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Matthias Lienhard committed Sep 13, 2023
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3 changes: 3 additions & 0 deletions CHANGELOG.md
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* planned new feature: during import of long reads, (optionally) correct for short exon alignment issues.
* separate new read import and classification of isoforms.

## [0.3.5]
* fixed a bug in domain plots, which was introduced in 0.3.4

## [0.3.4]
* fixing #8: AssertationError when unifying TSS/PAS between transcript
* improved domain plots: ORF start and end do not appear like exon exon boundaries.
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2 changes: 1 addition & 1 deletion VERSION.txt
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@@ -1 +1 @@
0.3.4
0.3.5
2 changes: 1 addition & 1 deletion docs/notebooks/01_prepare_data.ipynb
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"source": [
"## Demonstration Data\n",
"\n",
"To create an demonstration data set, we aligned the encode fastq files with minimap2, and sub-selected reads mapping to chromosome 8 only. All resulting files (~270 Mb) [can be downloaded here](https://oc-molgen.gnz.mpg.de/owncloud/s/gjG9EPiQwpRAyg3).\n",
"To create an demonstration data set, we aligned the encode fastq files with minimap2, and sub-selected reads mapping to chromosome 8 only. All resulting files (~270 Mb) [can be downloaded here](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd).\n",
"``` bash\n",
"\n",
"\n",
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97 changes: 53 additions & 44 deletions docs/notebooks/03_transcriptome_reconstruction.ipynb
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35 changes: 21 additions & 14 deletions docs/notebooks/03b_transcriptome_import.ipynb
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"name": "stderr",
"output_type": "stream",
"text": [
"INFO:This is isootools version 0.3.3\n"
"INFO:This is isootools version 0.3.5\n"
]
}
],
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"output_type": "stream",
"text": [
"INFO:importing reference from gff3 file demonstration_dataset/gencode.v42.chr_patch_hapl_scaff.annotation_sorted_chr8.gff3.gz\n",
"100%|█████████▉| 2.82M/2.82M [00:02<00:00, 1.36MB/s]\n",
"INFO:skipped the following categories: {'CDS', 'three_prime_UTR', 'five_prime_UTR'}\n",
"100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████▉| 2.82M/2.82M [00:02<00:00, 1.22MB/s]\n",
"INFO:skipped the following categories: {'five_prime_UTR', 'CDS', 'three_prime_UTR'}\n",
"WARNING:Missing genes! Found gene information in categories ['gene'] for 2540/5080 genes\n",
"INFO:adding samples \"GM12878_pooled\", \"K562_pooled\" from csv\n",
"100%|██████████| 2611/2611 [00:06<00:00, 391.00genes/s]\n"
"100%|███████████████████████████████████████████████████████████████████████████████████████████████████████████| 2611/2611 [00:09<00:00, 276.43genes/s]\n"
]
},
{
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" <th>0</th>\n",
" <td>GM12878_pooled</td>\n",
" <td>demonstration_dataset/demonstration_dataset_su...</td>\n",
" <td>NaN</td>\n",
" <td>GM12878_pooled</td>\n",
" <td>125138</td>\n",
" <td>0</td>\n",
" </tr>\n",
" <tr>\n",
" <th>0</th>\n",
" <td>K562_pooled</td>\n",
" <td>demonstration_dataset/demonstration_dataset_su...</td>\n",
" <td>NaN</td>\n",
" <td>125138</td>\n",
" <td>K562_pooled</td>\n",
" <td>142708</td>\n",
" <td>0</td>\n",
" </tr>\n",
" </tbody>\n",
"</table>\n",
"</div>"
],
"text/plain": [
" name file group \\\n",
"0 GM12878_pooled demonstration_dataset/demonstration_dataset_su... NaN \n",
"0 K562_pooled demonstration_dataset/demonstration_dataset_su... NaN \n",
" name file \\\n",
"0 GM12878_pooled demonstration_dataset/demonstration_dataset_su... \n",
"0 K562_pooled demonstration_dataset/demonstration_dataset_su... \n",
"\n",
" nonchimeric_reads chimeric_reads \n",
"0 125138 0 \n",
"0 125138 0 "
" group nonchimeric_reads chimeric_reads \n",
"0 GM12878_pooled 125138 0 \n",
"0 K562_pooled 142708 0 "
]
},
"execution_count": 2,
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"isoseq=Transcriptome.from_reference(annotation_fn)\n",
"\n",
"#specify the columns with the read counts per transcript\n",
"read_count_cols={'GM12878_pooled':'GM12878_sum_coverage','K562_pooled':'GM12878_sum_coverage'}\n",
"read_count_cols={'GM12878_pooled':'GM12878_sum_coverage','K562_pooled':'K562_sum_coverage'}\n",
"\n",
"# add the transcripts from the gtf file\n",
"id_map=isoseq.add_sample_from_csv(\n",
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"isoseq.sample_table"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
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6 changes: 3 additions & 3 deletions docs/notebooks/04_saturation_analysis.ipynb
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13 changes: 10 additions & 3 deletions docs/notebooks/05_qc.ipynb
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13 changes: 6 additions & 7 deletions docs/notebooks/06_filtering.ipynb
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"* define custom tags and filter expressions, to tailor filter queries.\n",
"\n",
"\n",
"This tutorial depends on the transcriptome file PacBio_isotools_substantial_isotools.pkl, which can be obtained with this [download link](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)"
"This tutorial assumes you have run the tutorial on [transcriptome reconstruction](03_transcriptome_reconstruction.html) already, and prepared the transcriptome pkl file *\"PacBio_isotools.pkl\"* based on the [demonstration data set](https://nc.molgen.mpg.de/cloud/index.php/s/zYe7g6qnyxGDxRd)."
]
},
{
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"import pandas as pd\n",
"\n",
"path='demonstration_dataset'\n",
"isoseq=Transcriptome.load(f'{path}/PacBio_isotools_substantial_isotools.pkl')"
"isoseq=Transcriptome.load(f'{path}/PacBio_isotools.pkl')"
]
},
{
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"text": [
"\n",
"These are the infos for this transcript:\n",
"exons: [[89757792, 89758233], [89762828, 89762982], [89765340, 89765496], [89769771, 89769929], [89771740, ...\n",
"exons: [[89757791, 89758233], [89762828, 89762982], [89765340, 89765496], [89769771, 89769929], [89771740, ...\n",
"strand: +\n",
"coverage: {'GM12878_a': 48, 'GM12878_b': 135, 'GM12878_c': 138, 'K562_a': 19, 'K562_b': 18, 'K562_c': 13}\n",
"TSS: {'GM12878_a': {89757763: 1, 89757766: 1, 89757778: 1, 89757782: 3, 89757783: 4, 89757784: 4, 8975778...\n",
"PAS: {'GM12878_a': {89790462: 3, 89791057: 3, 89790608: 5, 89790939: 3, 89790606: 3, 89790425: 1, 8979046...\n",
"annotation: (0, {'FSM': [1]})\n",
"TSS_unified: {'GM12878_a': {89757792: 48}, 'GM12878_b': {89757792: 135}, 'GM12878_c': {89757792: 138}, 'K562_a': ...\n",
"PAS_unified: {'GM12878_a': {89790463: 20, 89790983: 10, 89790606: 11, 89790940: 3, 89790525: 4}, 'GM12878_b': {89...\n",
"ORF: (89758060, 89790416, {'start': 268, 'length': 1623, 'start_codon': 'ATG', 'stop_codon': 'TAA', 'NMD'...\n",
"TSS_unified: {'GM12878_a': {89757791: 48}, 'GM12878_b': {89757791: 135}, 'GM12878_c': {89757791: 138}, 'K562_a': ...\n",
"PAS_unified: {'GM12878_a': {89790462: 20, 89790982: 10, 89790605: 11, 89790939: 3, 89790524: 4}, 'GM12878_b': {89...\n",
"direct_repeat_len: [3, 3, 4, 5, 7, 3, 5, 4, 6, 4]\n",
"downstream_A_content: 0.2\n"
]
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"name": "stderr",
"output_type": "stream",
"text": [
"100%|██████████| 10803/10803 [00:00<00:00, 15873.69genes/s]\n"
"100%|███████████████████████████████████████████████████████████████████████████████████████████████████████| 10803/10803 [00:00<00:00, 17189.88genes/s]\n"
]
}
],
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18 changes: 9 additions & 9 deletions docs/notebooks/08_alternative_splicing.ipynb
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