samsifter.filters package

Submodules

samsifter.filters.bam_2_sam module

Wrapper for SAMtools view.

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.

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.

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.

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
main()[source]

samsifter.filters.decompress module

Wrapper for GNU Gzip decompression functionality.

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.

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
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.

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

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
main()[source]

samsifter.filters.filter_read_pmds module

Created on Thu Dec 18 09:34:28 2014

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.

calc_avg_depth(depth_dist, ignore_uncovered=True)[source]

Calculate average depth from a coverage distribution.

Optionally ignores uncovered bases (first array element).

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
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.

integral_discrete(dist, limit)[source]

Integrate discrete distribution with stepsize 1 by simply adding up values.

integral_scaled(dist, limit)[source]

Integrate scaled discrete distribution with arbitrary stepsize.

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
lorenzify(depth_dist)[source]

Calculate Lorenz curve from coverage distribution.

lorenzify_b2b(depth_dist, ignore_uncovered=True)[source]

Calculate Lorenz curve from base2base coverage distribution.

main()[source]
plot_ccd(ax, depth_dist_cumsum, avg_depth)[source]

Create a bar plot of a cumulative coverage distribution.

plot_cd(ax, depth_dist, avg_depth)[source]

Create a bar plot of a cumulative coverage distribution.

plot_lorenz(ax, x, y)[source]

Create a Lorenz curve plot of a coverage distribution.

plot_lorenz_b2b(ax, x, y)[source]

Create a Lorenz curve plot of a coverage distribution.

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

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.

plot_sccd(ax, depth_dist_cumperc, avg_depth)[source]

Create a bar plot of a scaled cumulative coverage distribution.

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”

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
main()[source]

samsifter.filters.filter_ref_list module

Created on Thu Dec 18 09:34:28 2014

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
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

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
main()[source]

samsifter.filters.filter_taxon_list module

Created on Thu Dec 18 09:34:28 2014

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
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

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
main()[source]

samsifter.filters.filter_test module

Created on Fri Jan 16 11:55:23 2015

@author: aldehoff

main()[source]

samsifter.filters.remove_duplicates module

Wrapper for SAMtools rmdup

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

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

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

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