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    Èh&  ã                   @   sn  d dl Z dZeƒ Zeƒ ZdZg d¢ZdgZg d¢ZdgZ	ee e	 dg Z
dZg d	¢Zd
ddddœZg d¢ZdgZg d¢ZdZdZdZdZdZdZdZdZdZdZdZddgZdZd Zd!Zd"Z d#Z!d$Z"d%Z#d&Z$d'Z%d(Z&d)Z'd*Z(d+Z)d,Z*d)Z+d-Z,d.Z-d/Z.d0d1gZ/g d2¢Z0g d3¢Z1g d4¢Z2g d3¢Z3g d4¢Z4d&Z5d5Z6g d6¢Z7g d7¢Z8d8Z9d9Z:dZ;dZ<dZ=d:d;„ Z>d<d=„ Z?d>d?„ Z@dS )@é    N)é   é   )z.fqz.fastqú.bamz.fq.gzz	.fastq.gzr   )z.faz.fastaz.fa.gzz	.fasta.gzz.gfaz.sraé	   )z--12z-1z-2z-sz--mergedú
paired-endÚsinglez
mate-pairsúhq-mate-pairs)ÚpeÚsÚmpZhqmp)ÚpacbioZsangerÚnanoporeútrusted-contigsúuntrusted-contigsúfl-rnazassembly-graph)ÚecÚasÚmcZsccZtppzcontigs.fastazscaffolds.fastazraw_scaffolds.fastazassembly_graph.fastgz!assembly_graph_with_scaffolds.gfazcontigs.pathszraw_contigs.fastazscaffolds.pathszraw_scaffolds.pathsztranscripts.fastaztranscripts.pathsZhardZsoftzhmm_statistics.txtzgene_clusters.fastazdomain_graph.dotzlineages.csvZpipeline_stateZbiosynthetic_spades_hmmsÚcoronaspades_hmmsé   é   é   é7   é-   r   é
   é   é   éú   é!   é1   )r   r   r   )r   r   r   éM   )r   r   r   r    éc   r   Útmp)r   r   r   )r   r   r   r   r   r   r   Zread_conversionZlastc                 C   sH   d| |f }t j tjt|¡}t j t j |¡¡sDt  t j |¡¡ |S )Nzstage_%d_%s)	ÚosÚpathÚjoinÚargsÚ
output_dirÚpipeline_state_dirÚexistsÚdirnameÚmakedirs)Z	stage_numZstage_short_nameZstage_file_nameZstage_checkpoint_path© r,   ún/home/psgendb/BIRCHDEV/install/SPAdes-4.2.0-Linux/linux-x86_64/share/spades/spades_pipeline/options_storage.pyÚget_stage_filename_   s
    r.   c                   C   s(   t j o&t j o&t j o&t jo$t j  S ©N)r&   Zk_mersÚsingle_cellÚ
iontorrentÚmetaÚplasmidr,   r,   r,   r-   Úauto_K_allowedh   s    r4   c                   C   s   t jpt jpt jS r/   )r&   ÚbioÚcustom_hmmsÚcoronar,   r,   r,   r-   Úhmm_modek   s    r8   )Ar#   Zoriginal_k_mersÚdictÚdict_of_prefixesÚdict_of_rel2absÚMINIMAL_PYTHON_VERSIONÚBH_ALLOWED_READS_EXTENSIONSÚ(IONTORRENT_ONLY_ALLOWED_READS_EXTENSIONSÚ CONTIGS_ALLOWED_READS_EXTENSIONSÚGRAPH_ALLOWED_READS_EXTENSIONSÚALLOWED_READS_EXTENSIONSZMAX_LIBS_NUMBERZOLD_STYLE_READS_OPTIONSÚSHORT_READS_TYPESÚLONG_READS_TYPESÚGRAPH_READS_TYPESZSHORT_STAGES_NAMEÚcontigs_nameÚscaffolds_nameÚsecondary_scaffolds_nameÚassembly_graph_nameÚassembly_graph_name_gfaÚcontigs_pathsÚsecondary_contigs_nameÚscaffolds_pathsÚsecondary_scaffolds_pathsÚtranscripts_nameÚtranscripts_pathsÚfiltering_typesÚbgc_stats_nameZgene_clusters_nameÚdomain_graph_nameÚsewage_lineagesr(   Zbiosyntheticspades_hmmsr   ZMIN_KZMAX_KZ	RNA_MIN_KZRNA_MAX_LOWER_KZRNA_VIRAL_MAX_LOWER_KZ THRESHOLD_FOR_BREAKING_SCAFFOLDSZ)THRESHOLD_FOR_BREAKING_ADDITIONAL_CONTIGSZGAP_CLOSER_ENABLE_MIN_KZSCC_KZTHREADSZMEMORYZ
K_MERS_RNAZK_MERS_SHORTZ
K_MERS_150Z
K_MERS_250ZK_MERS_PLASMID_100ZK_MERS_PLASMID_LONGZ
ITERATIONSZTMP_DIRÚ READS_TYPES_USED_IN_CONSTRUCTIONZREADS_TYPES_USED_IN_RNA_SEQÚ
BASE_STAGEÚ
LAST_STAGEÚfirst_command_liner&   Zoriginal_dataset_datar.   r4   r8   r,   r,   r,   r-   Ú<module>   s~   	