samsifter.filters package
Submodules
samsifter.filters.bam_2_sam module
Wrapper for SAMtools view.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.calculate_pmds module
Wrapper for PMDtools score calculation.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.compress module
Wrapper for GNU Gzip compression functionality.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.count_taxon_reads module
Analysing filter step to measure read counts per taxon.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.decompress module
Wrapper for GNU Gzip decompression functionality.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.filter_read_conservation module
Identify highly conserved reads in a SAM file.
Filters reads assigned to multiple taxa with similar identity. Excludes reads
mapping to different accessions/taxa with similar alignment scores.
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item()[source]
Create FilterItem for this filter to be used in list and tree models.
Returns: | Object representing this filter in item-based models. |
Return type: | FilterItem |
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main()[source]
Executable to filter SAM files for reads with high conservation.
See --help for details on expected arguments. Takes input from
either STDIN, or optional, or positional arguments. Logs messages to
STDERR and writes processed SAM files to STDOUT.
samsifter.filters.filter_read_identity module
Wrapper for PMDtools identity filter functionality.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.filter_read_list module
Created on Thu Dec 18 09:34:28 2014
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.filter_read_pmds module
Created on Thu Dec 18 09:34:28 2014
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.filter_ref_coverage module
Identify reference accessions with uneven coverage in MALT’ed SAM files.
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calc_avg_depth(depth_dist, ignore_uncovered=True)[source]
Calculate average depth from a coverage distribution.
Optionally ignores uncovered bases (first array element).
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covered_length_from_cigar(cigar)[source]
Calculate length of reference covered by read from CIGAR operations.
- not counting padding, skipping or insertions into the reference
- not counting hard or soft clipped bases of the read
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get_gini_auc(x, y)[source]
Calculate Gini coefficient and area under Lorenz curve.
Expects arrays of x and y coordinates for a normalized Lorenz distribution.
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integral_discrete(dist, limit)[source]
Integrate discrete distribution with stepsize 1 by simply adding up values.
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integral_scaled(dist, limit)[source]
Integrate scaled discrete distribution with arbitrary stepsize.
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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lorenzify(depth_dist)[source]
Calculate Lorenz curve from coverage distribution.
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lorenzify_b2b(depth_dist, ignore_uncovered=True)[source]
Calculate Lorenz curve from base2base coverage distribution.
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main()[source]
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plot_ccd(ax, depth_dist_cumsum, avg_depth)[source]
Create a bar plot of a cumulative coverage distribution.
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plot_cd(ax, depth_dist, avg_depth)[source]
Create a bar plot of a cumulative coverage distribution.
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plot_lorenz(ax, x, y)[source]
Create a Lorenz curve plot of a coverage distribution.
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plot_lorenz_b2b(ax, x, y)[source]
Create a Lorenz curve plot of a coverage distribution.
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plot_nccd(ax, depth_dist_cumperc, avg_depth, max_depth, avg_depth_scaled, lci, color)[source]
Create a bar plot of a normalized cumulative coverage distribution.
Includes legend stating average scaled and total depth
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plot_rld(ax, length_dist, min_length, max_length, read_count, length_dist_total)[source]
Create a bar plot of a read length distribution.
Includes scaled expected distribution based on all reads in file.
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plot_sccd(ax, depth_dist_cumperc, avg_depth)[source]
Create a bar plot of a scaled cumulative coverage distribution.
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plot_scd(ax, depth_dist, avg_depth, ref_length, max_depth)[source]
Create a bar plot of a scaled cumulative coverage distribution.
samsifter.filters.filter_ref_identity module
Filters reference accessions with too few/many reads of high/low percent
identity in MALT’ed SAM files”
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.filter_ref_list module
Created on Thu Dec 18 09:34:28 2014
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.filter_ref_pmds module
Filter references with high attribution of ancient reads in a MALT’ed and
PMD’ed SAM file
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.filter_taxon_list module
Created on Thu Dec 18 09:34:28 2014
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.filter_taxon_pmds module
Filter taxa with high attribution of ancient reads in a MALT’ed and PMD’ed
SAM file
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
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main()[source]
samsifter.filters.filter_test module
Created on Fri Jan 16 11:55:23 2015
@author: aldehoff
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main()[source]
samsifter.filters.remove_duplicates module
Wrapper for SAMtools rmdup
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.sam_2_bam module
Wrapper for SAMtools view
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.sort_by_coordinates module
Wrapper for SAMtools sort
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
samsifter.filters.sort_by_names module
Wrapper for SAMtools sort
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item()[source]
Create item representing this tool in list and tree views.
Returns: | Item for use in item-based list and tree views. |
Return type: | FilterItem |
Module contents