Louis BECQUEY / RNANet

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Louis BECQUEY
550e1ac2 1 parent b5935bd6

updated command options list

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...@@ -60,13 +60,19 @@ The detailed list of options is below: ...@@ -60,13 +60,19 @@ The detailed list of options is below:
60 -h [ --help ] Print this help message 60 -h [ --help ] Print this help message
61 --version Print the program version 61 --version Print the program version
62 62
63 --f [ --full-inference ] Infer new mappings even if Rfam already provides some. Yields more copies of chains 63 +Select what to do:
64 - mapped to different families. 64 +--------------------------------------------------------------------------------------------------------------
65 --r 4.0 [ --resolution=4.0 ] Maximum 3D structure resolution to consider a RNA chain. 65 +-f [ --full-inference ] Infer new mappings even if Rfam already provides some. Yields more copies of
66 + chains mapped to different families.
66 -s Run statistics computations after completion 67 -s Run statistics computations after completion
67 --extract Extract the portions of 3D RNA chains to individual mmCIF files. 68 --extract Extract the portions of 3D RNA chains to individual mmCIF files.
68 --keep-hetatm=False (True | False) Keep ions, waters and ligands in produced mmCIF files. 69 --keep-hetatm=False (True | False) Keep ions, waters and ligands in produced mmCIF files.
69 - Does not affect the descriptors. 70 + Does not affect the descriptors.
71 +--no-homology Do not try to compute PSSMs and do not align sequences.
72 + Allows to yield more 3D data (consider chains without a Rfam mapping).
73 +
74 +Select how to do it:
75 +--------------------------------------------------------------------------------------------------------------
70 --3d-folder=… Path to a folder to store the 3D data files. Subfolders will contain: 76 --3d-folder=… Path to a folder to store the 3D data files. Subfolders will contain:
71 RNAcifs/ Full structures containing RNA, in mmCIF format 77 RNAcifs/ Full structures containing RNA, in mmCIF format
72 rna_mapped_to_Rfam/ Extracted 'pure' RNA chains 78 rna_mapped_to_Rfam/ Extracted 'pure' RNA chains
...@@ -74,16 +80,22 @@ The detailed list of options is below: ...@@ -74,16 +80,22 @@ The detailed list of options is below:
74 --seq-folder=… Path to a folder to store the sequence and alignment files. Subfolders will be: 80 --seq-folder=… Path to a folder to store the sequence and alignment files. Subfolders will be:
75 rfam_sequences/fasta/ Compressed hits to Rfam families 81 rfam_sequences/fasta/ Compressed hits to Rfam families
76 realigned/ Sequences, covariance models, and alignments by family 82 realigned/ Sequences, covariance models, and alignments by family
77 ---no-homology Do not try to compute PSSMs and do not align sequences. 83 +--maxcores=… Limit the number of cores to use in parallel portions to reduce the simultaneous
78 - Allows to yield more 3D data (consider chains without a Rfam mapping). 84 + need of RAM. Should be a number between 1 and your number of CPUs. Note that portions
85 + of the pipeline already limit themselves to 50% or 70% of that number by default.
86 +--archive Create tar.gz archives of the datapoints text files and the alignments,
87 + and update the link to the latest archive.
88 +--no-logs Do not save per-chain logs of the numbering modifications
79 89
90 +Select which data we are interested in:
91 +--------------------------------------------------------------------------------------------------------------
92 +-r 4.0 [ --resolution=4.0 ] Maximum 3D structure resolution to consider a RNA chain.
80 --all Build chains even if they already are in the database. 93 --all Build chains even if they already are in the database.
81 --only Ask to process a specific chain label only 94 --only Ask to process a specific chain label only
82 --ignore-issues Do not ignore already known issues and attempt to compute them 95 --ignore-issues Do not ignore already known issues and attempt to compute them
83 --update-homologous Re-download Rfam and SILVA databases, realign all families, and recompute all CSV files 96 --update-homologous Re-download Rfam and SILVA databases, realign all families, and recompute all CSV files
84 --from-scratch Delete database, local 3D and sequence files, and known issues, and recompute. 97 --from-scratch Delete database, local 3D and sequence files, and known issues, and recompute.
85 ---archive Create a tar.gz archive of the datapoints text files, and update the link to the latest archive 98 +
86 ---no-logs Do not save per-chain logs of the numbering modifications
87 ``` 99 ```
88 Options --3d-folder and --seq-folder are mandatory for command-line installations, but should not be used for installations with Docker. In the Docker container, they are set by default to the paths you provide with the -v options. 100 Options --3d-folder and --seq-folder are mandatory for command-line installations, but should not be used for installations with Docker. In the Docker container, they are set by default to the paths you provide with the -v options.
89 101
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