Scripts

BCModules.pm. . . . . . Biocluster specific sequence analysis modules<br> FM_ZygoAnalysis.pl. . . Specific script for analysis of Zygomycete run <br> IPR2latex.pl. . . . . . <br> IPR_reorder.pl. . . . . Used in MG_HMM workflow <br> ProteinModelSelection.pl<br> SeqAnalysis.pm. . . . . Perl module containing often-used subroutines for sequence processing<br> bio3d.R . . . . . . . . Loads Bio3D module and runs through steps to generate PCA plot<br> blast2krona.pl. . . . . Takes BLAST results and creates a Krona data file <br> bp_sreformat.pl . . . . <br> bp_ssearchparse.pl. . . Parses all ssearch files in the given directory; Gathers counts and sequences.<br> calcN50.pl. . . . . . . Test to calculate N50 value <br> cbind.pl. . . . . . . . Like cbind() in R <br> dephylip_tree.pl. . . . Dephylips Newick tree files<br> dinucl.pl . . . . . . . Calculates dinucleotide distribution for a given DNA string <br> fasta2go.pl . . . . . . Joins geneIDs to GO terms using previously established DBs <br> fasta2hmm.pl. . . . . . Pipeline for converting unaligned fasta files to hmm files<br> fasta2taxonomy.pl . . . Generates a taxonomy file from species in a Fasta description line <br> fastaClean.pl . . . . . Cleans up fasta descriptions (Not for general use; highly specific) <br> fastaSubset.pl. . . . . Takes a large fasta file and parses it into several smaller fasta files containing the desired number of sequences <br> fastaresize.pl. . . . . Rewrites a fasta file to be of a new width<br> gbk2pep.pl. . . . . . . Parses out translated regions from a genbank file<br> getPFAM.pl. . . . . . . Gets all PFAM IDs associated with a gene ID for a given organism<br> getSingleTax.pl . . . . Single use to get full taxonomy of a species <br> getTM.pl. . . . . . . . Parses the 6-9 TM sequences from a TMHMM results file <br> getTopHit.pl. . . . . . Gets the top hit from an m8 formatted blast results file <br> getaccnos.pl. . . . . . Gets names of all sequences in a .fasta file (this is done using seqcount.pl as well)<br> getkegg.pl. . . . . . . Parses a keggfile and downloads the genes <br> getscripts.pl . . . . . Produces README.md containing all of the custom scripts in ~/scripts<br> getseqfromfile.pl . . . Provide a sequence ID and a fasta flatfile (database) and the script will return the fasta-formatted sequence<br> getseqs.pl. . . . . . . Retrieve sequences from GenBank based accession numbers found in the input file<br> gffParse.pl . . . . . . <br> gimpvert.pl . . . . . . Converts gel-imager .tif images to .png files; opens in Gimp for optional editing<br> hashPFAM.pl . . . . . . Analyse flagellar patterns <br> hmmCount.pl . . . . . . General script to get counts from HMM results file <br> hmm_run.pl. . . . . . . Generates a shell script to run batch searches using either hmmsearch or hmmscan<br> hmmparse.pl . . . . . . Parses an HMM result file, scan or search<br> hmmparse_single.pl. . . <br> kegg.pl . . . . . . . . Queries the KEGG db to collect genes in a given pathway<br> mkpdf.R . . . . . . . . R script to use Sweave to convert LaTeX file to pdf and display<br> mkpl.pl . . . . . . . . Sets up perl skeleton script<br> mkpm.pl . . . . . . . . Sets up a perl module template with comments and standard info <br> parseByTax.pl . . . . . Trims an "out_table" file in accordance with a specific set of organisms <br> parseContacts.pl. . . . Parse Google Contacts csv file <br> patternAnalysis.pl. . . A script to analyze patterns in the flagella (gain/loss) search<br> pf2g.pl . . . . . . . . Takes a list of pfam IDs and maps them to go terms<br> print_all.R . . . . . . Loads Bio3D module and plots PCA using a variety of pre-defined color schemes<br> processHits.pl. . . . . Pulls out specific proteins from this Flagellar SSEARCH run <br> process_kegg.pl . . . . Process a KEGG record file<br> qiime_workflow.pl . . . Generate shell scripts for processing qiime Amend2009 files w/ UNITE db <br> qiime_workflow2.pl. . . Generate shell scripts for processing qiime Amazon_air files w/ UNITE db <br> rna-seq.R . . . . . . . <br> secretomePrediction.pl. Executes secretome workflow described by "Min et al. J Proteomics+Bioinformatics 2010" <br> seqlen.pl . . . . . . . Extracts sequence lengths from a fasta file<br> showPool.pl . . . . . . Takes pool input and highlights residues in Pymol<br> spc2tab.pl. . . . . . . Replaces multispace-delim files to tsv files <br> spc2us.pl . . . . . . . renamer script used for replacing spaces w/ underscores in filenames<br> split_fastq.pl. . . . . Splits a fastq file into a fasta and a qual file<br> splitup.pl. . . . . . . splits each sequence of a single multi-sequence fasta file into multiple single-sequence fasta files<br> ssearch_run.pl. . . . . Generates batch shell script for ssearches<br> ssearchrank.pl. . . . . Searches many FASTA search result files to get a better scoring match for a particular transcript<br> trin2gaf.pl . . . . . . Maps trinotate file to GO association file for GOSlim <br> unalign.pl. . . . . . . Un-aligns a fasta-formatted alignment<br>