Function list

For reference, here is the list of internal functions in TagDigger.

Core TagDigger program:

• combine_barcode_and_cutsite: Add restriction cut sites to the end of each barcode in a list
• tree_one_level: Take a set of sequences, sort them by the first letter, return a set of lists.
• tree_recursive: Build tree recursively for indexing sequences (either barcodes or tags) rapidly
• build_sequence_tree: Give each sequence a number to use for indexing, then build tree
• sequence_index_lookup: Lookup a sequence in an index tree, and get the index
• enumerate_cut_sites: Given an ambiguous cut site written in IUPAC codes, generate all possible cut sites
• find_tags_fastq: Make indexing trees for barcodes, cut sites, and tags, then go through a FASTQ file and count up instances of barcode*tag combos
• isFastq: Check the first four lines of a file, return 1 if is it an unzipped FASTQ file, 2 if it is gzipped FASTQ file, and 0 if it is neither or if it can't be opened
• readBarcodeKeyfile: Read in a csv file containing file names, barcodes, and sample names, and output a dictionary containing this information

Reading tags:

• compareTags: Find SNP alleles within a set of sequence tags representing the same locus
• readTags_UNEAK_FASTA: Read in pairs of tags from a FASTA file output by the TASSEL UNEAK pipeline
• readTags_Rows: Read a CSV of sequence tags, where each row has a marker name, an allele name, and a tag sequence
• readTags_Columns: Read a CSV of sequence tags, where each row has a marker name and two tag sequences representing two alleles
• readTags_Merged: Read a CSV of sequence tags, where each row has a marker name and a tag sequence with polymorphic nucleotides in square brackets separated by a forward slash
• readTags_Stacks: Read tags from the catalog format produced by Stacks
• readTags_TASSELSAM: Read tag sequences from a SAM file and match marker names using the same conventions as TASSEL-GBSv2
• readTags_pyRAD: Read the .alleles output from pyRAD and import tags
• readMarkerNames: Read in a simple list of marker names, and use for selecting markers to keep from a larger list of tags
• readTags_interactive: Interactively read in sequence tags
• sanitizeTags: Eliminate tags that will cause problems from the list (i.e. tags that are shorter versions of other tags)

TagDigger results export:

• combineReadCounts: Combine read counts across multiple libraries, merging samples with identical names

• writeCounts: Write a CSV file of tag counts

• extractMarkers: Get marker names, allele names, and indexes from tag names

• writeDiploidGeno: Write numeric diploid genotypes to a CSV file

• set_directory_interactive: Allow user to change working directory

Barcode splitter:

• reverseComplement: Make the reverse complement of a nucleotide sequence
• build_adapter_tree: Build a set of indexing trees, one for each barcode, for rapidly searching for adapter sequence at the end of a sequence
• findAdapterSeq: Find restriction site and/or adapters in a sequence, and give an index for slicing the string to remove them
• barcodeSplitter: Function to split one FASTQ file into multiple files by barcode, removing barcode and adapter sequence
• writeMD5sums: Write a CSV of file names and MD5 checksums, given a list of file names

Tag manager:

• exportFasta: Function to take a list of tags and export to a FASTA file for use in an alignment program such as Bowtie2 or BLAST
• varSitesByMarker: Across a set of tags as imported by a readTags function, make a dictionary of the positions of all variable sites for each marker
• readSAM: Read in a SAM file of alignment information for markers
• mergeTags: Given a list of sequences, produce an output string in "merged" format, with square brackets surrounding the variable region and a forward slash(es) separating the two or more variants
• mergedTagList: Given a list of tag names and tags such as those output by the readTags functions, output a list of marker names and a list of merged tag strings
• readTabularData: Read in a table of extra columns to include in tag database
• writeMarkerDatabase: Write a CSV giving sequence and other information for markers
• readMarkerDatabase: Read in a CSV file containing a SNP marker database as produced by writeMarkerDatabase
• lookupMarkerByTag: For a set of tags corresponding to one marker for the query, retrieve a set of markers with matching tags
• sortTagsBySeq: Take tags output by one of the readTags functions, and return tags and tag names in the same format but sorted by sequence (for binary search)
• compareTagSets: Compare two sets of tags, in the format output by the readTags function. Return a dictionary where the keys include all marker names from newtags, and the items are the marker names from oldtags (if found)
• consolidateTagSets: Allowing for multiple tags per marker, and for tag sets that do not completely overlap between old and new markers, make a consolidated set of tags and marker names
• allColumns: Combine all column names into one list
• consolidateExtraCols: Consolidate data from columns with the same column header

New functions to be incorporated into programs

• remove_monomorphic_loci: Given a set of imported tags, filter out any belonging to monomorphic loci