Perl scripts for genomic analysis:
AddMapMan.pl -Takes the output of MapMan annotation and adds results to a list of gene_IDs
AlignHomologs.pl -Aligns, trims and makes trees for each cluster from GroupSequences.pl
AllSelaginella.pl -Runs a command on all KRAUS, MOEL, UNC and WILD datasets
Blast2GTF -Convert homology info about the top blast hit of each sequence to GTF features
CheckMono.py -Determine if Selaginella sequence tree is congruent with species tree
ClusterHomologs.pl -Clusters sequences by blast eValue using single-linkage clustering
CombineCounts.pl, -Combine the output from DESeq for each species, providing counts and significance
CompareSets.pl -Compares the values in the first column of files and produces Venn diagram code
ContigStats.pl -Prints basic info about the sequences in a file
ConvertSeq.pl - Convert among a variety of sequence and alignment file formats
Ensembl.pl -Testing the functionality of the Ensembl API
ExtractEntrez.pl -Search for genbank accession numbers and generat a entrez query to limit blast results
FilterSeq.pl -filtering sequences on min and/or max length
FixTranscripts.pl -modifies GTF files to group exons from the same gene and indicate paralogs
GetOrthologGroup.py -Use blast results to add sequences to ortholog groups
GetSeq.pl -indexes fasta file and retrieves specified sequences
GetSeqsByGeneID.pl - Matches GeneIDs to contig names and outputs seqs matching list of GeneIDs
GroupSeqs.pl -Creates individual fasta files for each cluster identified by ClusterHomologs.pl
MakeConsensus.py -Creates consensus sequence from all sequences that group together from the specified species
NonRef.pl - Creates a file sequences that do not match a list of names
ParallelBatch.py -runs the specified command on all files in the specified folder using the specified number of nodes
rc.pl -Reverse-complement sequence
RemoveDuplicates.pl -Deletes sequences with duplicate names
RemoveSeqs.py -removes all sequences matching the search term from a file
RunPhyml.py -Wrapper to run PhyML on the specified file
ScafTranscritps.pl -Combines contigs that blast to the same reference gene
SelaginellaPipeline.py -Automatically runs all scriptable steps of my Selaginella workflow
SigDigits.pl -a simple script to trim all numbers in a csv file to the specified number of digits
Temp - a folder for quick scripts that do not need to be added to the repo
TopHit.pl -Excludes sub-optimal hits for each query and sub-optimal queries for each hit
trunc.pl -truncates sequences from STDIN
========================================================================================= Modules (Perl modules utilized by scripts in main folder):
FileParser.pl -subroutines to read and write GTF and (modified) blast tabular entries
HeathPy.py -custom python functions
========================================================================================= t Folder of test datasets
test.bl - seqs 1,2,5 and 6 cluster (1 and 5 are opposite strand of 2 and 6) and 3 and 4 cluster (same strand)
test.fa - two sequences (each 1225bp plus 220 -'s, 26 n's), names correspond to test.bl
test.gtf -gtf with 5 exon features (3 match the same ref gene (2 consecutive), one does not match ref)
raw_seq.txt - one sequence (1225bp plus 220 -'s, 26 n's) with no fasta header