get_homologues-est

This release has two main changes:

25022020: local BLAST jobs in get_homologues.pl are not splitted if proteomes < $BATCHSIZE; 2x speedup
26022020: fixed parse_pangenome_matrix.pl -p which was not parsing contig names correctly
26022020: added parse_pangenome_matrix.pl -p to test suite

get_homologues-est

This release ships with the following changes:

16122019: phyTools::constructDirectory now returns 1 if successful (thanks Ardy Kharabianmasouleh)
16122019: get_homologues[-est].pl now check return value of phyTools::constructDirectory
16122019: parse_pangenome_matrix.pl makes sure cloud occupancy < soft-core occupancy (thanks Sohini)
05012020: hcluster_pangenome_matrix.sh v5Jan2020, added option -P , added function cleanup_R_script, continuous color scale, only row dendrogram, fixed find command
12012020: hcluster_pangenome_matrix.sh v2.0_12Jan2020, major script update, see development notes with -D
22012020: hcluster_pangenome_matrix.sh v2.1_22Jan20
23012020: moved subs fisher_yates_shuffle short_path factorial calc_mean calc_std_deviation calc_memory_footprint warn_missing_soft to lib/pyTools.pm
23012020: moved subs get_string_with_previous_genomes split_Pfam_clusters to libs/marfil_homology.pm
23012020: created libs/HPCluster.pm to handle HPC cluster interaction, now supports SGE & LSF
24012020: get_homologues.pl & get_homologues-est.pl now import libs/HPCluster.pm
24012020: added cluster.conf.template
24012020: added ./install test
24012020: updated help message of _split_blast.pl and _split_hmmscan.pl
24012020: added download_genomes_ncbi.pl test
24012020: added test t/get_homologues.t
24012020: hcluster_pangenome_matrix.sh v2.2_22Jan20, removes intermediate silhouette-width genome table
27012020: added to Travis (Makefile, .travis.yml)
27012020: added transcripts2cdsCPP.pl to t/get_homologues.t
27012020: automatic Travis builds already in place, check badge in README.md
28012020: fixed stderr message printed out by warn_missing_soft
28012020: moved t/get_homologues.t to test_get_homologues.t
28012020: added sample_plasmids_gbk_homologues to support real tests with precomputed BLAST output
28012020: Travis tests now do real tests of get_homologues.pl, compare_clusters.pl & parse_pangenome_matrix.pl
28012020: Makefile removes tmp output of tests and also supports install target
31012020: added LSF and updated gridengine documentation in manuals
05022020: added slurm support and updated documentation
06022020: fixed macosx binaries and updated install.pl accordingly

binaries

Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl

get_homologues-est

This release ships with the following changes:

12092019: trailing tab removed from pangenome matrices (.tab) produced by compare_clusters.pl
12092019: compare_clusters.pl now also produces transposed matrices (.tab)
12092019: parse_pangenome_matrix.pl now warns if you pass it a transposed matrix (.tab)
28112919: updated manuals, flowcharts and tutorial

get_homologues-est

This release includes the following changes:

12042019: sort at the end of pfam_enrich.pl saved to file to avoid pipe errors
17062019: optimized if in subs parsing gbk files
19062019: download_genomes_ncbi.pl now can handle GCF_000261785.1 accessions, which are internally converted to GCA_000261785.1_05623
19062019: extract_*_genbank subs now add input filename to FASTA header to disambiguate sequences with non-unique ids
19062019: extract_gene_name adapted to new header format
05082019: fixed bug in extract_gene_from_genbank affecting files with CDS features without /translation, thanks Christian Sanchez
05082019: updated release.pl

get_homologues-est

This release includes the following changes:

03012019: fixed argument print out in transcripts2cds[CPP].pl
03012019: updated install.pl so that it downloads bin.tgz if blast is missing (likely to blast being updated)
04032019: fixed warning in check_BDBHs.pl when doing -m local .faa analyses
05032019: improved marfil_homology::sort_blast_results to minimize sort -m temp files
05032019: updated TODO.txt
11042019: fixed two bugs in pfam_enrich.pl that caused runtime warnings

get_homologues-est

This release includes the following changes:

02012019: updated BLAST+ to ncbi-blast-2.8.1+

binaries

Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl

get_homologues-est

This release includes the following changes:

03092018: added section 'Output files explained' to EST manual (thanks Lior Glick)
05092018: updated shebangs of some scripts and added use warnings instead of -w (thanks morgansobol)
10092018: aligned_coords checked before being added to FASTA headers @ get_homologues* (use Warnings)
10092018: pfam_hash keys checked before being used (use Warnings)
20092018: added #include <unistd.h> to bin/COGsoft/COGreadblast/bc.h so that it compiles ok

binaries

Compressed TAR file with binaries to be downloaded after cloning the source repository. This should be done with install.pl