def pb_isoseq_collapse(): """ Internal Iso-Seq pipeline, starting from an existing Iso-Seq job, continuing to collapse, continue to collapse, count and filter isoforms, requiring a reference genome GMAP dataset. """ return _core_isoseq_collapse(hq_isoforms_fq=to_entry("hq_isoforms_fq"), gmap_ref_ds=Constants.ENTRY_DS_GMAPREF, sample_prefix_pickle=to_entry("sample_prefix_pickle"))
def pb_isoseq_collapse(): """ Internal Iso-Seq pipeline, starting from an existing Iso-Seq job, continuing to collapse, continue to collapse, count and filter isoforms, requiring a reference genome GMAP dataset. """ return _core_isoseq_collapse( hq_isoforms_fq=to_entry("hq_isoforms_fq"), gmap_ref_ds=Constants.ENTRY_DS_GMAPREF, sample_prefix_pickle=to_entry("sample_prefix_pickle"))
def pb_isoseq2_collapse(): """ Internal Iso-Seq2 pipeline, starting from an existing Iso-Seq2 job, continuing to collapse, continue to collapse, count and filter isoforms, requiring a reference genome GMAP dataset. """ return _core_isoseq2_collapse(ws_json=to_entry('e_ws_json'), hq_isoforms_fq=to_entry('e_hq_isoforms_fq'), gmap_ref_ds=Constants.ENTRY_DS_GMAPREF, sample_to_uc_pickle_json=to_entry('e_sample_uc_json'))
def pb_isoseq2_collapse(): """ Internal Iso-Seq2 pipeline, starting from an existing Iso-Seq2 job, continuing to collapse, continue to collapse, count and filter isoforms, requiring a reference genome GMAP dataset. """ return _core_isoseq2_collapse( ws_json=to_entry('e_ws_json'), hq_isoforms_fq=to_entry('e_hq_isoforms_fq'), gmap_ref_ds=Constants.ENTRY_DS_GMAPREF, sample_to_uc_pickle_json=to_entry('e_sample_uc_json'))
def pb_isoseq_cluster_with_genome(): """ Internal Iso-Seq pipeline, starting from existing isoseq_flnc and isoseq_nfl datasets, continue to collapse, count and filter isoforms, requiring a reference genome GMAP dataset. """ b1 = _core_isoseq_cluster_chunk_by_bins(subreads_ds=Constants.ENTRY_DS_SUBREAD, ccs_ds=Constants.ENTRY_DS_CCS, flnc_ds=to_entry("e_flnc_fa"), nfl_ds=to_entry("e_nfl_fa")) b2 = _core_isoseq_collapse(hq_isoforms_fq="pbtranscript.tasks.combine_cluster_bins:4", gmap_ref_ds=Constants.ENTRY_DS_GMAPREF, sample_prefix_pickle="pbtranscript.tasks.combine_cluster_bins:7") return b1 + b2
def pb_isoseq_cluster_with_genome(): """ Internal Iso-Seq pipeline, starting from existing isoseq_flnc and isoseq_nfl datasets, continue to collapse, count and filter isoforms, requiring a reference genome GMAP dataset. """ b1 = _core_isoseq_cluster_chunk_by_bins( subreads_ds=Constants.ENTRY_DS_SUBREAD, ccs_ds=Constants.ENTRY_DS_CCS, flnc_ds=to_entry("e_flnc_fa"), nfl_ds=to_entry("e_nfl_fa")) b2 = _core_isoseq_collapse( hq_isoforms_fq="pbtranscript.tasks.combine_cluster_bins:4", gmap_ref_ds=Constants.ENTRY_DS_GMAPREF, sample_prefix_pickle="pbtranscript.tasks.combine_cluster_bins:7") return b1 + b2
def validate_entry_points(d): from pbsmrtpipe.pb_pipelines.pb_pipeline_constants import Constants, to_entry for ep in d['entryPoints']: eid = to_entry(ep['entryId']) if eid in Constants.ENTRY_FILE_TYPES: file_type_id = Constants.ENTRY_FILE_TYPES[eid].file_type_id if ep['fileTypeId'] != file_type_id: raise ValueError("Expected {r} for {e}, got {t}".format( r=file_type_id, e=eid, t=ep['fileTypeId']))
def pb_isoseq_cluster(): return _core_isoseq_cluster_chunk_by_bins( subreads_ds=Constants.ENTRY_DS_SUBREAD, ccs_ds=Constants.ENTRY_DS_CCS, flnc_ds=to_entry("e_flnc_fa"), nfl_ds=to_entry("e_nfl_fa"))
def pb_isoseq2_cluster(): return _core_isoseq2_cluster(subreads_ds=Constants.ENTRY_DS_SUBREAD, ccs_ds=Constants.ENTRY_DS_CCS, flnc_ds=to_entry("e_flnc_fa"), nfl_ds=to_entry("e_nfl_fa"))