some references to lamp/lamp.py in code still

[gawbul]

Following the name change, there are still some functions with the lamp name:

vespa $ ag lamp
vespa.py
166:For example: lamp.py help clean
453:### Details: handles general output assignment for LaMP functions
474:### Details: handles directory output assignment for laMP functions
580:                     'ENSPSIG':'Chinese_softshell_turtle', 'ENSPMAG':'Lamprey', 'ENSPPYG':'Orangutan',
640:### Function: lamp_codeml_reader:
641:### Details: LaMP codeML output reader
642:def lamp_codeml_reader (input_files):
643:    print 'LaMP: CodeML Reader'
824:### Function: lamp_branch_table:
825:### Details: LaMP function that creates a branch table from species tree
826:def lamp_branch_table(input_files):
827:    print 'LaMP: Branch Table Creator'
916:### Function: lamp_map_protein_gaps:
918:def lamp_map_protein_gaps(input_files):
919:    print 'LaMP: Mapping Nucleotide Alignments'
990:### Function: lamp_mrbayes_reader:
992:def lamp_mrbayes_reader (input_files):
993:    print 'LaMP: Reading MrBayes Output'
1019:### Function: lamp_infer_genetree:
1021:def lamp_infer_genetree (input_files):
1022:    print 'LaMP: Inferring GeneTree'
1091:### Function: lamp_link_input:
1093:def lamp_link_input(input_files):
1094:    print 'LaMP: Linking Input'
1145:### Function: lamp_codeml_setup:
1147:def lamp_codeml_setup(input_files):
1148:    print 'LaMP: CodeML Setup'
1394:### Function: lamp_subtrees:
1396:def lamp_subtrees(input_files):
1397:    print 'LaMP: Create SubTrees'
1586:### Function: lamp_metAl_compare:
1588:def lamp_metAl_compare (input_files):
1589:    print 'LaMP: metAl compare'
1697:### Function: lamp_setup_prottest:
1699:def lamp_setup_prottest(input_files):
1700:    print 'LaMP: ProtTest Setup'
1713:### Function: lamp_prottest_reader:
1715:def lamp_prottest_reader (input_files):
1716:    print 'LaMP: ProtTest Results Reader'
1765:### Function: lamp_setup_mrbayes:
1767:def lamp_setup_mrbayes (input_files):
1768:    print 'LaMP: MrBayes Setup'
1847:### Functions: lamp_setup_reciprocal_input
1849:def lamp_setup_reciprocal_input(input_files):
1951:### Functions: lamp_best_reciprocal_similarity_groups
1953:def lamp_best_reciprocal_similarity_groups(input_files):
1978:    print 'LaMP: Best-Reciprocal Groups'
2009:### Functions: lamp_similarity_groups
2011:def lamp_similarity_groups(input_files, reciprocality_check):
2031:        print 'LaMP: Reciprocal Groups'
2033:        print 'LaMP: Similarity Groups'
2069:### Function: lamp_clean:
2071:def lamp_clean (input_files):
2072:    print 'LaMP: Cleaning sequences'
2101:### Function: lamp_clean_ensembl:
2103:def lamp_clean_ensembl (input_files):
2104:    print 'LaMP: Cleaning ENSEBML sequences'
2148:### Function: lamp_reverse_complement:
2150:def lamp_reverse_complement (input_files):
2151:    print 'LaMP: Reverse Complementing Sequences'
2167:### Function: lamp_translate:
2169:def lamp_translate (input_files):
2170:    print 'LaMP: Translating Sequences'
2207:### Function: lamp_create_database:
2209:def lamp_create_database (input_files):
2216:    print 'LaMP: Creating Database'
2239:                print 'LaMP: Formatting BLAST Database'
2246:### Function: lamp_individual_sequences:
2248:def lamp_individual_sequences (input_files):
2266:    print 'LaMP: Creating Individual Sequences'
2284:### Function: lamp_split_in_groups:
2286:def lamp_split_in_groups (input_files):
2288:    print 'LaMP: Creating sequence groups'
2329:### Function: lamp_gene_selection:
2331:def lamp_gene_selection (input_files):
2349:    print 'LaMP: Gene selection'
2380:### Function: lamp_check_SGO:
2382:def lamp_check_SGO (input_files):
2385:    print 'LaMP: Checking SGO status'
2406:### Function: lamp_reduce_ensembl:
2408:def lamp_reduce_ensembl (input_files):
2409:    print 'LaMP: Reduce Ensembl Created Headers'
2662:                    lamp_clean_ensembl(command_input)
2664:                    lamp_clean(command_input)
2666:                    lamp_translate(command_input)
2668:                    lamp_reverse_complement(command_input)
2670:                    lamp_create_database(command_input,)
2672:                    lamp_individual_sequences(command_input)
2674:                    lamp_split_in_groups(command_input)
2676:                    lamp_gene_selection(command_input)
2678:                    lamp_check_SGO(command_input)
2680:                    lamp_reduce_ensembl(command_input)
2684:                    lamp_setup_reciprocal_input(command_input)
2686:                    lamp_best_reciprocal_similarity_groups(command_input)
2688:                    lamp_similarity_groups(command_input,True)
2690:                    lamp_similarity_groups(command_input,False)
2694:                    lamp_metAl_compare(command_input)
2696:                    lamp_setup_prottest(command_input)
2698:                    lamp_prottest_reader(command_input)
2700:                    lamp_setup_mrbayes(command_input)
2705:                    lamp_mrbayes_reader(command_input)
2707:                    lamp_branch_table(command_input)
2709:                    lamp_subtrees(command_input)
2711:                    lamp_map_protein_gaps(command_input)
2713:                    lamp_infer_genetree(command_input)
2715:                    lamp_link_input(command_input)
2717:                    lamp_codeml_setup(command_input)
2721:                    lamp_codeml_reader(command_input)

[gawbul]

Have submitted a pull request to fix the instances of lamp in vespa.py

[aewebb80]

Sorry for taking so long, I was away. Just updated these occurrences. Thanks!

[aewebb80]

I believe I approved the pull requests. Let me know if that isn't working.

[gawbul]

Cool, thanks @aewebb80. Have fixed a slight conflict with my branch, and it should be ready to merge and close now 😄