fixes; seed-run-job update to run from input file
Added routine to "flatten" Data::Dumper format. -- /gdp
added multiple value query capability to essentiality_data()
added essentiality_data retrieval method
Removed the config-based tracing.
allow spaces in abbr for roles in subsystems - fix pattern
Fixed typo in "pseudogene" rule of &hypo(). -- /gdp
spiff up the lock/unlock stuff
promote remaining orfs in rapid_propagation
added a little error checking to lock/unlock fids
introduce locks on features to block assignments
Use DAS configs from FIG/var instead of in Data so no chance of being wiped out by mirror.
Converted to provide BBH server support for Sprout.
remove debugging in all_bbhs
adding a new method for environmental genomes
add bbh server support
network coupling server support
Adding allow automatic update buttons
add add_to_subsystems
ignoring evidence codes in the transaction logs
killing error messages
restoring the ev_code_cron to almost right
hopefully fixing the evidence code bug
RAE: Adding docs to attributes
Added methods to support the genome statistics page. Updated some documentation.
RAE: updating IFC/DFC
Fixed some comments.
Fixed another bad return from coupling_and_evidence.
Fixed bad return from coupling_and_evidence.
Added SameFuncWhy. TD
minor reformatting
Fixed the documentation for bbhs.
Updated documentation.
changed format of search results for attributes again
changed format of search results for attributes
Enhanced "all_features" to match the SFXlate signature.
RAE: Adding BRC info
Fixed read_all_annotations to return an empty list if no annotations file exists.
Documented "uniprot_aliases_bulk".
Added documentation for "function_of_bulk".
Added documentation for the "is_genome" method.
Fixed the deprecated-boundary-method warning message.
Changed boundaries_of from a static to an instance method.
*** empty log message ***
Moved the network sims method to FIGRules.
Fixed two compile warnings, cleaned out some tabs.
just add comments to ToCall.pm
RAE: moving PIRSF to links
Drat, I thought I'd already turned off the sim debug logging.
make all assignments master assignments
Robustify netowrk sims code; change the timeout on the LWP::UserAgent, retry 10 times on failure.
bugfix.
Some changes to add_genome logic. (Only log after genome add completes; turn some formerly fatal errors into nonfatal with warnings so that we don't end up with a partially-added genome).
Added a method to read annotations directly from the flat files.
add normalizded bit scores to BBHs
Fixed a bad call to the Upstream function.
RAE: correcting error in transaction log
RAE: correcting error in transaction log
fix simserver bug
use Logs, not LOGS for GenomeLog
minor changes to logging correspondences
add ability to log arbitrary correspondences
add ability to show maps in log
crude version of show_log.cgi
added new logging
Turn off sim server support unless enabled in FIG_Config,for now. add dont_mark_complete to fig add_genome.
attempt to commit figfam stuff
to avoid getting clobbered
must have a role index on subsystem_index, added is_NMPDR_genome, etc.
fixes to usable_subsystem
Moved upstream region code into FIGRules so it can be used by Sprout.
pull master: off curator
leave master: on subsystem_curator
fix bug in perl, I think: watch out for make
usable_sub => usable_subsystem
minor changes to eliminate master:
fixes to making assignments based on consistency
Add support for readonly database instance, and for FileLocking module.
Fixed some compiler warnings.
Fixed some lines that were generating compiler warnings.
RAE: Yummy attributes
RAE: making 0 and -1 work
fixes to split_and_trim
RAE: Initial release of setting.cgi and format changes on subsys.cgi
Added helper methodsa for the Markups object.
Fixed incorrect POD for &subsystems_for_genome(). -- /gdp
Fixed to create user-data directories when they don't exist.
handle deleted fids in mapped_prot_ids
minor fixes to assignment for close strains
Fixed a bug in the user-data handler
add logging on update operations
Corrected typo in variable name that wasaborting compilation. -- /gdp
Fix Rob's bug.
RAE: Updating organisms.cgi for more genomes in cyanoseed
RAE: Swtiched to using SQL Count for the number of contigs
$/ fixes
fix of clustering
use is_genome checks for subsystems?
fixes for controlled vocab from NCI demo. fixes to accomodate RAE's changes in key_info. commit independent of other pkgs.
RAE: Updating POM -- pieces of metabolism
Add more sim compute stuff.
changes to support dynamic sims and updates
RAE: Adding NMPDR checkbox to subsys.cgi
RAE: Adding NMPDR checkbox to subsys.cgi
=head3 by_raw_alias usage: $peg = $fig->by_raw_alias($alias) Returns all FIG ids having the given alias. Unlike by_alias, we do not attempt any kind of normalization. I'm not sure this function is needed, but by_alias searches only in ext_alias table whereas here I'm searching in the features table. ext_alias does not have all external aliases which is keeping my code from working. In partic\ ular, it lacks EnsemblGene. It would be nice to combine these two functions. -Ed =cut =head3 get_cv_attributes A simple wrapper around get_attriubtes to return only those attributes that have meta_data indicating that the key is a controlled vocabulary. See get_attributes for description of arguments and return types. =cut
correction to is_deleted_fid
is_deleted_fid should return 0, if the argument is not a fid
Fine tuning of the add a feature software. (Still more to come in dealing with previously deleted features)
Minor changes to assign_function: Convert user of form master:xxx to master (clearly the intent) Clean-up and clarify flow
fixes to deleted_features, replace_features_with, etc
Converted the relative-to-absolute path code to use a system-independent PERL utility.
Greatly enhanced error checking and reporting for add_feature. Make sure feature does not already exist (return existing fid if this is the case).
Running version of adding a feature with a fid from the clearinghouse.
add_Feature additions
fix to verify_dir
RAE: Correcting what is meant by non-zero variant code
add subsystems_having_organisms
RAE: Adding statistics to protein families
added best_bbh_candidates_additional function
serious problem in setting max_expand in FIG::sims
RAE: Adding statistics to protein families
add abstract functional coupling
RAE: extending protein families
RAE: Changed attribute key to tag throughout
Added a method that can be used to determine whether the data is being taken from SEED or NMPDR.
Updating protein families
Added license words.
Don't save absolute paths in file_table in database; rather, strip them on file2N and restore on N2file.
Making attributes work for Ed
minor fix in reconizing aliases
correcting tag names
updating subsys.cgi so that it works with attributes again. Quickly, this time
correcting and extending get_distinct_keys
correcting return when no data supplied
removing error messages from attributes
major changes to attributes and protein families. There are changes to several modules to deal with new attributes database, and simultaneous updates to protein families
Added access methods for the UserData object. Fixed some documentation.
fixes to characterization of hypos
move cv files from Global to Global/CV
add search_cv_file as an encapsulation. cv, search_term -> ( (cv, term_id,term), ... ) I also have changes in index searching that I'm trying _not_ to commit. If you see wierdness, i messed up the commit so yell at me.
Fixed some documentation. Rewrote some ENV tests to avoid compiler warnings. Removed redundant variable declarations to avoid compiler warnings. Added a new method to test whether a role ID is an EC number.
Strip xxx identifiers from feature_aliases output.
Add run_gathering_output() for safe backtick-like functionality.
make add_cv_term give error status if passed empty strings.
make search_index_by_attribute be case insensitive.
How do you do this on just one line? Right now I used 2 lines (a bunch of times)
$user =~ s/^\s*//g;
$user =~ s/\s*$//g;
key_info: modify to return nothing if the passed key has no associated data (rather than returning empty hash). search_index: modify to call search_index_by_attributes so that attributes are included in the search without building glimpse indexes search_index_by_attribues: supports search_index. Also, in search_index, turned off old attribute search.
key_info() was returning and empty hash to say it had nothing that matches a key. this was making downstream code very confusing. so now i return nothing if there's no match for the key.
add new sub, add_cv_term($user, $peg, $vocab, $id, $term);
=head3 add_cv_term
Add a controlled vocabulary term to a peg. Pass in the peg, the vocab
name, the termId, and the term (see next paragraph). returns error string
if problem, else returns nothing.
my $status = $fig->add_cv_term( "master:EdF",
"fig|9606.3.peg.26823", "MyVocab", "1234", "A thing of wonder.");
if ($status) {print "error adding cv term: $status\n";}
Controlled vocabulary is read-only text associated with a peg. Each
is a triple, namely (vocab name, termId, term text). The termId is an
id that is used in the particulary vocabulary and the term text is the
actual term. For example, the GO has the term "U12-type nuclear mRNA
branch site recognition" with termId GO:0000371. Thus, the triplet is
(GO, GO:0000371, "U12-type nuclear mRNA branch site recognition").
Don't be confused by the GO: in GO:0000371. We don't add the GO:.
That's just what GO decided to do.
termIds can not have ';' in them.
This routine encapsulates our present implementation via attributes.
=cut
protein families again
Assorted relative-path fixes. remove length check in indexing function assignments.
fixed key_info
changing the format of attribute_keys
Added new documentation. Fixed attributes to prevent return of duplicate items.
Workaround for peg.synonyms file that has multiple entries.
Broad minor fixes to make the SEED use relative paths throughout. (The motivation this is to fully enable hiding the actual location of a running SEED system behind a web proxy so that things like NMPDR protein page references can be made stable across multiple releases). This involved things like the following: Changing $cgi->url() to $cgi->url(-relative => 1) Changing $cgi->self_url() to $cgi->url(-relative => 1, -query => 1, -path_info => 1) Changing the definition of FIG::cgi_url() to return "." (this may break something, but I haven't found it yet).
Added the "compute_clusters" method for use by UnvSubsys. Added a "FIG" method for compatability with SFXlate. Added more documentation.
add find_by_attribute. this takes a single string argument. it returns triples, (featureId, key, value) of all attributes in which the search string is a substring of either key or value. the search is via the attribute table, not via the glimpse indexes so tha searches immediately after edits of attributes work.
minor fix to not include xxx entries in expanded sims
adding more functions with external ids
loading external ids and external protein families
remove debug
fixes to update_uniq_id_data
fix display_subsys.cgi
Correcting display of classifications
fixes to display of reactions
add functiontion to FIG.pm to get active subsystems for a genome
Converted tabs to spaces to fix indenting.
upgrade sigs.cgi to run under Sprout
Added `formatdb` invocation to &add_genome(). Changed "VERBOSE" flag name to "FIG_VERBOSE". -- /gdp
make annotation requests by master return all non-assignment annotations.
Make annotations_made_fast return new Annotation objects instead of arrays of data. Add the Annotation object.
Remove the debugging file setting in add_annotations_batch.
Add $fig->add_annotations_batch() that does filehandle conservation and uses COPY TABLE instead of INSERT to add annotations to the database. Now used by 'fig add_annotations' so that large annotation file installs don't take overnight.
Force is_deleted_fid to set the value of $/ that it wants, since use of that method within a loop with $/ set to something else breaks is_deleted_fid. Darn global input record separator.
Add FIG::by_genome_id for sorting genome ID lists. Add $fig->extract_assignments_from_annoatations to transform the output of annotations_made_fast to a list of the current assignments (per the annotations data).
make package_annotations use $fig->annotations_made_fast. Add date parsing to FIG.pm ($fig->parse_date) using Date::Parse if available.
Tweaked tracing, added more documentation, fixed so that the annotations will work properly in environments where the number of characters in a file is different from the number of bytes.
Fixed &possibly_truncated() so that it does not blow up on non-PEG features. -- /gdp
Invoked `assess_completeness` from &add_genomes(). -- /gdp
Adding menus to subsys.cgi
fixes to calling starts
fixes to call_starts
Adding more details to organisms.cgi and correcting get_key_values
removing blank lines from attribute_keys
NMPDR updates
*** empty log message ***
Fixed change_attribute to work properly if the attribute value has quotes in it.
Fixed "add_attributes" to work correctly when quotes are present in attribute values.
Modified &to_aliases to make "TYPE" argument optional instead of mandatory. -- /gdp
Changed "add_feature" to save the return from the INSERT into the feature table so that it can be viewed during debugging.
More diagram changes. Add new simple start page.
Updated "add_feature" to allow the caller to specify the feature ID.
adding fig versus kegg
fix to multi-functional roles
New interface for subsys.cgi, but it is commented out at the moment
fixes to bugs in calling starts
adding options to add_genome
Make enqueue_similarities ignore a $fig argument if invoked as a method call. Add a $time_made argument to add_annotation.
Modified &possibly_truncated() to accept either FID or location. -- /gdp
Modified &possibly_truncated() to accept either FID or location. -- /gdp
Adding a force to the add_genomes
Support gif/png/jpeg file type detection on diagram upload. Support the multiple file types on packaging for clearinghouse.
Add support for creating and parsing diagram data as part of subsystem clearinghouse packages.
Changed attributes to capital-case in order to prevent the avalanche of compile-time warnings.
update stuff relating to protein families
Cosmetic changes to make clear that &display_id_and_seq() and &display_seq() take sequence-pointers, not sequences. -- /gdp
fixes to pick_gene_boundaries
Publish/install changes for reactions.
Support "fig load_all N" and "fig load_all list"
commit code to expand regions of similarity to PEGs and to recall starts
Fixed some POD comments.
Added "upstream_of" method to compute upstream sequences. Cleaned up some documentation.
7-26-05
altering location in FIG.pm
standardize returned DNA to lower case, as per GJO's request. -- /gdp
More final touches for Attributes code
minor chagnes to attributes
Updating attributes code in seed
Updating attributes code
Making attributes interface work
minor changes to subsys_vectors to allow complete genomes
minor changes to subsys_vectors.cgi
Changing attributes and modifying protein.cgi with show/hides
updates to build protein families
making index_subsystems work
added index subsystems to subsys.cgi
Changed proteinfamilies.cgi
Tweak tracing.
Initial release of proteinfamilies.cgi into the wild
commiting FIG.pm::clean_spaces to remove leading, trailing, and extra spaces. Please use it
Fixed the environment-variable tracing so that it does not override previous tracing options if they were set.
finally
Add some more gene name mapping stuff. Add Tracer environment variable for affecting tracing. Fix typo in invocation of load_coupling.
Replaced tabs with spaces to make indenting device-independent. Moved "Open" and "OpenDir" to the Tracer.pm module. Added more POD documentation.
Add genome/peg id mapping routines. (For functional coupling support).
add new protein family routines
add new protein family routines
disable old protein families
Ross change commit after cleanup
Added Open and OpenDir methods for streamlining file and directory operations.
fixes to cached pin displays
adding correspondence.cgi
re-add couipling routines
*** empty log message ***
*** empty log message ***
major change to BBHs (use precomputed)
Fixed typo in &hypo(), and added new rule. -- /gdp
install precomputed functional coupling data
add test for existence of relation that works only under Postgres
added subsystems_roles method to FIG.pm
Code for similarity request export.
fix bug in search_indexes
Bundle of misc bob changes, including sim computation code and search-for-substring.
fixes to using trees under subsystems
fix indexing search code
add css generation modules
add assign_to_close_strains
revised on Monday
minor fix to select tag/values
minor fix to select tag/values
handle missing annotations file gracefully
Fix bunged index search
search_index now returns attributes
changed genome stats to show attributes
Re-enable "duplicates" in sims. Multiple regions of matching is common in eukaryotic sequences, and only seeing one is disorienting.
changed tag/value pairs completely. Ooops!
many changes to key/value pairs to make them work
changing pir corresepondence
Added a script to load pir superfamilies in the background. This will download all the data and install it. Changed pir.cgi to background this job as it takes a while.
add update_subsys_conflicts to fig.pl
fix to asses_completeness
Add genome_with_md5sum. Warn on FigGFF errors only if you're bob.
changing attributes returned back to variables
minor changes to rae.cgi
add make_pu from ids and seqs
broaden set of acceptable aliases as dbxrefs
Removed constraint that sims request had to be by a fig ID. Ross seems to have solved the orginal problem that names that could not be mapped returned a representitive ID with undefined length, which crashed sims(). Now failure to map a name returns an empty list, and sims graceful returns an empty list of similarities.
A few similarities tweeks. Move the submit button on the default protein page (to shorten the line slightly). Remove a debug statement that was writing to the error log.
Add options to Similarities to override Max expand when asking for FIG IDs. It gets annoying to have to constantly increase the value, and it is not predictable how many sims will need to be expanded to get any desired number of FIG IDs.
fix to best_bbh_candidates and added fill_subsys
When sorting similarities by percent identity or bit score per position, include a penalty for very sort sequences, so that they do not randomly appear much higher in the similaries list than they should. The current treatment for this is roughly a two standard deviation penalty. The original behavior is still available as non-star versions. The "help" information has been updated (and other aspects clarified as well).
update hypo
Fix end condition test on expand_raw_sims to promptly return.
remove ddd: in front of some organisms (mostly uniprot)
change spaces to _s in subsystem names
make the gff stuff work again.
Put the FigGFF code in a require for now. Add fast anno lookup.
Add general-purpose GFF writing stuff.
Minor fix in expand_raw_sims so that it stops when it should
Initial commit of organisms.cgi which allows separate entry pages for different groups of organisms
fix for mapped_prot_ids
Making tag/value pairs work
Making tag/value pairs work
Many new options for similarities
Add contig_md5sum.
Add support for computing MD5 checksums for contigs and genomes. The checksum of a genome is defined as the checksum of its signature file. The signature file consists of tab-separated lines, one for each contig, ordered by the contig id. Each line contains the contig ID, the length of the contig in nucleotides, and the MD5 checksum of the nucleotide data, with uppercase letters forced to lower case. The signature file is written by index_contigs to The genome's md5 checksum is written by index_contigs to <genomedir>/MD5SUM. The md5.c code here is extracted from the Perl Digest::MD5 module. We use the perl configuration to build it so that it will work correctly on 64-bit architectures.
disconnect get_attributes until I can talk to Rob
added highlight by peg attribute to subsystem
tweaks to coloring ss by oa
Added color by organism attributes to subsystems page
Added attribute editing to the protein.cgi page
Big updates to FIG.pm for the addition of methods to properly handle attributes. Also modified genome_statistics to take advantage of these new methods. load_attributes will load genomes and other attributes but doesn't not yet use the new methods (but should), and Attributes.html is some docs.
major changes in notion of function and load_attributes
filters for data mining
add reset_curator.cgi
highlight subsystems with no genomes attached
Fix subsystem_classification in FIG.pm
Moved the subsystem_classification getting/setting into subsys.pm where it belongs, and so I ammended FIG.pm. Also added the boxes on the subsystem page so you can see the classifications.
minor change to FIG::subsystem_classification
Initial addition of subsys_summary.cgi and minor modification of FIG.pm
changes to subsystem_classification
fix routine for locating candidates for a role in a genome
Minor changes to pir.cgi and added subsystem_classification to FIG.pm
many fixes to extending subsystems
Add some pod to FIG.pm
update
added all_for_genome, etc
Add subsystems_for_genome.
no message
head -1 should be head -n 1
add pegs_in_subsystems
no message
fix bugs introduced into by_alias function
Time stamp individual load steps
fix dumb typo.
Add peg_in_gendb and genome_in_gendb
add get_system_name() call.
fix to scoring fc
More fixes for Sprout integration.
sprout debugging
no message
no message
I ran into a bug today where I was using by_alias to look up aliases
for the peg-mapping code, and one of the aliases was DR6', with a
single-quote. Because the code in by_alias doesn't quote its argument,
the SQL failed with a syntax error.
The perl DBI library has a mechanism designed to solve this
problem. If you use ? in a sql string where you want to substitute an
argument from code, DBI will do the appropriate quoting for you. I've
made this accessible via the SQL method in the DBrtns module, so the
by_alias code now looks like this:
if (($relational_db_response = $rdbH->SQL("SELECT id FROM ext_alias WHERE ( alias = ? )", undef, $alias))
and works properly in the face of $alias having a single-quote in
it. I believe this mechanism is also more efficient. Note the second
argument of SQL is a verbose flag, which means that any bound
variables (to replace ?s in the query) have to start at the third
argument.
I've also made a change in the SQL method such that the query is done
inside an eval{} block, and if it fails, the error is reraised using
confess so that it is possible to see the full backtrace so you can
find in the source where the bad query was.
fix disambiguating maps
add check to assign_function
add option to not create a release info file to get_release_info()
p2p changes.
fix stupid error in cleaning up aliases
automatically generate aliases from mapped IDs
minor fix to FIG.pm and addition of generate_kegg_map_ec_tables
fixes to assigned_function
allow set of seeks to cores for bbhs
Minor changes to FIG.pm POD
Changes to subsys.cgi that warn if a subsystem doesn't exist
raw time for annotations
fix a comment
add checking for subsystems
Add subsystem_roles() method. Add status callback to translate_pegs. Remove setting of sticky bit in verify_dir.
add higher-level construct support
untested changes to extract_genomes - copy-all-but in Global
allow external IDs on subsystem displays
add is_complete function to FIG.pm
fix bug in subsys.cgi and add Literature to Global
Adding some pod
stupid error in FIG.pm
fix bound in find_role_in_org
added function all_features_detailed will return fig_id, location, type as array
fill_in_cell for Heiko
added homologs_in_clusters.cgi
fix to by_alias
fixes to UniProt IDs on chromosomal_clusters.cgi
fixes to generalize chromosomal_clusters.cgi for UniProt
peg links generalized to fid links
fixes to subsystem code
remove extra EOLs on changed locations
fixes to change_location_of_feature
More fixes for sprout support.
Added number of contigs to menu
more DAS fixes
Changes for DAS integration
minor fixes to exporting sets
doc fix
Possible fix for beg_of and contig_of More p2p stuff
Some contig manipulation stuff, more p2p stuff.
$fig->adjacent_genes was not returning adjacent genes
remove print
Mods for P2P update stuff.
subsystem_genomes should return just genomes with an operational variant
remove inappropriate setting of g+s bit
Fixed errors in POD documentation. -- /gdp
add attributes as key-value pairs attached to fids
Add domain-based selection to genomes function. Used to generate domain-specfic genome lists.
minor fixes
add new subsystem interface
added adjacent_genes() and supporting methods
set current user
minor changes to indexing translations
sort sims into the correct order
fix evil bug in index searches
sort sims by bit score
Fix a typo in annotations_made and start adding infrastructure to fix genes_in_region issues
have function_of append to end of lines
update feature alterations
Fixed major error in org_of
handle changes to feature locations
add abilities to add, delete and update features
straighten out FIG.pm
interface for Bielefeld in FIG.pm
fix errors relating to read_annotations
major fix in read_annotations in FIG.pm
fixes to aliases_of
Colorize organisms by domain in similarities list. Changes protein.cgi and FIG.pm
fix order on genes returned in a region
sort links
handle bug that lost notes for subsystems
Added out-of-bounds checks to &extract_seq(), plus debugging information for loci whose sequences could not be extracted.
updates to ssa2.cgi and warnings when assignments fail
Add "umask 0" to fig.pm to ensure all new files are world writable.
More sim/askfor/pool stuff. Make fig load_all show progress. Fix run_in_background to do the right thing with an open db handle.
Add assignments_made_for_protein expand some code for readability.
handle names of subsystems just a bit better
Add assignments_made_full, which returns the date and id of person who made the assignment. assignments_made now just maps the result of assignments_made. Add some comments.
Modifications to fix & finish up the automated subsystem extension.
New map support.
add background job support.
Add background job support
Add scalar decl to is_bacterial and friends.
add more funcs for tutorials
add some scalar annotations; add find_role_in_org
Guard the rquire of figrpc in case we don't have the necessary modules installed for it.
Add capability for :scalar :list :remote annotations to FIG interface. This works with modules that are declared as subclasses of FIGAttributes.
reorder load of databases just slightly
Fixed typo in pod-documentation
Added check for "defined" status of filehandle reads from <SSA>; removed various "masking" redefinitions of "my" variables.
Fixed typos in various $fig->genome_*() accessor functions.
fix typo.
Add $force_load argument to get_subsystem; results in the discarding of the cached subsystem if there is one.
add subsystems_for_peg
fix the call to figrpc
added redirect in FIG constructor to create a FIGrpc if the FIG_URL environment variable is set
make bbhs sensitive to lengths of match - watch out for fused proteins
precomputed BBHs
untested changes to extract_genomes
attempt to change FIG.pm to keep mac-1 up
doh, had left a debug print in there
add genome_and_peg_of
Factor out the subsystem caching.
cache subsystem objects, since they can be expensive to create.
Beginning of sim queueing stuff. First implementation of Subsystem object, with FIG::peg_in_subsystem_cell implemented in terms of it.
Changed name of genome-size access method to \&genome_szdna($genome_id) to match the SQL keyword; added \&genome_pegs($genome) and \&genome_rnas($genome) to return number of PEGs and RNAs, resp.
Added access method \&genome_size($genome_id) to return the number of base-pairs in an organism\'s contig files.
add file_head and file_read
fix error in tutorial
fixes to similarities
make aliases include external aliases
allow comma-separated contiguous regions in dna_seq argument list
add all_contigs
fixes on memory leak and genome version
set max open files to 50
support addition of links to pegs
fixed up links
fix add_genome
more protection around the code that pokes at the clearing house, in case xmlrpc libs are missing
Add comment.
Comment out import of Clearinghouse until we get the env updated.
tools for query
Clearinghouse publishing stuff
fix to definition of bbh
basic query tools
make sure that external_calls produces one function for each peg
tools for McCune to build expert automated assignments
make load_all build blast dbs for fig proteins
fixes to index.cgi to blast against all complete
fixes to best_candidates
fixes to best_bbh_candidates
fix a bad bug in assignment permissions
pass back more detailed data for candidates for a role
more intelligent candidates for function
fixes in auto assignments
allow p2p to send me epoch dates, rather than readable dates
turn off warning messages for translation failures when translating PEG ids
More P2P fixes. Add setgid to the mkdir/chmod's.
fixes to candidates for a role
p2p for updating release
p2p changes
attempt to fix package/install for p2p
move PEG translation into FIG.pm
removes ## markers in FIG.pm
removes ## markers in FIG.pm and fixed Blast.pm
Make get_local_hostname check for a FIGdisk/config/hostname file and use that as the local hostname if present.
better peg mapping when importing spreadsheets
includes errors
improvements on importing subsystems
export subsystems stuff
Broke a semicolon-chained set of commands in &delete_genomes() into separate &run() invocations, so that if any of them fail, the delete operation will abort. -- /gdp
Fixed failure to declare two variables in routine &read_fasta_record(). -- /gdp
Added routine &read_fasta_record(). -- /gdp