{ "info": { "author": "Leiden University Medical Center", "author_email": "sasc@lumc.nl", "bugtrack_url": null, "classifiers": [ "Development Status :: 3 - Alpha", "License :: OSI Approved :: MIT License", "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.5", "Programming Language :: Python :: 3.6", "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3 :: Only" ], "description": "# collect-columns\n\nThis tool retrieves a column from each in a set of tables and compiles into a single table.\nOptionally, additional attributes from the associated GTF/GFF file may be added to the output\ntables.\n\n## Installation\nInstall from PyPI: `pip install collect-columns`\n\nInstall from github:\n* Clone the repository: `git clone https://github.com/biowdl/collect-columns.git`\n* Enter the repository: `cd collect-columns`\n* Install using pip: `pip install .`\n\n## Usage\n```\ncollect-columns output_path input_files...\n```\n\nIt assumes that all input count tables are in the same format.\nBy default the format is assumed to be headerless and tab separated, with the\nfirst column being the feature identifiers and the second the values of interest.\nThe output table will use the same separator as the input tables and contain\na header. The `feature` column will contain the feature identifiers, the value\ncolumns will be named after the input files or according to the names given\nthrough the `-n` option, which takes a list of names as argument.\n\nIn order to use a different input format the following options can be given:\n\n| option | arguments | definition |\n|:-:|:-:|:-|\n| `-f` | a number | The index of the column containing the feature identifiers. |\n| `-c` | a number | The index of the column containing the values/counts. |\n| `-s` | a character | The separator.|\n| `-H` | | Indicates that the table has a header. |\n\nTo add additional attributes from a GTF/GFF, the following options can be given:\n\n| option | arguments | definition |\n|:-:|:-:|:-|\n| `-a` | a list of words | The attributes to be added to the output table. |\n| `-g` | a path | The gtf file from which the attributes will be retrieved. |\n| `-F` | a word | The attribute used to map rows in the input tables to gtf record. Defaults to `gene_id`. |\n\n### Examples\n#### HTSeq-count\nUsing the output from HTSeq-count as input the following command:\n```\ncollect-columns all.tsv s1.tsv s2.tsv\n```\nwill result in a table like:\n\n| feature | s1.tsv | s2.tsv |\n|:-------:|:------:|:------:|\n| MSTRG.1 | 10 | 11 |\n| MSTRG.2 | 60 | 12 |\n| ... | ... | ... |\n\n#### Stringtie\nUsing stringtie abundance output as input, the following command:\n```\ncollect-columns all.FPKM s1.abundance s2.abundance \\\n -c 7 \\\n -H \\\n -a ref_gene_id gene_name \\\n -g merged.gtf \\\n -n sample1 sample2\n```\nwill result in a table like:\n\n| feature | ref_gene_id | gene_name | sample1 | sample2 |\n|:-------:|:-----------:|:---------:|:-------------:|:-----------:|\n| MSTRG.1 | g_1 | gene_1 | 185151.953125 | 151.964231 |\n| MSTRG.2 | g_2 | gene_2 | 100160.070312 | 1160.030213 |\n| ... | ... | ... | ... | ... |\n\n\n", "description_content_type": "text/markdown", "docs_url": null, "download_url": "", "downloads": { "last_day": 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