Replace zcat (#94)

* D3-Enhancements (#78)

* Sam/try plots (#71)

* Fix batch mode pandas warning. (#70)

* refactor to call method on DataFrame, rather than Series.
Removes warning.

* Fix pandas future warning in CRISPRessoWGS

---------

Co-authored-by: Cole Lyman <[email protected]>

* Functional

* Cole/fix status file name (#69)

* Update config file logging messages

This removes printing the exception (which is essentially a duplicate),
and adds a condition if no config file was provided. Also changes `json`
to `config` so that it is more clear.

* Fix divide by zero when no amplicons are present in Batch mode

* Don't append file_prefix to status file name

* Place status files in output directories

* Update tests branch for file_prefix addition

* Load D3 and plotly figures with pro with multiple amplicons

* Update batch

* Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix

Before this fix, when using a file_prefix the second run that was compared
would not be displayed as a data in the first figure of the report.

* Import CRISPRessoPro instead of importing the version

When installed via conda, the version is not available

* Remove `get_amplicon_output` unused function from CRISPRessoCompare

Also remove unused argparse import

* Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests

* Allow for matching of multiple guides in the same amplicon

* Fix pandas FutureWarning

* Change test branch back to master

---------

Co-authored-by: Sam <[email protected]>

* Try catch all futures

* Fix test fail plots

* Point test to try-plots

* Fix d3 not showing and plotly mixing with matplotlib

* Use logger for warnings and debug statements

* Point tests back at master

---------

Co-authored-by: mbowcut2 <[email protected]>
Co-authored-by: Cole Lyman <[email protected]>

* Sam/fix plots (#72)

* Fix batch mode pandas warning. (#70)

* refactor to call method on DataFrame, rather than Series.
Removes warning.

* Fix pandas future warning in CRISPRessoWGS

---------

Co-authored-by: Cole Lyman <[email protected]>

* Functional

* Cole/fix status file name (#69)

* Update config file logging messages

This removes printing the exception (which is essentially a duplicate),
and adds a condition if no config file was provided. Also changes `json`
to `config` so that it is more clear.

* Fix divide by zero when no amplicons are present in Batch mode

* Don't append file_prefix to status file name

* Place status files in output directories

* Update tests branch for file_prefix addition

* Load D3 and plotly figures with pro with multiple amplicons

* Update batch

* Fix bug in CRISPRessoCompare with pointing to report datas with file_prefix

Before this fix, when using a file_prefix the second run that was compared
would not be displayed as a data in the first figure of the report.

* Import CRISPRessoPro instead of importing the version

When installed via conda, the version is not available

* Remove `get_amplicon_output` unused function from CRISPRessoCompare

Also remove unused argparse import

* Implement `get_matching_allele_files` in CRISPRessoCompare and accompanying unit tests

* Allow for matching of multiple guides in the same amplicon

* Fix pandas FutureWarning

* Change test branch back to master

---------

Co-authored-by: Sam <[email protected]>

* Try catch all futures

* Fix test fail plots

* Fix d3 not showing and plotly mixing with matplotlib

---------

Co-authored-by: mbowcut2 <[email protected]>
Co-authored-by: Cole Lyman <[email protected]>

* Remove token from integration tests file

* Provide sgRNA_sequences to plot_nucleotide_quilt plots

* Passing sgRNA_sequences to plot

* Refactor check for determining when to use CRISPREssoPro or matplotlib for Batch plots

* Add max-height to Batch report samples

* Change testing branch

* Fix wrong check for large Batch plots

* Fix typo and move flexiguide to debug (#77)

* Change flexiguide output to debug level

* Fix typo in fastp merged output file name

* Adding id tags for d3 script enhancements

* pointing to test branch

* Add amplicon_name parameter to allele heatmap and line plots

* Add function to extract quantification window regions from include_idxs

* Scale the quantification window according to the coordinates of the sgRNA plot

* added c2pro check, added space in args.json

* Correct the quantification window indexes for multiple guides

* Fix name of nucleotide conversion plot when guides are not the same

* Fix jinja variables that aren't found

* Fix multiple guide errors where the wrong sgRNA sequence was associated in d3 plot

* Remove unneeded variable and extra whitespace

* Switch test branch to master

---------

Co-authored-by: Samuel Nichols <[email protected]>
Co-authored-by: mbowcut2 <[email protected]>
Co-authored-by: Cole Lyman <[email protected]>

* Replace zcat with gunzip -c in `get_most_frequent_reads`

---------

Co-authored-by: Trevor Martin <[email protected]>
Co-authored-by: Samuel Nichols <[email protected]>
Co-authored-by: mbowcut2 <[email protected]>

CRISPResso2/CRISPRessoShared.py

@@ -782,13 +782,13 @@ def get_most_frequent_reads(fastq_r1, fastq_r2, number_of_reads_to_consider, fas
 
     view_cmd_1 = 'cat'
     if fastq_r1.endswith('.gz'):
-        view_cmd_1 = 'zcat'
+        view_cmd_1 = 'gunzip -c'
     file_generation_command = "%s %s | head -n %d " % (view_cmd_1, fastq_r1, number_of_reads_to_consider * 4)
 
     if fastq_r2:
         view_cmd_2 = 'cat'
         if fastq_r2.endswith('.gz'):
-            view_cmd_2 = 'zcat'
+            view_cmd_2 = 'gunzip -c'
         min_overlap_param = ""
         if min_paired_end_reads_overlap:
             min_overlap_param = "--overlap_len_require {0}".format(min_paired_end_reads_overlap)