ipyrad/assemble/rawedit.py
def parse_pair_results(data, sample, res):
    """ parse results from cutadapt for paired data"""
    LOGGER.info("in parse pair mod results\n%s", res)   
    ## set default values
    sample.stats_dfs.s2["trim_adapter_bp_read1"] = 0
    sample.stats_dfs.s2["trim_adapter_bp_read2"] = 0    
    sample.stats_dfs.s2["trim_quality_bp_read1"] = 0
    sample.stats_dfs.s2["trim_quality_bp_read2"] = 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

    lines = res.strip().split("\n")
    qprimed = 0
    for line in lines:
        ## set primer to catch next line
        if "Quality-trimmed" in line:
            qprimed = 1

        ## grab read1 and read2 lines when qprimed
        if "Read 1:" in line:
            if qprimed:
                value = int(line.split()[2].replace(",", ""))
                sample.stats_dfs.s2["trim_quality_bp_read1"] = value

        if "Read 2:" in line:
            if qprimed:
                value = int(line.split()[2].replace(",", ""))
                sample.stats_dfs.s2["trim_quality_bp_read2"] = value
                qprimed = 0

        if "Read 1 with adapter:" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["trim_adapter_bp_read1"] = value

        if "Read 2 with adapter:" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["trim_adapter_bp_read2"] = value

        if "Total read pairs processed:" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["reads_raw"] = value

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

        if "Pairs with too many N" in line:
            value = int(line.split()[5].replace(",", ""))
            sample.stats_dfs.s2["reads_filtered_by_Ns"] = value

        if "Pairs 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"), 
             OPJ(data.dirs.edits, sample.name+".trimmed_R2_.fastq.gz")
             )]

    else:
        print("No reads passed filtering in Sample: {}".format(sample.name))
def parse_pair_results(data, sample, res):
    """ parse results from cutadapt for paired data"""
    LOGGER.info("in parse pair mod results\n%s", res)   
    ## set default values
    sample.stats_dfs.s2["trim_adapter_bp_read1"] = 0
    sample.stats_dfs.s2["trim_adapter_bp_read2"] = 0    
    sample.stats_dfs.s2["trim_quality_bp_read1"] = 0
    sample.stats_dfs.s2["trim_quality_bp_read2"] = 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

    lines = res.strip().split("\n")
    qprimed = 0
    for line in lines:
        ## set primer to catch next line
        if "Quality-trimmed" in line:
            qprimed = 1

        ## grab read1 and read2 lines when qprimed
        if "Read 1:" in line:
            if qprimed:
                value = int(line.split()[2].replace(",", ""))
                sample.stats_dfs.s2["trim_quality_bp_read1"] = value

        if "Read 2:" in line:
            if qprimed:
                value = int(line.split()[2].replace(",", ""))
                sample.stats_dfs.s2["trim_quality_bp_read2"] = value
                qprimed = 0

        if "Read 1 with adapter:" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["trim_adapter_bp_read1"] = value

        if "Read 2 with adapter:" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["trim_adapter_bp_read2"] = value

        if "Total read pairs processed:" in line:
            value = int(line.split()[4].replace(",", ""))
            sample.stats_dfs.s2["reads_raw"] = value

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

        if "Pairs with too many N" in line:
            value = int(line.split()[5].replace(",", ""))
            sample.stats_dfs.s2["reads_filtered_by_Ns"] = value

        if "Pairs 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"), 
             OPJ(data.dirs.edits, sample.name+".trimmed_R2_.fastq.gz")
             )]

    else:
        print("No reads passed filtering in Sample: {}".format(sample.name))
def parse_pair_results ( data , sample , res ) : LOGGER . info ( "in parse pair mod results\n%s" , res ) ## set default values sample . stats_dfs . s2 [ "trim_adapter_bp_read1" ] = 0 sample . stats_dfs . s2 [ "trim_adapter_bp_read2" ] = 0 sample . stats_dfs . s2 [ "trim_quality_bp_read1" ] = 0 sample . stats_dfs . s2 [ "trim_quality_bp_read2" ] = 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 lines = res . strip ( ) . split ( "\n" ) qprimed = 0 for line in lines : ## set primer to catch next line if "Quality-trimmed" in line : qprimed = 1 ## grab read1 and read2 lines when qprimed if "Read 1:" in line : if qprimed : value = int ( line . split ( ) [ 2 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "trim_quality_bp_read1" ] = value if "Read 2:" in line : if qprimed : value = int ( line . split ( ) [ 2 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "trim_quality_bp_read2" ] = value qprimed = 0 if "Read 1 with adapter:" in line : value = int ( line . split ( ) [ 4 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "trim_adapter_bp_read1" ] = value if "Read 2 with adapter:" in line : value = int ( line . split ( ) [ 4 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "trim_adapter_bp_read2" ] = value if "Total read pairs processed:" in line : value = int ( line . split ( ) [ 4 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_raw" ] = value if "Pairs that were too short" in line : value = int ( line . split ( ) [ 5 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_filtered_by_minlen" ] = value if "Pairs with too many N" in line : value = int ( line . split ( ) [ 5 ] . replace ( "," , "" ) ) sample . stats_dfs . s2 [ "reads_filtered_by_Ns" ] = value if "Pairs 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" ) , OPJ ( data . dirs . edits , sample . name + ".trimmed_R2_.fastq.gz" ) ) ] else : print ( "No reads passed filtering in Sample: {}" . format ( sample . name ) )
parse results from cutadapt for paired data
parse results from cutadapt for paired data