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change tutorial tables to option-list
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@mehrdadbakhtiari
mehrdadbakhtiari committed Mar 26, 2019
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83 changes: 26 additions & 57 deletions docs/tutorial.rst
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Expand Up @@ -74,51 +74,30 @@ Summary of options:

Input/output options:

+-------------------------------+---------------------------------------------------------------------------------+
| -a/--alignment_file <file> | alignment file in SAM/BAM/CRAM format |
+-------------------------------+---------------------------------------------------------------------------------+
| -r/--reference_filename <file>| path to a FASTA-formatted reference file for CRAM files. |
+-------------------------------+---------------------------------------------------------------------------------+
| -f/--fasta <file> | Fasta file containing raw reads |
+-------------------------------+---------------------------------------------------------------------------------+
| -p/--pacbio | set this flag if input file contains PacBio reads instead of Illumina reads |
+-------------------------------+---------------------------------------------------------------------------------+
| -n/--nanopore | set this flag if input file contains Nanopore MinION reads instead of Illumina |
+-------------------------------+---------------------------------------------------------------------------------+
| -o/--outfile <file> | file to write results. adVNTR writes output to stdout if oufile is not specified|
+-------------------------------+---------------------------------------------------------------------------------+
| -of/--outfmt <format> | output format. Allowed values are {text, bed} [text] |
+-------------------------------+---------------------------------------------------------------------------------+
-f, --alignment_file <file> alignment file in SAM/BAM/CRAM format
-r, --reference_filename <file> path to a FASTA-formatted reference file for CRAM files.
-f, --fasta <file> Fasta file containing raw reads
-p, --pacbio set this flag if input file contains PacBio reads instead of Illumina reads
-n, --nanopore set this flag if input file contains Nanopore MinION reads instead of Illumina
-o, --outfile <file> file to write results. adVNTR writes output to stdout if oufile is not specified
-of, --outfmt <format> output format. Allowed values are {text, bed} [text]

Algorithm options:

+---------------------------+--------------------------------------------------------------------------------+
| -fs/--frameshift | set this flag to search for frameshifts in VNTR instead of copy number. |
+---------------------------+--------------------------------------------------------------------------------+
| -e/--expansion | set this flag to determine long expansion from PCR-free data |
+---------------------------+--------------------------------------------------------------------------------+
| -c/--coverage <float> | average sequencing coverage in PCR-free sequencing |
+---------------------------+--------------------------------------------------------------------------------+
| --haploid | set this flag if the organism is haploid |
+---------------------------+--------------------------------------------------------------------------------+
| -naive/--naive | use naive approach for PacBio reads |
+---------------------------+--------------------------------------------------------------------------------+
-fs, --frameshift set this flag to search for frameshifts in VNTR instead of copy number.
-e, --expansion set this flag to determine long expansion from PCR-free data
-c, --coverage <float> average sequencing coverage in PCR-free sequencing
--haploid set this flag if the organism is haploid
-naive, --naive use naive approach for PacBio reads

Other options:

+---------------------------+--------------------------------------------------------------------------------+
| -h/--help | show this help message and exit |
+---------------------------+--------------------------------------------------------------------------------+
| --working_directory <path>| working directory for creating temporary files needed for computation |
+---------------------------+--------------------------------------------------------------------------------+
| -m/--models <file> | file containing VNTRs information [vntr_data/hg19_VNTRs.db] |
+---------------------------+--------------------------------------------------------------------------------+
| -t/--threads <int> | number of threads [4] |
+---------------------------+--------------------------------------------------------------------------------+
| -u/--update | set this flag to iteratively update the model |
+---------------------------+--------------------------------------------------------------------------------+
| -vid/--vntr_id <text> | comma-separated list of VNTR IDs |
+---------------------------+--------------------------------------------------------------------------------+
-h, --help show this help message and exit
--working_directory <path> working directory for creating temporary files needed for computation
-m, --models <file> file containing VNTRs information [vntr_data/hg19_VNTRs.db]
-t, --threads <int> number of threads [4]
-u, --update set this flag to iteratively update the model
-vid, --vntr_id <text> comma-separated list of VNTR IDs


View VNTRs
Expand All @@ -134,27 +113,17 @@ The structure of VNTR and its genomic coordinate are required.

Required arguments:

+-----------------------+----------------------------------------------------------------+
| -r/--reference <text> | Reference genome |
+-----------------------+----------------------------------------------------------------+
| -c/--chromosome <text>| Chromosome (e.g. chr1) |
+-----------------------+----------------------------------------------------------------+
| -p/--pattern <text> | First repeating pattern of VNTR in forward (5' to 3') direction|
+-----------------------+----------------------------------------------------------------+
| -s/--start <int> | Start coordinate of VNTR in forward (5' to 3') direction |
+-----------------------+----------------------------------------------------------------+
| -e/--end <int> | End coordinate of VNTR in forward (5' to 3') direction |
+-----------------------+----------------------------------------------------------------+
-r, --reference <text> Reference genome
-c, --chromosome <text> Chromosome (e.g. chr1)
-p, --pattern <text> First repeating pattern of VNTR in forward (5' to 3') direction
-s, --start <int> Start coordinate of VNTR in forward (5' to 3') direction
-e, --end <int> End coordinate of VNTR in forward (5' to 3') direction

Other options:

+-------------------------+--------------------------------+
| -g/--gene <text> |Gene name |
+-------------------------+--------------------------------+
| -a/--annotation <text> |Annotation of VNTR region |
+-------------------------+--------------------------------+
| -h/--help |show this help message and exit |
+-------------------------+--------------------------------+
-g, --gene <text> Gene name
-a, --annotation <text> Annotation of VNTR region
-h, --help show this help message and exit

You can use :code:`--update` in genotyping step to iteratively update the model using real data.

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