From 4ab196385d33a11caab272626abc49625e262357 Mon Sep 17 00:00:00 2001 From: ljyanesm Date: Thu, 14 Jan 2021 15:19:17 +0000 Subject: [PATCH 01/35] Adds details to docs about 'attributes' metrics --- docs/Algorithms.rst | 34 ++++++++++++++++++++-- docs/Usage/Daijin.rst | 68 +++++++++++++++++++++---------------------- 2 files changed, 66 insertions(+), 36 deletions(-) diff --git a/docs/Algorithms.rst b/docs/Algorithms.rst index 60f699c62..ff58b1def 100644 --- a/docs/Algorithms.rst +++ b/docs/Algorithms.rst @@ -323,9 +323,13 @@ Metrics belong to one of the following categories: * **Locus**: these metrics refer to features of the transcript in relationship to all other transcripts in its locus, eg how many of the introns present in the locus are present in the transcript. These metrics are calculated by Mikado during the picking phase, and as such their value can vary during the different stages as the transcripts are shifted to different groups. -* **External**: these metrics are derived from accessory data that is recovered for the transcript during the run time. Examples include data regarding the number of introns confirmed by external programs such as PortCullis, or the BLAST score of the best hits. +* **External**: these metrics are derived from accessory data that is recovered for the transcript during the run time. Examples include data regarding the number of introns confirmed by external programs such as Portcullis, or the BLAST score of the best hits. -.. hint:: Starting from version 1 beta8, Mikado allows to use externally defined metrics for the transcripts. These can be accessed using the keyword "external." within the configuration file. See the :ref:`relevant section ` for details. +* **Attributes**: these metrics are extracted at runtime from attributes present in the input files. An example of this could be the TPM or FPKM values assigned to transcripts by rna expression analysis software. + +.. hint:: Starting from version 1 beta8, Mikado allows to use externally defined metrics for the transcripts. These can be accessed using the keyword "external." within the *configuration* file. See the :ref:`relevant section ` for details. + +.. hint:: Starting from version 2, Mikado allows to use attribute defined metrics for the transcripts. These can be accessed using the keyword "attributes." within the *scoring* file. See the :ref:`relevant section ` for details. .. important:: Starting from Mikado 1 beta 8, it is possible to use metrics with values between 0 and 1 directly as scores, without rescaling. This feature is available only for metrics whose values naturally lie between 0 and 1, or that are boolean in nature. @@ -667,6 +671,32 @@ As external metrics allow Mikado to accept any arbitrary metric for each transcr .. note:: also for external metrics, it is necessary to add a suffix to them if they are invoked more than once in an expression (see the :ref:`tutorial `). An invocation of e.g. "external.samples_expressed.mono" and "external.samples_expressed.multi", to distinguish between monoexonic and multiexonic transcripts, would be perfectly valid and actually *required* by Mikado. Notice the double use of the dot (".") as separator. Its usage as such is the reason that it cannot be present in the name of the metric itself (so, for example, "has.coverage.gaps" would be an invalid metric name). +.. attributes-metrics: + +Attributes metrics +------------------ +Starting from version 2, Mikado allows the usage of metrics defined in the attributes of the input files, these metrics behave as the rest of the metrics but they are gathered at runtime from the input datasets. It is important to note that these metrics must be equivalent in all the inputs and are by default initialised to "0" when a transcript does not have an attribute defining the metric. The default initialisation value can be overridden in the scoring file. + +Attribute metrics along with the required **rescaling** parameter, can define a *rtype* parameter as one of (float, int or bool) which will be used to cast the value of the attribute internally, and a *percentage* boolean which indicates that the values are in the 0-100 range and enables a transformation to the 0-1 range so that these can be used as 'raw' scores (see the :ref:`scoring algorithm section <_scoring_algorithm>`). + +An example for the usage of these metrics could be:: + + Chr5 Cufflinks transcript 26581218 26583874 1000 - . gene_id "cufflinks_star_at.23551";transcript_id "cufflinks_star_at.23551.1";exon_number "1";FPKM "0.4343609420";conf_hi "0.577851";frac "0.751684";cov "11.982854";conf_lo "0.293994";percentage_score "42.42" + Chr5 Cufflinks exon 26581218 26581528 . - . gene_id "cufflinks_star_at.23551";transcript_id "cufflinks_star_at.23551.1"; + Chr5 Cufflinks exon 26583335 26583874 . - . gene_id "cufflinks_star_at.23551";transcript_id "cufflinks_star_at.23551.1"; + + +If the scoring file defines: + +.. code-block:: yaml + + scoring: + # [ ... other metrics ... ] + - attributes.FPKM: {rescaling: max} + - attributes.frac: {rescaling: max, use_raw: true} + - attributes.percentage_score: {rescaling: max, use_raw: true, percentage: true} + +The same scoring rules defined previously will apply to metrics obtained from the transcript's attributes. .. _padding: diff --git a/docs/Usage/Daijin.rst b/docs/Usage/Daijin.rst index 7ec720f02..272f9b6a3 100644 --- a/docs/Usage/Daijin.rst +++ b/docs/Usage/Daijin.rst @@ -288,45 +288,45 @@ Running the pipeline Daijin executes the pipeline in two distinct phases, *assemble* and *mikado*. Both commands have the same command line interface, namely:: - $ daijin assemble --help - usage: daijin assemble [-h] [-c HPC_CONF] [-d] [--jobs N] [--cores [N]] + $ daijin assemble --help + usage: daijin assemble [-h] [-c HPC_CONF] [-d] [--jobs N] [--cores [N]] [--threads N] [--no_drmaa] [--rerun-incomplete] [--forcerun TARGET [TARGET ...]] [--detailed-summary] [--list] [--dag] config - positional arguments: - config Configuration file to use for running the transcript - assembly pipeline. - - optional arguments: - -h, --help show this help message and exit - -c HPC_CONF, --hpc_conf HPC_CONF - Configuration file that allows the user to override - resource requests for each rule when running under a - scheduler in a HPC environment. - -d, --dryrun Do a dry run for testing. - --jobs N, -J N Maximum number of cluster jobs to execute - concurrently. - --cores [N], -C [N] Use at most N cores in parallel (default: 1000). - --threads N, -t N Maximum number of threads per job. Default: None (set - in the configuration file) - --no_drmaa, -nd Use this flag if you wish to run without DRMAA, for - example, if running on a HPC and DRMAA is not - available, or if running locally on your own machine - or server. - --rerun-incomplete, --ri - Re-run all jobs the output of which is recognized as - incomplete. - --forcerun TARGET [TARGET ...], -R TARGET [TARGET ...] - Force the re-execution or creation of the given rules - or files. Use this option if you changed a rule and - want to have all its output in your workflow updated. - --detailed-summary, -D - Print detailed summary of all input and output files - --list, -l List resources used in the workflow - --dag Do not execute anything and print the redirected - acylic graph of jobs in the dot language. + positional arguments: + config Configuration file to use for running the transcript + assembly pipeline. + + optional arguments: + -h, --help show this help message and exit + -c HPC_CONF, --hpc_conf HPC_CONF + Configuration file that allows the user to override + resource requests for each rule when running under a + scheduler in a HPC environment. + -d, --dryrun Do a dry run for testing. + --jobs N, -J N Maximum number of cluster jobs to execute + concurrently. + --cores [N], -C [N] Use at most N cores in parallel (default: 1000). + --threads N, -t N Maximum number of threads per job. Default: None (set + in the configuration file) + --no_drmaa, -nd Use this flag if you wish to run without DRMAA, for + example, if running on a HPC and DRMAA is not + available, or if running locally on your own machine + or server. + --rerun-incomplete, --ri + Re-run all jobs the output of which is recognized as + incomplete. + --forcerun TARGET [TARGET ...], -R TARGET [TARGET ...] + Force the re-execution or creation of the given rules + or files. Use this option if you changed a rule and + want to have all its output in your workflow updated. + --detailed-summary, -D + Print detailed summary of all input and output files + --list, -l List resources used in the workflow + --dag Do not execute anything and print the redirected + acylic graph of jobs in the dot language. The available command parameters are: From e99501fb8cfc596317df8e8394e46687119cbb7f Mon Sep 17 00:00:00 2001 From: ljyanesm Date: Thu, 14 Jan 2021 17:12:28 +0000 Subject: [PATCH 02/35] Formatting --- docs/Usage/Configure.rst | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/docs/Usage/Configure.rst b/docs/Usage/Configure.rst index bcbdef50f..edc9d2981 100644 --- a/docs/Usage/Configure.rst +++ b/docs/Usage/Configure.rst @@ -57,9 +57,7 @@ Selected command line parameters: - *--seed*: random seed for full reproducibility of Mikado runs. - *--list*: the argument to this option specifies the input annotation files for Mikado. See above. -Command line help: - -.. code-block:: +Command line help:: $ mikado configure --help usage: Mikado configure [-h] [--full] [--seed SEED] [--minimum-cdna-length MINIMUM_CDNA_LENGTH] [--max-intron-length MAX_INTRON_LENGTH] [--scoring SCORING] [--copy-scoring COPY_SCORING] @@ -182,6 +180,7 @@ Global options The following options apply to all programs in the Mikado pipeline, and they refer to general parameters such as logging verbosity, number of threads, etc. Parameters: + - *threads*: this is the number of processes/threads that will be requested by the Mikado programs. This parameter can be overridden on the command line. - *seed*: random seed specification, to ensure maximum reproducibility of the run. .. _start-methods: @@ -542,8 +541,7 @@ Parameters regarding the clustering of transcripts in loci This section influences how Mikado clusters transcripts in its multi-stage selection. The available parameters are: -- *flank*: numerical. When constructing :ref:`Superloci `, Mikado will use this value as the maximum distance -between transcripts for them to be integrated within the same superlocus. +- *flank*: numerical. When constructing :ref:`Superloci `, Mikado will use this value as the maximum distance between transcripts for them to be integrated within the same superlocus. - *cds_only*: boolean. If set to true, during the :ref:`picking stage ` Mikado will consider only the **primary ORF** to evaluate whether two transcripts intersect. Transcripts which eg. share introns in their UTR but have completely unrelated CDSs will be clustered separately. Disabled by default. - *purge*: boolean. If true, any transcript failing the :ref:`specified requirements ` will be purged out. Otherwise, they will be assigned a score of 0 and might potentially appear in the final output, if no other transcript is present in the locus. - *simple_overlap_for_monoexonic*: boolean. During the :ref:`second clustering `, by default monoexonic transcripts are clustered together even if they have a very slight overlap with another transcript. Manually setting this flag to *false* will cause Mikado to cluster monoexonic transcripts only if they have a minimum amount of cDNA and CDS overlap with the other transcripts in the holder. @@ -627,8 +625,7 @@ This section determines how Mikado will deal with :ref:`chimeras `) that will **never** have the transcripts split. -.. hint:: cDNAs, reference transcripts, and the like should end up in the "skip" category. These are, after all, transcripts -that are presupposed to be originated from a single RNA molecule and therefore without fusions. +.. hint:: cDNAs, reference transcripts, and the like should end up in the "skip" category. These are, after all, transcripts that are presupposed to be originated from a single RNA molecule and therefore without fusions. - *blast_check*: boolean. Whether to execute the check on the BLAST hits. If set to *false*, Mikado will operate in the *split* mode, unless *execute* is set to *false* (execute takes precedence over the other parameters). - *blast_params*: this section contains the settings relative to the *permissive*, *lenient* and *stringent* mode. From 7de6bca71b4c51028610dd0087378c06d81f904e Mon Sep 17 00:00:00 2001 From: ljyanesm Date: Thu, 14 Jan 2021 17:13:43 +0000 Subject: [PATCH 03/35] Revert style to default Makes some text appear too large on the screen (menu and lists) --- docs/_static/theme_overrides.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/_static/theme_overrides.css b/docs/_static/theme_overrides.css index 0a7f506f2..37d715760 100644 --- a/docs/_static/theme_overrides.css +++ b/docs/_static/theme_overrides.css @@ -27,7 +27,7 @@ tt { body { font-family: {{ theme_bodyfont }}; - font-size: 150%; + /*font-size: 150%;*/ background-color: {{ theme_footerbgcolor }}; color: #000; margin: 0; From 2148833c52f12ac5adfedfc849823ae56446ab9e Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Thu, 25 Feb 2021 10:09:45 +0000 Subject: [PATCH 04/35] Ported the changes made by @ljyanesm to the docs --- docs/Algorithms.rst | 34 +++++++++++++++- docs/Usage/Configure.rst | 16 ++++---- docs/Usage/Daijin.rst | 68 ++++++++++++++++---------------- docs/_static/theme_overrides.css | 19 ++++----- 4 files changed, 84 insertions(+), 53 deletions(-) diff --git a/docs/Algorithms.rst b/docs/Algorithms.rst index 60f699c62..ff58b1def 100644 --- a/docs/Algorithms.rst +++ b/docs/Algorithms.rst @@ -323,9 +323,13 @@ Metrics belong to one of the following categories: * **Locus**: these metrics refer to features of the transcript in relationship to all other transcripts in its locus, eg how many of the introns present in the locus are present in the transcript. These metrics are calculated by Mikado during the picking phase, and as such their value can vary during the different stages as the transcripts are shifted to different groups. -* **External**: these metrics are derived from accessory data that is recovered for the transcript during the run time. Examples include data regarding the number of introns confirmed by external programs such as PortCullis, or the BLAST score of the best hits. +* **External**: these metrics are derived from accessory data that is recovered for the transcript during the run time. Examples include data regarding the number of introns confirmed by external programs such as Portcullis, or the BLAST score of the best hits. -.. hint:: Starting from version 1 beta8, Mikado allows to use externally defined metrics for the transcripts. These can be accessed using the keyword "external." within the configuration file. See the :ref:`relevant section ` for details. +* **Attributes**: these metrics are extracted at runtime from attributes present in the input files. An example of this could be the TPM or FPKM values assigned to transcripts by rna expression analysis software. + +.. hint:: Starting from version 1 beta8, Mikado allows to use externally defined metrics for the transcripts. These can be accessed using the keyword "external." within the *configuration* file. See the :ref:`relevant section ` for details. + +.. hint:: Starting from version 2, Mikado allows to use attribute defined metrics for the transcripts. These can be accessed using the keyword "attributes." within the *scoring* file. See the :ref:`relevant section ` for details. .. important:: Starting from Mikado 1 beta 8, it is possible to use metrics with values between 0 and 1 directly as scores, without rescaling. This feature is available only for metrics whose values naturally lie between 0 and 1, or that are boolean in nature. @@ -667,6 +671,32 @@ As external metrics allow Mikado to accept any arbitrary metric for each transcr .. note:: also for external metrics, it is necessary to add a suffix to them if they are invoked more than once in an expression (see the :ref:`tutorial `). An invocation of e.g. "external.samples_expressed.mono" and "external.samples_expressed.multi", to distinguish between monoexonic and multiexonic transcripts, would be perfectly valid and actually *required* by Mikado. Notice the double use of the dot (".") as separator. Its usage as such is the reason that it cannot be present in the name of the metric itself (so, for example, "has.coverage.gaps" would be an invalid metric name). +.. attributes-metrics: + +Attributes metrics +------------------ +Starting from version 2, Mikado allows the usage of metrics defined in the attributes of the input files, these metrics behave as the rest of the metrics but they are gathered at runtime from the input datasets. It is important to note that these metrics must be equivalent in all the inputs and are by default initialised to "0" when a transcript does not have an attribute defining the metric. The default initialisation value can be overridden in the scoring file. + +Attribute metrics along with the required **rescaling** parameter, can define a *rtype* parameter as one of (float, int or bool) which will be used to cast the value of the attribute internally, and a *percentage* boolean which indicates that the values are in the 0-100 range and enables a transformation to the 0-1 range so that these can be used as 'raw' scores (see the :ref:`scoring algorithm section <_scoring_algorithm>`). + +An example for the usage of these metrics could be:: + + Chr5 Cufflinks transcript 26581218 26583874 1000 - . gene_id "cufflinks_star_at.23551";transcript_id "cufflinks_star_at.23551.1";exon_number "1";FPKM "0.4343609420";conf_hi "0.577851";frac "0.751684";cov "11.982854";conf_lo "0.293994";percentage_score "42.42" + Chr5 Cufflinks exon 26581218 26581528 . - . gene_id "cufflinks_star_at.23551";transcript_id "cufflinks_star_at.23551.1"; + Chr5 Cufflinks exon 26583335 26583874 . - . gene_id "cufflinks_star_at.23551";transcript_id "cufflinks_star_at.23551.1"; + + +If the scoring file defines: + +.. code-block:: yaml + + scoring: + # [ ... other metrics ... ] + - attributes.FPKM: {rescaling: max} + - attributes.frac: {rescaling: max, use_raw: true} + - attributes.percentage_score: {rescaling: max, use_raw: true, percentage: true} + +The same scoring rules defined previously will apply to metrics obtained from the transcript's attributes. .. _padding: diff --git a/docs/Usage/Configure.rst b/docs/Usage/Configure.rst index 81efa5d60..edc9d2981 100644 --- a/docs/Usage/Configure.rst +++ b/docs/Usage/Configure.rst @@ -57,9 +57,7 @@ Selected command line parameters: - *--seed*: random seed for full reproducibility of Mikado runs. - *--list*: the argument to this option specifies the input annotation files for Mikado. See above. -Command line help: - -.. code-block:: +Command line help:: $ mikado configure --help usage: Mikado configure [-h] [--full] [--seed SEED] [--minimum-cdna-length MINIMUM_CDNA_LENGTH] [--max-intron-length MAX_INTRON_LENGTH] [--scoring SCORING] [--copy-scoring COPY_SCORING] @@ -182,6 +180,7 @@ Global options The following options apply to all programs in the Mikado pipeline, and they refer to general parameters such as logging verbosity, number of threads, etc. Parameters: + - *threads*: this is the number of processes/threads that will be requested by the Mikado programs. This parameter can be overridden on the command line. - *seed*: random seed specification, to ensure maximum reproducibility of the run. .. _start-methods: @@ -513,6 +512,9 @@ After selecting the best model for each locus, Mikado will backtrack and try to # is retained compared to the primary or any other valid AS. Default: false. # - valid_ccodes: Valid class codes for AS events. Valid codes are in categories # 'Alternative splicing', 'Extension' (with junction F1 lower than 100%), and Overlap (exluding m). Default: j, J, g, G, C, h + # - max_utr_length: Maximum length of the UTR for AS events. Default: 10e6 (i.e. no limit) + # - max_fiveutr_length: Maximum length of the 5'UTR for AS events. Default: 10e6 (i.e. no limit) + # - max_threeutr_length: Maximum length of the 5'UTR for AS events. Default: 10e6 (i.e. no limit) # - min_score_perc: Minimum score threshold for subsequent AS events. Only transcripts with a score at least (best) * value are retained. # - only_confirmed_introns: bring back AS events only when their introns are either present in the primary transcript or in the set of confirmed introns. # - pad: boolean switch. If true, Mikado will pad all the transcript in a gene so that their ends are the same @@ -539,8 +541,7 @@ Parameters regarding the clustering of transcripts in loci This section influences how Mikado clusters transcripts in its multi-stage selection. The available parameters are: -- *flank*: numerical. When constructing :ref:`Superloci `, Mikado will use this value as the maximum distance -between transcripts for them to be integrated within the same superlocus. +- *flank*: numerical. When constructing :ref:`Superloci `, Mikado will use this value as the maximum distance between transcripts for them to be integrated within the same superlocus. - *cds_only*: boolean. If set to true, during the :ref:`picking stage ` Mikado will consider only the **primary ORF** to evaluate whether two transcripts intersect. Transcripts which eg. share introns in their UTR but have completely unrelated CDSs will be clustered separately. Disabled by default. - *purge*: boolean. If true, any transcript failing the :ref:`specified requirements ` will be purged out. Otherwise, they will be assigned a score of 0 and might potentially appear in the final output, if no other transcript is present in the locus. - *simple_overlap_for_monoexonic*: boolean. During the :ref:`second clustering `, by default monoexonic transcripts are clustered together even if they have a very slight overlap with another transcript. Manually setting this flag to *false* will cause Mikado to cluster monoexonic transcripts only if they have a minimum amount of cDNA and CDS overlap with the other transcripts in the holder. @@ -624,8 +625,7 @@ This section determines how Mikado will deal with :ref:`chimeras `) that will **never** have the transcripts split. -.. hint:: cDNAs, reference transcripts, and the like should end up in the "skip" category. These are, after all, transcripts -that are presupposed to be originated from a single RNA molecule and therefore without fusions. +.. hint:: cDNAs, reference transcripts, and the like should end up in the "skip" category. These are, after all, transcripts that are presupposed to be originated from a single RNA molecule and therefore without fusions. - *blast_check*: boolean. Whether to execute the check on the BLAST hits. If set to *false*, Mikado will operate in the *split* mode, unless *execute* is set to *false* (execute takes precedence over the other parameters). - *blast_params*: this section contains the settings relative to the *permissive*, *lenient* and *stringent* mode. @@ -745,4 +745,4 @@ Parameters: Technical details ~~~~~~~~~~~~~~~~~ -The configuration file obeys a specific schema defined by the :class:`Mikado.configuration.daijin_configuration` or the :class:`Mikado.configuration.configuration`. Every time a Mikado utility is launched, it checks the configuration file against the schema defined by those classes to validate it. +The configuration file obeys a specific JSON schema which can be found at :download:`Mikado/configuration/configuration_blueprint.json `. Every time a Mikado utility is launched, it checks the configuration file against the schema to validate it. The schema contains non-standard "Comment" and "SimpleComment" string arrays which are used at runtime to generate the comment strings in the YAML output. diff --git a/docs/Usage/Daijin.rst b/docs/Usage/Daijin.rst index 7ec720f02..272f9b6a3 100644 --- a/docs/Usage/Daijin.rst +++ b/docs/Usage/Daijin.rst @@ -288,45 +288,45 @@ Running the pipeline Daijin executes the pipeline in two distinct phases, *assemble* and *mikado*. Both commands have the same command line interface, namely:: - $ daijin assemble --help - usage: daijin assemble [-h] [-c HPC_CONF] [-d] [--jobs N] [--cores [N]] + $ daijin assemble --help + usage: daijin assemble [-h] [-c HPC_CONF] [-d] [--jobs N] [--cores [N]] [--threads N] [--no_drmaa] [--rerun-incomplete] [--forcerun TARGET [TARGET ...]] [--detailed-summary] [--list] [--dag] config - positional arguments: - config Configuration file to use for running the transcript - assembly pipeline. - - optional arguments: - -h, --help show this help message and exit - -c HPC_CONF, --hpc_conf HPC_CONF - Configuration file that allows the user to override - resource requests for each rule when running under a - scheduler in a HPC environment. - -d, --dryrun Do a dry run for testing. - --jobs N, -J N Maximum number of cluster jobs to execute - concurrently. - --cores [N], -C [N] Use at most N cores in parallel (default: 1000). - --threads N, -t N Maximum number of threads per job. Default: None (set - in the configuration file) - --no_drmaa, -nd Use this flag if you wish to run without DRMAA, for - example, if running on a HPC and DRMAA is not - available, or if running locally on your own machine - or server. - --rerun-incomplete, --ri - Re-run all jobs the output of which is recognized as - incomplete. - --forcerun TARGET [TARGET ...], -R TARGET [TARGET ...] - Force the re-execution or creation of the given rules - or files. Use this option if you changed a rule and - want to have all its output in your workflow updated. - --detailed-summary, -D - Print detailed summary of all input and output files - --list, -l List resources used in the workflow - --dag Do not execute anything and print the redirected - acylic graph of jobs in the dot language. + positional arguments: + config Configuration file to use for running the transcript + assembly pipeline. + + optional arguments: + -h, --help show this help message and exit + -c HPC_CONF, --hpc_conf HPC_CONF + Configuration file that allows the user to override + resource requests for each rule when running under a + scheduler in a HPC environment. + -d, --dryrun Do a dry run for testing. + --jobs N, -J N Maximum number of cluster jobs to execute + concurrently. + --cores [N], -C [N] Use at most N cores in parallel (default: 1000). + --threads N, -t N Maximum number of threads per job. Default: None (set + in the configuration file) + --no_drmaa, -nd Use this flag if you wish to run without DRMAA, for + example, if running on a HPC and DRMAA is not + available, or if running locally on your own machine + or server. + --rerun-incomplete, --ri + Re-run all jobs the output of which is recognized as + incomplete. + --forcerun TARGET [TARGET ...], -R TARGET [TARGET ...] + Force the re-execution or creation of the given rules + or files. Use this option if you changed a rule and + want to have all its output in your workflow updated. + --detailed-summary, -D + Print detailed summary of all input and output files + --list, -l List resources used in the workflow + --dag Do not execute anything and print the redirected + acylic graph of jobs in the dot language. The available command parameters are: diff --git a/docs/_static/theme_overrides.css b/docs/_static/theme_overrides.css index e904a4594..37d715760 100644 --- a/docs/_static/theme_overrides.css +++ b/docs/_static/theme_overrides.css @@ -3,7 +3,7 @@ .wy-nav-content { /* padding: 1.618em 3.236em; */ height: 100%; - max-width: none; + max-width: 80%; margin: auto; } @@ -24,11 +24,12 @@ tt { font-size: 130%; } -/*body {*/ -/* font-family: {{ theme_bodyfont }};*/ -/* font-size: 150%;*/ -/* background-color: {{ theme_footerbgcolor }};*/ -/* color: #000;*/ -/* margin: 0;*/ -/* padding: 0;*/ -/*}*/ + +body { + font-family: {{ theme_bodyfont }}; + /*font-size: 150%;*/ + background-color: {{ theme_footerbgcolor }}; + color: #000; + margin: 0; + padding: 0; +} From e4a5374005bc8a11ca0a55d0e5b31261ea36bacb Mon Sep 17 00:00:00 2001 From: Luca Venturini Date: Thu, 25 Feb 2021 12:16:15 +0000 Subject: [PATCH 05/35] Clarifying the input list files for configure/prepare, as well as expanding on strand, redundancy and ORF checks during prepare. --- docs/Library/Mikado.scales.rst | 4 - .../Mikado.serializers.blast_serializer.rst | 4 - docs/Library/Mikado.transcripts.rst | 1 - .../Mikado.transcripts.transcript_methods.rst | 2 - docs/Library/Mikado.utilities.rst | 6 - docs/References.rst | 3 +- docs/Usage/Configure.rst | 36 +++--- docs/Usage/Prepare.rst | 114 ++++++++++++------ 8 files changed, 102 insertions(+), 68 deletions(-) diff --git a/docs/Library/Mikado.scales.rst b/docs/Library/Mikado.scales.rst index 566f26c4b..e3aefd2ee 100644 --- a/docs/Library/Mikado.scales.rst +++ b/docs/Library/Mikado.scales.rst @@ -22,10 +22,6 @@ Submodules Mikado.scales.class_codes Mikado.scales.compare Mikado.scales.contrast - Mikado.scales.contrast - Mikado.scales.contrast - Mikado.scales.f1 - Mikado.scales.f1 Mikado.scales.resultstorer Module contents diff --git a/docs/Library/Mikado.serializers.blast_serializer.rst b/docs/Library/Mikado.serializers.blast_serializer.rst index 10d241c4f..5bcec5af8 100644 --- a/docs/Library/Mikado.serializers.blast_serializer.rst +++ b/docs/Library/Mikado.serializers.blast_serializer.rst @@ -7,13 +7,9 @@ Submodules .. toctree:: :maxdepth: 4 - Mikado.serializers.blast_serializer.aln_string_parser - Mikado.serializers.blast_serializer.aln_string_parser Mikado.serializers.blast_serializer.aln_string_parser Mikado.serializers.blast_serializer.blast_serialiser Mikado.serializers.blast_serializer.btop_parser - Mikado.serializers.blast_serializer.btop_parser - Mikado.serializers.blast_serializer.btop_parser Mikado.serializers.blast_serializer.hit Mikado.serializers.blast_serializer.hsp Mikado.serializers.blast_serializer.query diff --git a/docs/Library/Mikado.transcripts.rst b/docs/Library/Mikado.transcripts.rst index d1adc50b8..604f4a730 100644 --- a/docs/Library/Mikado.transcripts.rst +++ b/docs/Library/Mikado.transcripts.rst @@ -15,7 +15,6 @@ Submodules .. toctree:: :maxdepth: 4 - Mikado.transcripts.clique_methods Mikado.transcripts.reference_gene Mikado.transcripts.transcript Mikado.transcripts.transcriptchecker diff --git a/docs/Library/Mikado.transcripts.transcript_methods.rst b/docs/Library/Mikado.transcripts.transcript_methods.rst index 38836f7fc..1441ae2ea 100644 --- a/docs/Library/Mikado.transcripts.transcript_methods.rst +++ b/docs/Library/Mikado.transcripts.transcript_methods.rst @@ -7,8 +7,6 @@ Submodules .. toctree:: :maxdepth: 4 - Mikado.transcripts.transcript_methods.finalizing - Mikado.transcripts.transcript_methods.printing Mikado.transcripts.transcript_methods.retrieval Mikado.transcripts.transcript_methods.splitting diff --git a/docs/Library/Mikado.utilities.rst b/docs/Library/Mikado.utilities.rst index 6c9ac6c49..8ea346127 100644 --- a/docs/Library/Mikado.utilities.rst +++ b/docs/Library/Mikado.utilities.rst @@ -9,17 +9,11 @@ Submodules Mikado.utilities.dbutils Mikado.utilities.f1 - Mikado.utilities.f1 - Mikado.utilities.f1 Mikado.utilities.file_type Mikado.utilities.intervaltree - Mikado.utilities.intervaltree - Mikado.utilities.intervaltree Mikado.utilities.log_utils Mikado.utilities.namespace Mikado.utilities.overlap - Mikado.utilities.overlap - Mikado.utilities.overlap Module contents --------------- diff --git a/docs/References.rst b/docs/References.rst index 97b8c6141..211c75857 100644 --- a/docs/References.rst +++ b/docs/References.rst @@ -44,4 +44,5 @@ References .. [PYinterval] https://github.com/chaimleib/intervaltree .. [BXPython] https://bitbucket.org/james_taylor/bx-python/overview .. [Snakeviz] https://jiffyclub.github.io/snakeviz/ -.. [PASA] **Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies** Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D. et al. *Nucleic Acids Res*, 2003, 31, 5654-5666. doi:10.1093/nar/gkg770 \ No newline at end of file +.. [PASA] **Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies** Haas, B.J., Delcher, A.L., Mount, S.M., Wortman, J.R., Smith Jr, R.K., Jr., Hannick, L.I., Maiti, R., Ronning, C.M., Rusch, D.B., Town, C.D. et al. *Nucleic Acids Res*, 2003, 31, 5654-5666. doi:10.1093/nar/gkg770 +.. [GffRead] **GFF Utilities: GffRead and GffCompare** Pertea, G. and Pertea, M. *F1000*, 2020, 9, ISCB Comm J-304. doi:10.12688/f1000research.23297.2 \ No newline at end of file diff --git a/docs/Usage/Configure.rst b/docs/Usage/Configure.rst index edc9d2981..8a9dc60d3 100644 --- a/docs/Usage/Configure.rst +++ b/docs/Usage/Configure.rst @@ -30,20 +30,27 @@ The fields in this file are as follows, for each row: ..