zagrosman / scripts Goto Github PK

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