ipyrad/assemble/rawedit.py
def parse_single_results(data, sample, res1):
    """ parse results from cutadapt into sample data"""

    ## set default values 
    #sample.stats_dfs.s2["reads_raw"] = 0
    sample.stats_dfs.s2["trim_adapter_bp_read1"] = 0
    sample.stats_dfs.s2["trim_quality_bp_read1"] = 0
    sample.stats_dfs.s2["reads_filtered_by_Ns"] = 0
    sample.stats_dfs.s2["reads_filtered_by_minlen"] = 0
    sample.stats_dfs.s2["reads_passed_filter"] = 0

    ## parse new values from cutadapt results output
    lines = res1.strip().split("\n")
    for line in lines:

        if "Total reads processed:" in line:
            value = int(line.split()[3].replace(",", ""))
            sample.stats_dfs.s2["reads_raw"] = value

        if "Reads with adapters:" in line:
            value = int(line.split()[3].replace(",", ""))
            sample.stats_dfs.s2["trim_adapter_bp_read1"] = value

        if "Quality-trimmed" in line:
            value = int(line.split()[1].replace(",", ""))
            sample.stats_dfs.s2["trim_quality_bp_read1"] = value

        if "Reads that were too short" in line:
            value = int(line.split()[5].replace(",", ""))
            sample.stats_dfs.s2["reads_filtered_by_minlen"] = value

        if "Reads with too many N" in line:
            value = int(line.split()[5].replace(",", ""))
            sample.stats_dfs.s2["reads_filtered_by_Ns"] = value
   
        if "Reads written (passing filters):" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["reads_passed_filter"] = value

    ## save to stats summary
    if sample.stats_dfs.s2.reads_passed_filter:
        sample.stats.state = 2
        sample.stats.reads_passed_filter = sample.stats_dfs.s2.reads_passed_filter
        sample.files.edits = [
            (OPJ(data.dirs.edits, sample.name+".trimmed_R1_.fastq.gz"), 0)]
        ## write the long form output to the log file.
        LOGGER.info(res1)

    else:
        print("{}No reads passed filtering in Sample: {}".format(data._spacer, sample.name))
def parse_single_results(data, sample, res1):
    """ parse results from cutadapt into sample data"""

    ## set default values 
    #sample.stats_dfs.s2["reads_raw"] = 0
    sample.stats_dfs.s2["trim_adapter_bp_read1"] = 0
    sample.stats_dfs.s2["trim_quality_bp_read1"] = 0
    sample.stats_dfs.s2["reads_filtered_by_Ns"] = 0
    sample.stats_dfs.s2["reads_filtered_by_minlen"] = 0
    sample.stats_dfs.s2["reads_passed_filter"] = 0

    ## parse new values from cutadapt results output
    lines = res1.strip().split("\n")
    for line in lines:

        if "Total reads processed:" in line:
            value = int(line.split()[3].replace(",", ""))
            sample.stats_dfs.s2["reads_raw"] = value

        if "Reads with adapters:" in line:
            value = int(line.split()[3].replace(",", ""))
            sample.stats_dfs.s2["trim_adapter_bp_read1"] = value

        if "Quality-trimmed" in line:
            value = int(line.split()[1].replace(",", ""))
            sample.stats_dfs.s2["trim_quality_bp_read1"] = value

        if "Reads that were too short" in line:
            value = int(line.split()[5].replace(",", ""))
            sample.stats_dfs.s2["reads_filtered_by_minlen"] = value

        if "Reads with too many N" in line:
            value = int(line.split()[5].replace(",", ""))
            sample.stats_dfs.s2["reads_filtered_by_Ns"] = value
   
        if "Reads written (passing filters):" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["reads_passed_filter"] = value

    ## save to stats summary
    if sample.stats_dfs.s2.reads_passed_filter:
        sample.stats.state = 2
        sample.stats.reads_passed_filter = sample.stats_dfs.s2.reads_passed_filter
        sample.files.edits = [
            (OPJ(data.dirs.edits, sample.name+".trimmed_R1_.fastq.gz"), 0)]
        ## write the long form output to the log file.
        LOGGER.info(res1)

    else:
        print("{}No reads passed filtering in Sample: {}".format(data._spacer, sample.name))
def parse_single_results ( data , sample , res1 ) : ## set default values  #sample.stats_dfs.s2["reads_raw"] = 0 sample . stats_dfs . s2 [ "trim_adapter_bp_read1" ] = 0 sample . stats_dfs . s2 [ "trim_quality_bp_read1" ] = 0 sample . stats_dfs . s2 [ "reads_filtered_by_Ns" ] = 0 sample . stats_dfs . s2 [ "reads_filtered_by_minlen" ] = 0 sample . stats_dfs . s2 [ "reads_passed_filter" ] = 0 ## parse new values from cutadapt results output lines = res1 . strip ( ) . split ( "\n" ) for line in lines : if "Total reads processed:" in line : value = int ( line . split ( ) [ 3 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_raw" ] = value if "Reads with adapters:" in line : value = int ( line . split ( ) [ 3 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "trim_adapter_bp_read1" ] = value if "Quality-trimmed" in line : value = int ( line . split ( ) [ 1 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "trim_quality_bp_read1" ] = value if "Reads that were too short" in line : value = int ( line . split ( ) [ 5 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_filtered_by_minlen" ] = value if "Reads with too many N" in line : value = int ( line . split ( ) [ 5 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_filtered_by_Ns" ] = value if "Reads written (passing filters):" in line : value = int ( line . split ( ) [ 4 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_passed_filter" ] = value ## save to stats summary if sample . stats_dfs . s2 . reads_passed_filter : sample . stats . state = 2 sample . stats . reads_passed_filter = sample . stats_dfs . s2 . reads_passed_filter sample . files . edits = [ ( OPJ ( data . dirs . edits , sample . name + ".trimmed_R1_.fastq.gz" ) , 0 ) ] ## write the long form output to the log file. LOGGER . info ( res1 ) else : print ( "{}No reads passed filtering in Sample: {}" . format ( data . _spacer , sample . name ) )
parse results from cutadapt into sample data
parse results from cutadapt into sample data