Example of data redundency  


Var name: in_seq_user_nosum:
Key: test_User
Val: >test_User
MAATWAGGGTAMMM

Var name: in_sqonly
Key: test_User
Val: MAATWAGGGTAMMM


Var name: in_seq_user
Key: len
Val: HASH(0xb178830)
Key: all_summary
Val: test_User
Key: test_User
Val: >test_User
MAATWAGGGTAMMM

Var name: in_seq
Key: test
val: >test_User
MAATWAGGGTAMMM

  

 

Functions calls from TarO_indevel.pl

Function (package:name) Function description
  • Clust_int_taro::num_seqs()
  
  • TarO_indevel::read_fasta_adduser_cleanup()
  • TarO_indevel::read_fasta_subset_fromstring()
  • TarO_indevel::read_fasta()
  • TarO_indevel::read_fasta_seqonly()
  
  • TarO_indevel::write_fasta_updatevars
  
  • TarO_indevel::check_output ()
  
  • TarO_indevel::stat_files()
  
  • Clust_int_taro::wait_for_cluster
  
  • Clust_int_taro::psiblast_newclust_localDB()
  
  • Blast_pars::psiblastout()
  
  • Clust_int_taro->initialise()
  • TarO_indevel::process_summary()
  • TarO_indevel::copy_attributes()
  • Blast_pars::assign_match()
  • TarO_indevel::assign_object_field()
  • TarO_indevel::order_seqs_blas()
  • Clust_int_taro::num_seqs()
  • Clust_int_taro::tidy_up()
  • Clust_int_taro::blast_newclus_pri()
  • Clust_int_taro::rpsblast_newclus_pri()
  • TarO_indevel::read_muscle_msa_fa()
  • TarO_indevel::cleanup_fasta_strict()
  • TarO_indevel::calc_gravy_pI_clus()
  • TarO_indevel::readin_globplot_output()
  • TarO_indevel::readin_disembl_output()
  • TarO_indevel::parse_ronn_finalout()
  • TarO_indevel::readin_tm_oo()
  • TarO_indevel::parse_jnet_finalout()
  • TarO_indevel::clean_jnet_for_jalview()
  • MIME::Lite()
  
  • TarO_indevel::write_fasta_count_seqs()
  • TarO_indevel::write_fasta()
  
TarO_indevel::read_tabdelim()  
  • TarO_indevel::dbtab_uniref_tophit()
  • TarO_indevel::dbtab_Astral_blast_tophit()
  • TarO_indevel::dbtab_TargetDB_blast_tophit()
  • TarO_indevel::dbtab_RPS_blast_tophit()
  • TarO_indevel::dbtab_annotation()
  • TarO_indevel::dbtab_display_main()
  
Taro_inDevel::$vars content Key verbose val 0
Key orig_in val /fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO1381/TO1381.fasta
Key minimal_upload val 0
Key input val /fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO1381/TO1381.user.fasta
Key block_size val 50
Key perlscripts val /homes/www-refine/SSPF_TO1/TarO_newclus
Key spec_overw val 0
Key tmp_clus_dir val /local/gjb_lab/refine/tmp/refine
Key debug val 0
Key overwrite val 0
Key uniq_intag val TO1381
Key out_dir val /fc_gpfs/gjb_lab/www-refine/pipeline_newclus/TO1381
Key max_num_msa_seqs val 10
Key dat_files val /homes/www-refine/SSPF_TO1/TarO_newclus/databases
Key uemail val P.V.Troshin@dundee.ac.uk
Key outfile_ext val .user.fasta
Key usr_id val 87
Key jobs_dir val /homes/www-refine/NOBACK/pipeline_results/raw_pipe_out_newclus
Key db_qid val 1381
Key psiblast_localdb val /local/gjb_lab/refine/tmp/refinepipe/db