U \d@sddlmZddlmZddlZddlZddlZddlZddl m Z ddZ ddZ d d Z d d Zd dZddZddZddZddZdS))division)statsN)SeqIOc Cs:tt}i}z"t|jdks$tt|d}Wnvtt fk rn}z| d|t dW5d}~XYntk r}z| d|t dW5d}~XYnX|v|D]j}z | d}t| d}Wn<tk r}z| d|t dW5d}~XYqX|||<qW5QRX|d||S) a6Parse an abundance or coverage file The abundance/coverage file is a flat file of the format "genome_idabundance" or "genome_idcoverage" Args: abundance_file (string): the path to the abundance file Returns: dict: genome_id as keys, abundance as values rrz Failed to open abundance file:%sNzAbundance file seems empty: %sz!Failed to read abundance file: %szLoaded abundance file: %s)logging getLogger__name__osstatst_sizeAssertionErroropenIOErrorOSErrorerrorsysexitsplitfloat IndexErrorinfo)Zabundance_filelogger abundance_dicfelineZ genome_id abundancer,lib/python3.8/site-packages/iss/abundance.pyparse_abundance_files,  r cCs&i}t|}|D]}d|||<q|S)zGenerate uniform abundance distribution from a number of records Args: record_list (list): a list of record.id Returns: dict: a dictionary with records as keys, abundance as values rlen) record_listr n_recordsrecordrrruniform8s r&cCsJi}t|}tjjdd|d}|t|}t||D]\}}|||<q4|S)zGenerate scaled halfnormal abundance distribution from a number of records Args: record_list (list): a list of record.id Returns: dict: a dictionary with records as keys, abundance as values gg?)locZscalesize)r"rZhalfnormrvssumzipr#rr$dist dist_scaledr%rrrr halfnormalIs   r/cCsFi}t|}tjj|d}|t|}t||D]\}}|||<q0|S)zGenerate scaled exponential abundance distribution from a number of records Args: record_list (list): a list of record.id Returns: dict: a dictionary with records as keys, abundance as values r()r"nprandom exponentialr*r+r,rrrr3]s   r3cCsFi}t|}tjj|d}|t|}t||D]\}}|||<q0|S)zGenerate scaled lognormal abundance distribution from a number of records Args: record_list (list): a list of record.id Returns: dict: a dictionary with records as keys, abundance as values r0)r"r1r2 lognormalr*r+r,rrrr4qs   r4cCs^i}t|}tjjd|d}d|tjj|d}|t|}t||D]\}}|||<qH|S)zGenerate scaled zero-inflated lognormal abundance distribution from a number of records Args: record_list (list): a list of record.id Returns: dict: a dictionary with records as keys, abundance as values g?)pr(rr0) r"rZ bernoullir)r1r2r4r*r+)r#rr$Z zero_inflatedr-r.r%rrrrzero_inflated_lognormals   r6cCs||}|||}|S)aCalculate the coverage of a genome in a metagenome given its size and abundance Args: total_n_reads (int): total amount of reads in the dataset species_abundance (float): abundance of the species, between 0 and 1 read_length (int): length of the reads in the dataset genome_size (int): size of the genome Returns: float: coverage of the genome r)Z total_n_readsZspecies_abundanceZ read_lengthZ genome_sizeZn_readsZcoveragerrr to_coverages  r7c Cstt}|d}zt|d}Wn:tk rZ}z|d|tdW5d}~XYn6X|*|D]\}}| d||fqjW5QRXdS)zWrite the abundance dictionary to a file Args: abundance_dic (dict): the abundance dictionary output (str): the output file name z_abundance.txtwzFailed to open output file: %srNz%s %s ) rrr rPermissionErrorrrritemswrite)routputrZoutput_abundancerrr%rrrrto_files r=c sJg}D] }|ddt|dDqtt|t|}||}fdd|D}t|||D]\}} i} |krrzJt|d} | 2t| d} dd| D}tdd |D} W5QRXWn$t k r}zW5d }~XYqrXtd d |D} |D]$}t |}| || }|| |j <q qr| }| | |S) aMComputes the abundance dictionary for a mix of complete and draft genomes Args: genomes (list): list of all input records draft (list): draft genome files distribution (function): distribution function to use output (str): output file Returns: dict: the abundance dictionary cSsg|] }|jqSr)name.0r%rrr szdraft..Zfastacsi|]\}}|kr||qSrr)r@kvdraftrr szdraft..rcSsg|]}|qSrrr?rrrrAscss|]}t|VqdSNr!r?rrr szdraft..Ncss|]}t|VqdSrGr!r?rrrrHs)extendrparselistsetr:r=rr* Exceptionr"idcopyupdate)ZgenomesrEZ distributionr<Z draft_recordsdrZcomplete_genomes_abundancekeyrZ draft_dicrZ fasta_fileZ total_lengthrr%lengthZcontig_abundanceZfull_abundance_dicrrDrrEs<        rE)Z __future__rZscipyrr rrZnumpyr1ZBiorr r&r/r3r4r6r7r=rErrrrs   (