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csvgather

Utility for gathering multiple character-separated value files and joining into a single matrix. Similar to csvjoin from the csvkit package, or the join function of csvtk, except allows column headers to be renamed based on the filename. This is an extremely common operation in, e.g. bioinformatic analyses, when the same utility, which produces a file with static headers, is run for many samples, differing only in some portion of the filename.

For example, the RNA-Seq gene expression quantification tool kallisto produces a directory that contains a file that is always named abundance.tsv, which has columns

target_id length eff_length est_counts tpm

To differentiate between samples, the directory is often named to include the sample name, e.g. sample_A__kallisto_counts/abundance.tsv. Downstream analysis steps often require the est_counts columns from many samples files to be concatenated into a single matrix file. A simple join operation on the first field of these files would produce a file with identical column names, making such operations useless. This utility enables field-specific name transforms based on input file. For example:

csvgather -j 0 -f est_counts -t "s:est_counts:{dir}:" -t "s:__kallisto_counts::" sample_*__kallisto_counts/abundance.tsv

This command joins all of the abundance.tsv files on the first column value, selects only the columns est_counts from each file, transforms the column name of each column to include the directory name of the corresponding file, and then transforms again to remove the __kallisto_counts part, leaving only the sample name.

Maybe I'll try to integrate this utility into csvkit one day.

Installation

You can install using pip:

pip install csvgather

Usage

Usage: csvgather.py [options] [-j PATT]... [-f PATT]... [-t STR]... <csv_fn>...

Options:
  -h --help               This helpful help help help help is a weird word
  -d STR --delimiter=STR  Character(s) to use as the delimiter in the output,
                          can be multiple characters [default:  ]
  -o PATH --output=PATH   Output to file [default: stdout]
  -j COL --join=COL       Column(s) to join on. Can take one of four forms:
                            - 0-based integer indicating column index, can be
                              negative to index from the end of the columns
                            - a half closed interval of 0-based integers to
                              specify a range of columns (e.g. 0:4 or 0:-1)
                            - a regular expression that will use any columns it
                              matches as the join columns
                            - a pair of regular expressions to specify a range
                              of columns (e.g. geneName:strand will start with
                              the column geneName and end with column strand)
                          If more than one column matches, then a warning is
                          issued but the join continues on the aggregate of the
                          columns. ':' or special regular expression characters
                          (e.g. +, *, [, ], etc) in column names must be
                          wrapped in [], e.g. '[:]'. Can be specified multiple
                          times, in which case all selected columns are unioned
                          together [default: 0]
  -f COL --field=COL      Column(s) to select fields for concatenation. Uses
                          the same format as -j option. May be specified
                          multiple times and any matching columns will be
                          included. Column selection occurs before application
                          of transformations (-t). Joined columns are not
                          included in the field match [default: .]
  -t STR --transform=STR  A string of the form "s:patt:repl:[gi]" to apply to
                          every column name. The special strings {path}, {dir},
                          {fn}, and {basename} can be used in the repl string to
                          refer to the full path, parent directory name, file
                          name, and filename without extension (i.e. [.][^.]*$)
                          removed. May be specified multiple times, in which
                          case the transformations will be performed
                          sequentially in the order specified on the command
                          line [default: s:.:.:]
  --join-type=STR         Type of join, one of 'outer', 'inner', or 'left'.
                          outer will create a row for every distinct value in
                          the -j column(s), inner will report only rows that
                          are found in all files, and left will join files from
                          left to right [default: outer]
  --empty-val=VAL         The value to use when an outer or left join does not
                          find a corresponding row in a file [default: ]
  --comment=CHARS         Characters to be considered comments in input files
                          and will be skipped. Can be any number of characters
                          e.g. #@- [default: #]