Remove unused parameters from the configuration file #158
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lucventurini
added a commit
that referenced
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Mar 27, 2019
…l NOT duplicate information when the 'daijin' option is invoked
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Seems ok, we will need to likely change the following to perhaps but can be confirmed once we have the padding finalised I believe the values below are not used by Mikado but rather by Daijin, can we add a comment to indicate how they are used. reference: |
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Hi @swarbred , for the time being. Regarding this: reference:
genome: genome.fa
max_intron: 4500000
min_intron: 20"genome" is used by Mikado itself. |
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Yes, the external.yaml to drive GMC was made a long time ago. Must have taken it from the Melia Azaderach or Quillaja saponaria annotation (just like any other input for the GMC tests). |
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Great. As this is the case, I will close the issue. |
lucventurini
added a commit
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Jun 18, 2019
* This should address #173 (both configuration file and docs) and #158 * Fix #181 and small bug fix for parsing Mikado annotations. * Progress for #142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for #142) * #142: corrected and tested the issue with one-off exons, for padding. * This should fix and test #142 for good. * Removed spurious warning/error messages * #142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * #142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * #142: fixing previous commit * Pushing the fix for #182 onto the development branch * Fix #183 * Fix #183 and previous commit * #183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * #177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s.
lucventurini
added a commit
that referenced
this issue
Jun 18, 2019
* Solved a small bug in the Gene class * This commit should fix some of the performance issues found in Mikado compare when testing in the all vs all (issue #166). * Updated the CHANGELOG. * Slight improvements to the generic GFLine class and to the to_gff wrapper * Solved some assorted bugs, from stop_codon parsing in GTF2 (for Augustus) to avoiding a very costly pragma check on MIDX databases. * Now Mikado util stats will only return one value for the mode, making the table parsable * Solved some small bugs introduced by changing the mode for mikado util stats * Dropping automated support for Python3.5. The conda environment cannot be created successfully, too many packages have not been updated in the original repositories. * Updating the conda environment to reflect that only Python>=3.6 is now accepted * Various fixes for managing correctly BED12 files. * Fix for the previous commit breaking TRAVIS * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (#166) and fix for #172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (#137) potentially also fixing #172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing #175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on #142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue #174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * #174: this should provide a solution to the issue, which is however only temporary. To be tested. * #174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * #174: peppered the failing block with try-except statements. * #174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed #176 * BROKEN. Progress on #142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing #155. * #174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * #166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix #142. * Development (#178) * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (#166) and fix for #172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (#137) potentially also fixing #172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing #175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on #142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue #174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * #174: this should provide a solution to the issue, which is however only temporary. To be tested. * #174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * #174: peppered the failing block with try-except statements. * #174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed #176 * BROKEN. Progress on #142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing #155. * #174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * #166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix #142. * Update Singularity.centos.def Changed python to python3 during %post, otherwise it will use the system python2.7... * Fixed small bug in external metrics handling * Update Singularity.centos.def * Development (#184) * This should address #173 (both configuration file and docs) and #158 * Fix #181 and small bug fix for parsing Mikado annotations. * Progress for #142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for #142) * #142: corrected and tested the issue with one-off exons, for padding. * This should fix and test #142 for good. * Removed spurious warning/error messages * #142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * #142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * #142: fixing previous commit * Pushing the fix for #182 onto the development branch * Fix #183 * Fix #183 and previous commit * #183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * #177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s.
lucventurini
added a commit
that referenced
this issue
Jun 19, 2019
* Solved a small bug in the Gene class * This commit should fix some of the performance issues found in Mikado compare when testing in the all vs all (issue #166). * Updated the CHANGELOG. * Slight improvements to the generic GFLine class and to the to_gff wrapper * Solved some assorted bugs, from stop_codon parsing in GTF2 (for Augustus) to avoiding a very costly pragma check on MIDX databases. * Now Mikado util stats will only return one value for the mode, making the table parsable * Solved some small bugs introduced by changing the mode for mikado util stats * Dropping automated support for Python3.5. The conda environment cannot be created successfully, too many packages have not been updated in the original repositories. * Updating the conda environment to reflect that only Python>=3.6 is now accepted * Various fixes for managing correctly BED12 files. * Fix for the previous commit breaking TRAVIS * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (#166) and fix for #172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (#137) potentially also fixing #172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing #175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on #142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue #174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * #174: this should provide a solution to the issue, which is however only temporary. To be tested. * #174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * #174: peppered the failing block with try-except statements. * #174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed #176 * BROKEN. Progress on #142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing #155. * #174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * #166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix #142. * Development (#178) * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (#166) and fix for #172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (#137) potentially also fixing #172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing #175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on #142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue #174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * #174: this should provide a solution to the issue, which is however only temporary. To be tested. * #174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * #174: peppered the failing block with try-except statements. * #174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed #176 * BROKEN. Progress on #142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing #155. * #174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * #166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix #142. * Update Singularity.centos.def Changed python to python3 during %post, otherwise it will use the system python2.7... * Fixed small bug in external metrics handling * Update Singularity.centos.def * This should address #173 (both configuration file and docs) and #158 * Fix #181 and small bug fix for parsing Mikado annotations. * Progress for #142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for #142) * #142: corrected and tested the issue with one-off exons, for padding. * This should fix and test #142 for good. * Removed spurious warning/error messages * #142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * #142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * #142: fixing previous commit * Pushing the fix for #182 onto the development branch * Fix #183 * Fix #183 and previous commit * #183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * #177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s. * Development (#184) * This should address #173 (both configuration file and docs) and #158 * Fix #181 and small bug fix for parsing Mikado annotations. * Progress for #142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for #142) * #142: corrected and tested the issue with one-off exons, for padding. * This should fix and test #142 for good. * Removed spurious warning/error messages * #142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * #142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * #142: fixing previous commit * Pushing the fix for #182 onto the development branch * Fix #183 * Fix #183 and previous commit * #183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * #177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s.
lucventurini
added a commit
to lucventurini/mikado
that referenced
this issue
Feb 11, 2021
… config files now will NOT duplicate information when the 'daijin' option is invoked
lucventurini
added a commit
to lucventurini/mikado
that referenced
this issue
Feb 11, 2021
* Solved a small bug in the Gene class * This commit should fix some of the performance issues found in Mikado compare when testing in the all vs all (issue EI-CoreBioinformatics#166). * Updated the CHANGELOG. * Slight improvements to the generic GFLine class and to the to_gff wrapper * Solved some assorted bugs, from stop_codon parsing in GTF2 (for Augustus) to avoiding a very costly pragma check on MIDX databases. * Now Mikado util stats will only return one value for the mode, making the table parsable * Solved some small bugs introduced by changing the mode for mikado util stats * Dropping automated support for Python3.5. The conda environment cannot be created successfully, too many packages have not been updated in the original repositories. * Updating the conda environment to reflect that only Python>=3.6 is now accepted * Various fixes for managing correctly BED12 files. * Fix for the previous commit breaking TRAVIS * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (EI-CoreBioinformatics#166) and fix for EI-CoreBioinformatics#172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (EI-CoreBioinformatics#137) potentially also fixing EI-CoreBioinformatics#172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing EI-CoreBioinformatics#175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on EI-CoreBioinformatics#142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue EI-CoreBioinformatics#174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * EI-CoreBioinformatics#174: this should provide a solution to the issue, which is however only temporary. To be tested. * EI-CoreBioinformatics#174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * EI-CoreBioinformatics#174: peppered the failing block with try-except statements. * EI-CoreBioinformatics#174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed EI-CoreBioinformatics#176 * BROKEN. Progress on EI-CoreBioinformatics#142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing EI-CoreBioinformatics#155. * EI-CoreBioinformatics#174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * EI-CoreBioinformatics#166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix EI-CoreBioinformatics#142. * Development (EI-CoreBioinformatics#178) * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (EI-CoreBioinformatics#166) and fix for EI-CoreBioinformatics#172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (EI-CoreBioinformatics#137) potentially also fixing EI-CoreBioinformatics#172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing EI-CoreBioinformatics#175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on EI-CoreBioinformatics#142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue EI-CoreBioinformatics#174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * EI-CoreBioinformatics#174: this should provide a solution to the issue, which is however only temporary. To be tested. * EI-CoreBioinformatics#174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * EI-CoreBioinformatics#174: peppered the failing block with try-except statements. * EI-CoreBioinformatics#174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed EI-CoreBioinformatics#176 * BROKEN. Progress on EI-CoreBioinformatics#142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing EI-CoreBioinformatics#155. * EI-CoreBioinformatics#174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * EI-CoreBioinformatics#166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix EI-CoreBioinformatics#142. * Update Singularity.centos.def Changed python to python3 during %post, otherwise it will use the system python2.7... * Fixed small bug in external metrics handling * Update Singularity.centos.def * Development (EI-CoreBioinformatics#184) * This should address EI-CoreBioinformatics#173 (both configuration file and docs) and EI-CoreBioinformatics#158 * Fix EI-CoreBioinformatics#181 and small bug fix for parsing Mikado annotations. * Progress for EI-CoreBioinformatics#142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for EI-CoreBioinformatics#142) * EI-CoreBioinformatics#142: corrected and tested the issue with one-off exons, for padding. * This should fix and test EI-CoreBioinformatics#142 for good. * Removed spurious warning/error messages * EI-CoreBioinformatics#142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * EI-CoreBioinformatics#142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * EI-CoreBioinformatics#142: fixing previous commit * Pushing the fix for EI-CoreBioinformatics#182 onto the development branch * Fix EI-CoreBioinformatics#183 * Fix EI-CoreBioinformatics#183 and previous commit * EI-CoreBioinformatics#183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * EI-CoreBioinformatics#177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s.
lucventurini
added a commit
to lucventurini/mikado
that referenced
this issue
Feb 11, 2021
* Solved a small bug in the Gene class * This commit should fix some of the performance issues found in Mikado compare when testing in the all vs all (issue EI-CoreBioinformatics#166). * Updated the CHANGELOG. * Slight improvements to the generic GFLine class and to the to_gff wrapper * Solved some assorted bugs, from stop_codon parsing in GTF2 (for Augustus) to avoiding a very costly pragma check on MIDX databases. * Now Mikado util stats will only return one value for the mode, making the table parsable * Solved some small bugs introduced by changing the mode for mikado util stats * Dropping automated support for Python3.5. The conda environment cannot be created successfully, too many packages have not been updated in the original repositories. * Updating the conda environment to reflect that only Python>=3.6 is now accepted * Various fixes for managing correctly BED12 files. * Fix for the previous commit breaking TRAVIS * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (EI-CoreBioinformatics#166) and fix for EI-CoreBioinformatics#172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (EI-CoreBioinformatics#137) potentially also fixing EI-CoreBioinformatics#172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing EI-CoreBioinformatics#175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on EI-CoreBioinformatics#142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue EI-CoreBioinformatics#174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * EI-CoreBioinformatics#174: this should provide a solution to the issue, which is however only temporary. To be tested. * EI-CoreBioinformatics#174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * EI-CoreBioinformatics#174: peppered the failing block with try-except statements. * EI-CoreBioinformatics#174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed EI-CoreBioinformatics#176 * BROKEN. Progress on EI-CoreBioinformatics#142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing EI-CoreBioinformatics#155. * EI-CoreBioinformatics#174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * EI-CoreBioinformatics#166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix EI-CoreBioinformatics#142. * Development (EI-CoreBioinformatics#178) * Switched to PySam for loading and fetching from genome files. Also, improved massively the speed of tests. * Fixed previous commit * Fixed travis bug * Refactoring of check_index for Mikado compare (EI-CoreBioinformatics#166) and fix for EI-CoreBioinformatics#172 * Now Mikado will merge touching (NOT overlapping) exons coming from BED12 files. This should fix an issue with halLiftover * This commit should fix a bunch of tests for when Mikado is installed with SUDO privileges (EI-CoreBioinformatics#137) potentially also fixing EI-CoreBioinformatics#172. * Corrected a bug in the printing of transcriptomic BED12 files, corrected a bug in the serialisation of ORFs * Fixed previous breakage * Moved the code for checking the index into gene_dict. Also, now GeneDict allows access to positions as well. * Minor edit to assigner * Fixing previously broken commit * Solving a bug which rendered the exclude_utr/protein_coding flags of mikado compare useless. * Adding the GZI index to the tests directory to avoid permission errors. Addressing EI-CoreBioinformatics#175 * Corrected some testing. Moreover, now Mikado supports the BED12+1 format (ie gffread --bed output) * Adding a maximum intron length for the default scoring configuration files. * BROKEN. Proceeding on EI-CoreBioinformatics#142. Now the padding algorithm is aware of where a transcript finishes (intron vs exon). Moreover, we need to change the data structure for padding to a *directional* graph and keep in mind the distance needed to pad a transcript, to solve ambiguous cases in a deterministic (rather than random) way. * Issue EI-CoreBioinformatics#174: modification to the abstractlocus.py file, to try to solve the issue found by @cschuh. * EI-CoreBioinformatics#174: this should provide a solution to the issue, which is however only temporary. To be tested. * EI-CoreBioinformatics#174: making the implicit "for" cycle explicit. Hopefully this should help pinpoint the error better. * EI-CoreBioinformatics#174: peppered the failing block with try-except statements. * EI-CoreBioinformatics#174: this should solve it. Now missing external scores in the database will cause Mikado to explicitly fail. * Fixed EI-CoreBioinformatics#176 * BROKEN. Progress on EI-CoreBioinformatics#142, the code runs, but the tests are broken. **This might be legitimate as we changed the behaviour of the code.** * Closing EI-CoreBioinformatics#155. * EI-CoreBioinformatics#174: Now Mikado pick will die informatively if the SQLite3 database has not been found. * EI-CoreBioinformatics#166: fixed some issues with self-compare * BROKEN. We have to verify that the padding functions also on the 5' end, but we need to make a new test for that. The test development is in progress. * The padding now should be tested and correct. * Fixed previous commit. This should fix EI-CoreBioinformatics#142. * Update Singularity.centos.def Changed python to python3 during %post, otherwise it will use the system python2.7... * Fixed small bug in external metrics handling * Update Singularity.centos.def * This should address EI-CoreBioinformatics#173 (both configuration file and docs) and EI-CoreBioinformatics#158 * Fix EI-CoreBioinformatics#181 and small bug fix for parsing Mikado annotations. * Progress for EI-CoreBioinformatics#142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for EI-CoreBioinformatics#142) * EI-CoreBioinformatics#142: corrected and tested the issue with one-off exons, for padding. * This should fix and test EI-CoreBioinformatics#142 for good. * Removed spurious warning/error messages * EI-CoreBioinformatics#142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * EI-CoreBioinformatics#142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * EI-CoreBioinformatics#142: fixing previous commit * Pushing the fix for EI-CoreBioinformatics#182 onto the development branch * Fix EI-CoreBioinformatics#183 * Fix EI-CoreBioinformatics#183 and previous commit * EI-CoreBioinformatics#183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * EI-CoreBioinformatics#177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s. * Development (EI-CoreBioinformatics#184) * This should address EI-CoreBioinformatics#173 (both configuration file and docs) and EI-CoreBioinformatics#158 * Fix EI-CoreBioinformatics#181 and small bug fix for parsing Mikado annotations. * Progress for EI-CoreBioinformatics#142 - this should fix the wrong ORF calculation for cases when the CDS was open at the 5' end. * Fixed previous commit (always for EI-CoreBioinformatics#142) * EI-CoreBioinformatics#142: corrected and tested the issue with one-off exons, for padding. * This should fix and test EI-CoreBioinformatics#142 for good. * Removed spurious warning/error messages * EI-CoreBioinformatics#142: solved a bug which caused truncated transcripts at the 5' end not to be padded. * EI-CoreBioinformatics#142: solved a problem which caused a false abort for transcripts on the - strand with changed stop codon. * EI-CoreBioinformatics#142: fixing previous commit * Pushing the fix for EI-CoreBioinformatics#182 onto the development branch * Fix EI-CoreBioinformatics#183 * Fix EI-CoreBioinformatics#183 and previous commit * EI-CoreBioinformatics#183: now Mikado configure will set a seed when generating the configuration file. The seed will be explicitly mentioned in the log. * EI-CoreBioinformatics#177: made ORF loading slightly faster with pysam. Also made XML serialisation much faster using SQL sessions and multiprocessing.Pool instead of queues. * Solved annoying bug that caused Mikado to crash with TAIR GFF3s.
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Currently the configuration file has a little bit of legacy flags.
One such flags, for example, is "strand_specific" under the "prepare" section.
Ideally, we should clean up the file to make sure that such legacy parts do not engender confusion in the user.
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