Avril Coghlan avrilcoghlan
avrilcoghlan
/ get_treefam_family_seqs2.pl
Created
March 1, 2013 14:18
Perl script that prints out all the protein sequences in a particular TreeFam family
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script get_treefam_family_seqs.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 19-Nov-08. | |
| # Updated 19-Nov-08. | |
| # | |
| # For the TreeFam project. | |
| # |
avrilcoghlan
/ list_treefam_families.pl
Created
March 1, 2013 14:20
Perl script that makes a list of all families in the TreeFam mysql database
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script list_treefam_families.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 27-Feb-07. | |
| # Updated 6-Dec-07. | |
| # | |
| # This perl script makes a list of families in the TreeFam mysql database. | |
| # |
avrilcoghlan
/ store_treefam_full_nt_alns.pl
Created
March 1, 2013 14:25
Perl script that retrieves the full nucleotide alignments for TreeFam families, and stores them in a Perl pickle
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script store_treefam_full_nt_alns.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 3-Apr-09. | |
| # | |
| # For the TreeFam project. | |
| # | |
| # This perl script connects to the TreeFam database and stores |
avrilcoghlan
/ store_treefam_orthostrap.pl
Created
March 1, 2013 14:29
Perl script that retrieves orthology bootstrap values for ortholog pairs for a particular pair of species from the TreeFam database, and stores the orthology bootstrap values in a Perl pickle
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script store_treefam_orthostrap.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 4-Apr-09. | |
| # | |
| # For the TreeFam project. | |
| # | |
| # This perl script connects to the TreeFam database and stores the orthology |
avrilcoghlan
/ store_treefam_species.pl
Created
March 1, 2013 14:32
Perl script that retrieves a list of all the fully sequenced species that are in the TreeFam database, and stores them in a Perl pickle
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script store_treefam_species.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 3-Apr-09. | |
| # | |
| # For the TreeFam project. | |
| # | |
| # This perl script connects to the TreeFam database and stores |
avrilcoghlan
/ store_treefam_trees.pl
Created
March 1, 2013 14:35
Perl script that retrieves all trees from the TreeFam database, and stores them in a Perl pickle
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script store_treefam_trees.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 3-Apr-09. | |
| # | |
| # For the TreeFam project. | |
| # | |
| # This perl script connects to the TreeFam database and stores |
avrilcoghlan
/ treefam_QC1.pl
Created
March 1, 2013 14:39
Perl script that finds TreeFam proteins that have a strong match to a family in the TreeFam mysql hmmer_matches table, but where the gene was not added to the 'fam_genes' table for the family or to any family.
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script treefam_QC1.pl | |
| # Written by Avril Coghlan (a.coghlan:ucc.ie) | |
| # 9-Dec-08. | |
| # Edited 9-Jan-09. | |
| # | |
| # This perl script finds TreeFam proteins that have a strong match to a family | |
| # in the treefam mysql hmmer_matches table, but where the gene was not added to the |
avrilcoghlan
/ treefam_QC2.pl
Created
March 1, 2013 14:41
Perl script that finds TreeFam families that are lacking a tree in the 'trees' table of the TreeFam mysql database.
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script treefam_QC2.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 3-Feb-09. | |
| # | |
| # This perl script finds TreeFam families that are lacking a tree in the | |
| # 'trees' table. | |
| # |
avrilcoghlan
/ treefam_QC3.pl
Created
March 1, 2013 14:42
Perl script that finds cases where a TreeFam family is listed in the TreeFam mysql database, but has no genes listed in the 'fam_genes' table.
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script treefam_QC3.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 3-Feb-09. | |
| # | |
| # This perl script finds cases where there is a TreeFam family listed in the | |
| # 'familyA' or 'familyB' or 'familyC' tables, but it has no genes listed in | |
| # the 'fam_genes' table. |
avrilcoghlan
/ treefam_QC4.pl
Created
March 1, 2013 14:44
Perl script that finds TreeFam proteins that have a match to a family in the TreeFam mysql 'hmmer_matches' table, but where the gene does not appear in the 'genes' table.
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| #!/usr/local/bin/perl | |
| # | |
| # Perl script treefam_QC4.pl | |
| # Written by Avril Coghlan ([email protected]) | |
| # 3-Feb-09. | |
| # | |
| # This perl script finds TreeFam proteins that have a match to a family | |
| # in the treefam mysql hmmer_matches table, but where the gene does not | |
| # appear in the 'genes' table. |