Returns a list of taxa from a taxa file

Parses a VCF file and retains the location of all SNPs in the genome as a list of tupples

Main function comparing the information contained in a VCF file between pairs of technical replicates. The relevant statistics will be stored

Parses an Fst file from vcftools. Returns a dictionary with the chromosome and postition as key and fst value as value. If he fst_range a

Returns a list of taxa from a taxa file

Removes invariable sites from a VCF file. This assumes that the genotype columns start at the 10th column until the last column :param vc

Gets a loci list, and a loci file and filters it. It then saves the data in GPhoCS format.

Counts the number of '//', adds that number to the string and prints it to stdout.

Grabs a VCF file and adds "SNP_##" to the end of the line, to match those outputed by PDGspider when converting to to other formats.

Parse the VCF and return a list with the loci that contain SNPs.

Parses a VCF file and plots the frequency of the number of alternative SNPs for each taxon

Parses the list of arguments as implemented in argparse.

Parses a BLAST tabular format with the following fields: "qseqid sseqid qlen evalue nident length sstart send" Returns a dict identified

Computes a triangular matrix for D' and r2 for each combinaiton in genotype_list

Takes a list of sequences and returns a single consensus sequence. There is an assumption that sequences have the same sequence lenght.

Converts a genotype string from the vcf ("0|0") into an actual genotype ("A"), provided the variants for that particular site

Converts a vcf file into bcg format according to the taxa provided for parental populations (p1 and p2) and hybrid population

The parsing of the .loci file and creation and writting of consensus sequences to output_file are performed together to improve performance.

Writes the output in fasta format. Arguments as in phy_writer function

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Filters a VCF file so that only one SNP per locus (the one closer to the center) is retained

Filters a vcf_file so that it includes only the SNPs from the fst_storage

Filters a VCF to ensure that loci are at least *dist* apart

Filters a VCF file so that only one SNP per locus (the first) is retained

Filters a VCF file so that only one random SNP per locus is retained.

Filters the chromossome positions of a vcf_file that are contained in the bad_loci_file. :param vcf_file: string, path to the vcf file

Uses the vcf module to parse and retrieve data from a VCF file. The data is returned as a list of lists

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Gets relative frequencies from VCF data

Reads the subset loci from a file and returns a list with it.

Takes a list of tuples with SAM file names as first element and their correspoding dictionaries as second element. Returns basic statistics

Returns a dictionary with pop identifier as key and taxa as a list of strings. In the pop file, each populations should be in one line, start

Gets a list of sequences from a SAM file according to a chromosome name and position. It also assumes that reads are 90bp long

Parses a GFF file to look for the annotation corresponding to the zone provided in the BLAST data dictionary. Prints the output in the pr

:param vcf_file: path to vcf file :param p1: list, taxa to count shared polymorphisms :param p2: list, reference taxa

Parses a file with a loci list (one entry per line). Returns a set with the loci numbers on the list.

Parses a list with loci order numbers and returns a set with those values.

Gets a loci list, a .loci file and sequence names and filters the .loci file according to the loci list. Returns a dict {seqname: sequence}

Parses the .loci file and prints the lines that belong to a loci from the vcf file.

Gets a loci list, and a loci file and sequence names and filters the loci file according to the loci list. Returns a dict {seqname: sequence}

Handle everything.

Main function. Runs all the others, based on the given input file name.

Parses the ".bf" file outputted by Bayenv2 and returns the SNPs with putative associations.

Main function that controls what to do.

Reads a .geste file and changes "1 X" to "2 X 0" for consistency. Prints everything to stdout, so you ight want to use a shell redirect.

Main function. Calls the argparser and the runner function.

Parses an alignment in an OrderedDict format {taxon: seq} and returns a similar alignment OrderedDict with the variable positions not present in th

Replaces the full text on the SNP name for something sensible & returns it.

Transposes the columns back into a phylip file.

Parses an association summary file and return a list with the reported loci.

Parses csv file with similar format to the one generated by Tracer Example: time; mean; median; hpd lower 95; hpd upper 95

Pareses a txt file with one environment variable name per line and returns a list with these values.

Parses a GESTE file and retuns a dict with: {"SNP_num":["FreqAp1\tFreqBp1","FreqAp2\tFreqBp2",...]}.

Parses a hardy-weinberg output file, corrects p-values according to a FDR and generates several plots to visualize the hwe results

Writes a phylip file from a loci file, according to the positions in the VCF. Variable positions that are not present in the VCF are soft masked

Parses an outlier summary file and returns a list with the outlier SNPs.

Parses a txt file in which each line contains three columns with the name of the pair and the replicate names for each pair, which must match

Parses a population file and returns a list in which the index of the taxon names correspond to their positions in the qfile

Parses a population file and returns an orderedDict object with the population name as keys and the corresponding list of samples as values

Parses a meanQ file from fastStructure and returns a list of lists, with the values of each taxon in each element of the root list

Parses a SAM file and retains each mapping location in the genome, along with the coverage. :param sam_file: string, path to SAM file

Parses the VCF file and returns a dictionary with the loci (chromossomes) as keys and a list of positions as values.

Parses a vcf file and prints only the requested lines (either only neutral or only under selection)

Parses a VCF file and returns a list of genotypes

Parses the VCF but retains the variation information. This is done when converting a VCF directly to phylip without using a .loci file. The result

Writes the output ready to submit to RAxML or other phylogeny programs, along with a partitions file. Based on seqnames dict {seqname: sequenc

Writes the output ready to submit to RAxML or other phylogeny program. Based on seqnames dict {seqname: sequence}

Creates a bar plot for the heterozygous files

This function plots the four error rates for each assembly stats provided by the multi_stats argument. It calculates the mean error for each

Plots the qvals. If pops are provided, plot them as well

This function will calculate and plot four error rates from a single assembly (i.e., vcf file). The error rates are: - Total locus error

Prints the number of loci in the VCF file

Reads a phylip file and retunrs the data in columns.

Manages what gets run and runs it.

Defines wether a locus segregates the two groups For now only works with full segregation

Removes any columns that contain singleton sites. Returns any columns that don't contain sigleton sites.

Parses the singleton/doubleton output file