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xpore v1.0
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ploy-np committed Mar 7, 2021
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47 changes: 26 additions & 21 deletions docs/source/scripts.rst
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Expand Up @@ -14,31 +14,36 @@ Output files from `nanopolish eventalgin`. Please refer to :ref:`Data preparatio

* Usage example

====================== ========== =================== ============================================================================================================
Argument name(s) Required Default value Description
====================== ========== =================== ============================================================================================================
--eventalign=FILE Yes NA Eventalign filepath, the output from nanopolish.
--summary=FILE Yes NA Eventalign summary filepath, the output from nanopolish.
--out_dir=DIR Yes NA Output directory.
--ensembl=NUM No 91 Ensembl version for gene-transcript mapping.
--species=STR No homo_sapiens Species for ensembl gene-transcript mapping.
--genome No False To run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates.
--n_processes=NUM No 1 Number of processes to run.
--readcount_max=NUM No 1000 Maximum read counts per gene.
--resume No False With this argument, the program will resume from the previous run.
====================== ========== =================== ============================================================================================================
================================= ========== =================== ============================================================================================================
Argument name(s) Required Default value Description
================================= ========== =================== ============================================================================================================
--eventalign=FILE Yes NA Eventalign filepath, the output from nanopolish.
--summary=FILE Yes NA Eventalign summary filepath, the output from nanopolish.
--out_dir=DIR Yes NA Output directory.
--ensembl=NUM No 91 Ensembl version for gene-transcript mapping.
--species=STR No homo_sapiens Species for ensembl gene-transcript mapping.
--customised_genome No False If customised genome provided.
--reference_name No NA fasta reference name.
--annotation_name No NA gtf annotation name.
--gtf_path_or_url No NA gtf file path or url.
--transcript_fasta_paths_or_urls No NA Transcript fasta paths or urls.
--skip_eventalign_indexing No False To skip indexing the eventalign nanopolish output.
--genome No False To run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates.
--n_processes=NUM No 1 Number of processes to run.
--readcount_max=NUM No 1000 Maximum read counts per gene.
--resume No False With this argument, the program will resume from the previous run.
================================= ========== =================== ============================================================================================================

* Output

====================== ============== ===============================================================================================================================================================
File name File type Description
====================== ============== ===============================================================================================================================================================
`eventalign.combined` csv Read segmentation information where multiple segments from `nanopolish eventalign` are aggregated per position.
`eventalign.index` csv File index indicating the position in the `eventalign.combin` file where the segmentation information of each read index is stored, allowing a random access.
`eventalign.log` txt Read indexes being processed.
`data.json` json Intensity level mean for each position.
`data.index` csv File index indicating the position in the `data.json` file where the intensity level means across positions of each gene is stored, allowing a random access.
`data.log` txt Gene ids being processed.
eventalign.index csv File index indicating the position in the `eventalign.txt` file (the output of nanopolish eventalign) where the segmentation information of each read index is stored, allowing a random access.
data.json json Intensity level mean for each position.
data.index csv File index indicating the position in the `data.json` file where the intensity level means across positions of each gene is stored, allowing a random access.
data.log txt Gene ids being processed.
data.readcount csv Summary of readcounts per gene.
====================== ============== ===============================================================================================================================================================

``xpore-diffmod``
Expand All @@ -65,7 +70,7 @@ Argument name(s) Required Default value Description
====================== =============== =================================================================================================================================================
File name File type Description
====================== =============== =================================================================================================================================================
`diffmod.table` csv Output table information of differential modification rates. Please refer to :ref:`Output table description <outputtable>` for the full description.
`diffmod.log` txt Gene/Transcript ids being processed.
diffmod.table csv Output table information of differential modification rates. Please refer to :ref:`Output table description <outputtable>` for the full description.
diffmod.log txt Gene/Transcript ids being processed.
====================== =============== =================================================================================================================================================

8 changes: 4 additions & 4 deletions xpore/scripts/dataprep.py
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Expand Up @@ -34,12 +34,12 @@ def get_args():
# Use customised db
# These arguments will be passed to Genome from pyensembl
optional.add_argument('--customised_genome', dest='customised_genome', help='if customised genome provided.',default=False,action='store_true')
optional.add_argument('--reference_name', dest='reference_name', help='reference name.',type=str)
optional.add_argument('--annotation_name', dest='annotation_name', help='annotation name.',type=str)
optional.add_argument('--reference_name', dest='reference_name', help='fasta reference name.',type=str)
optional.add_argument('--annotation_name', dest='annotation_name', help='gtf annotation name.',type=str)
optional.add_argument('--gtf_path_or_url', dest='gtf_path_or_url', help='gtf file path or url.',type=str)
optional.add_argument('--transcript_fasta_paths_or_urls', dest='transcript_fasta_paths_or_urls', help='transcript fasta paths or urls.',type=str)

optional.add_argument('--skip_eventalign_index', dest='skip_eventalign_index', help='skip indexing the eventalign nanopolish output.',default=False,action='store_true')
optional.add_argument('--skip_eventalign_indexing', dest='skip_eventalign_indexing', help='skip indexing the eventalign nanopolish output.',default=False,action='store_true')

# parser.add_argument('--features', dest='features', help='Signal features to extract.',type=list,default=['norm_mean'])
optional.add_argument('--genome', dest='genome', help='to run on Genomic coordinates. Without this argument, the program will run on transcriptomic coordinates',default=False,action='store_true')
Expand Down Expand Up @@ -642,7 +642,7 @@ def main():
misc.makedirs(out_dir) #todo: check every level.

# (1) For each read, combine multiple events aligned to the same positions, the results from nanopolish eventalign, into a single event per position.
if not args.skip_eventalign_index:
if not args.skip_eventalign_indexing:
parallel_index(eventalign_filepath,summary_filepath,chunk_size,out_dir,n_processes,resume)

# (2) Create a .json file, where the info of all reads are stored per position, for modelling.
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