Development #117
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Development #117
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Refactoring temporary json file concatenation
* Uncomment dask dataframe import. * Remove json output type from list of parquet incompatible formats. * Specify dtypes for dask dataframe read from json. * Enable reading json files into dask dataframe and writing as parquet file. * Enable files to be read in binary mode for all output formats. * Change json output field for j gene from score to assigner_score. * Revert change in line position to read file in binary mode. * Converting IMGT positions from integers or floats to string. * Coerce raw_position to be stringtype. * Add schema for JSON fields datatypes to override when writing to parquet. * Additional schema attributes. * Convert schema to full pyarrow schema for full dataset. * Add columns desired order and dtypes for dataframe metadata. * Reorder dtype fields. * Remove unneeded column and dtype information. * Edit json reading and parquet writing code. * Add additional schema attributes involved in BCR. * Reorder schema fields. * Reorder pyarrow schema.
… already assigned V gene
… end of the V and/or the 3' end of the J
* Replace string dtypes to object dtypes. * Add function attribute to indicate if parquet will be written to `write_output` function. * Write parquet files directly in place of temporary JSON files. * Add flag to ignore datatype conversion errors when casting integer columns with NaNs, and change output file name. * Edit concat_outputs to simply move files instead for parquet files generated from json output. * Edit file path from string concatenation to os path join. * Minor edit to ps.path.join. * Added if statement to check if file exists before attempting to delete temporary file. * Add `.snappy` file extension to parquet files. * Simplified file name to simply moving to directory instead. * Simplify specifying columns by changing `schema.names` to `dtypes`. * Parse strings of dictionary into dictionary with `json.loads` before loading into dataframe. * Read in temporary parquet files, repartition and write back parquet files. * Remove setting writing metadata file in parquet to False as it's the default function argument. * Remove unused imports. * Remove if condition to check for temp files before deleting them.
* Fix chunking of fastq files * ignore vscode
* Replace double quotation marks to single quotes for consistency with rest of codebase. * Add empty line at EOF. * Allow matplotlib to be installed to the latest version since scanpy has upgraded their matplotlib support. * Add comments to better explain code edits.
…nctions (no need for a matrix)
Add support to write in parquet format
Preprocessing
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