UCore¶
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ursgal.ucore.
calculate_mass
(mz, charge)¶ Calculate mass function
Keyword Arguments: - mz (float) – mz of molecule/peak
- charge (int) – charge for calculating mass
Returns: calculated mass
Return type: float
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ursgal.ucore.
calculate_mz
(mass, charge)¶ Calculate m/z function
Keyword Arguments: - mass (float) – mass for calculating m/z
- charge (int) – charge for calculating m/z
Returns: calculated m/z
Return type: float
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ursgal.ucore.
convert_dalton_to_ppm
(da_value, base_mz=1000.0)¶ Convert the precision in Dalton to ppm
Keyword Arguments: - da_value (float) – Dalton value to transform
- base_mz (float) – factor for transformation
Returns: value in ppm
Return type: float
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ursgal.ucore.
convert_ppm_to_dalton
(ppm_value, base_mz=1000.0)¶ Normalize the precision in ppm to 1000 Dalton
Keyword Arguments: - ppm_value (float) – parts per million value to transform
- base_mz (float) – factor for transformation
Returns: value in Dalton
Return type: float
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ursgal.ucore.
count_distinct_psms
(csv_file_path=None, psm_defining_colnames=None)¶ Returns a counter based on PSM-defining column names (i.e spectrum & peptide, but also score field because sometimes the same PSMs are reported with different scores…).
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ursgal.ucore.
digest
(sequence, enzyme, count_missed_cleavages=None, no_missed_cleavages=False)¶ Amino acid digest function
Keyword Arguments: - sequence (str) – amino acid sequence to digest
- enzyme (tuple) – enzyme properties used for cleavage (‘aminoacid(s)’, ‘N/C(terminus)’) e.g. (‘KR’,’C’) for trypsin
- count_missed_cleavages (int) – number of miss cleavages allowed
Returns: list of digested peptides
Return type: list
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ursgal.ucore.
merge_duplicate_psm_rows
(csv_file_path=None, psm_counter=None, psm_defining_colnames=None, psm_colnames_to_merge_multiple_values={}, joinchar='<|>', overwrite_file=True)¶ Rows describing the same PSM (e.g. when two proteins share the same peptide) are merged to one row.
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ursgal.ucore.
merge_rowdicts
(list_of_rowdicts, psm_colnames_to_merge_multiple_values, joinchar='<|>')¶ Merges CSV rows. If the column values are conflicting, they are joined with a character (joinchar).
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ursgal.ucore.
parse_fasta
(io)¶ Small function to efficiently parse a file in fasta format.
Keyword Arguments: io (obj) – openend file obj (fasta file) Yields: tuple – fasta_id and sequence
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ursgal.ucore.
print_current_params
(params, old_params=None)¶ Function to print current params
Keyword Arguments: params (dict) – parameter dict to print
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ursgal.ucore.
reformat_peptide
(regex_pattern, unimod_name, peptide)¶ reformats the MQ and Novor peptide string to ursgal format (ac)SSSLM(ox)RPGPSR –> SSSLMRPGPSR#Acetyl:0;Oxidation:5
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ursgal.ucore.
terminal_supports_color
()¶ Returns True if the running system’s terminal supports color, and False otherwise. Source: https://github.com/django/django/blob/master/django/core/management/color.py