flowcraft.templates.trimmomatic_report module¶
Purpose¶
This module is intended parse the results of the Trimmomatic log for a set of one or more samples.
Expected input¶
The following variables are expected whether using NextFlow or the
main()
executor.
log_files
: Trimmomatic log files.- e.g.:
'Sample1_trimlog.txt Sample2_trimlog.txt'
- e.g.:
Generated output¶
trimmomatic_report.csv
: Summary report of the trimmomatic logs for all samples
Code documentation¶
-
flowcraft.templates.trimmomatic_report.
parse_log
(log_file)[source]¶ Retrieves some statistics from a single Trimmomatic log file.
This function parses Trimmomatic’s log file and stores some trimming statistics in an
OrderedDict
object. This object contains the following keys:clean_len
: Total length after trimming.total_trim
: Total trimmed base pairs.total_trim_perc
: Total trimmed base pairs in percentage.5trim
: Total base pairs trimmed at 5’ end.3trim
: Total base pairs trimmed at 3’ end.
Parameters: - log_file : str
Path to trimmomatic log file.
Returns: - x :
OrderedDict
Object storing the trimming statistics.
-
flowcraft.templates.trimmomatic_report.
write_report
(storage_dic, output_file, sample_id)[source]¶ Writes a report from multiple samples.
Parameters: - storage_dic : dict or
OrderedDict
Storage containing the trimming statistics. See
parse_log()
for its generation.- output_file : str
Path where the output file will be generated.
- sample_id : str
Id or name of the current sample.
- storage_dic : dict or