def create_library_unique_peptides_combined(all_psm_list):
full_peptide_set = ming_psm_library.PeptideVariantSet("Combined")
for psm_set in all_psm_list:
peptide_set = ming_psm_library.PeptideVariantSet("Test")
peptide_set.add_psms_set(psm_set)
peptide_set.filter_to_fdr(0.01)
full_peptide_set.add_variant_set(peptide_set)
return full_peptide_set
def create_library_variant_consistency(all_psm_list):
full_peptide_set = ming_psm_library.PeptideVariantSet("Combined")
for psm_set in all_psm_list:
peptide_set = ming_psm_library.PeptideVariantSet("Test")
peptide_set.add_psms_set(psm_set)
full_peptide_set.add_variant_set(peptide_set)
for variant in full_peptide_set.peptide_list:
library_creation_utilities.check_variant_psm_consistency(variant)
return full_peptide_set
def create_library_minimum_replicate_count(all_psm_list):
full_peptide_set = ming_psm_library.PeptideVariantSet("Combined")
for psm_set in all_psm_list:
peptide_set = ming_psm_library.PeptideVariantSet("Test")
peptide_set.add_psms_set(psm_set)
full_peptide_set.add_variant_set(peptide_set)
full_peptide_set_new = ming_psm_library.PeptideVariantSet("Combined")
for variant in full_peptide_set.peptide_list:
if variant.get_spectrum_count() > 1:
full_peptide_set_new.add_variant(variant)
return full_peptide_set_new
def create_library_unique_peptides_filtered(all_psm_list,
fdr=0.01,
filter_by_length=False):
full_peptide_set = ming_psm_library.PeptideVariantSet("Combined")
for psm_set in all_psm_list:
peptide_set = ming_psm_library.PeptideVariantSet("Test")
peptide_set.add_psms_set(psm_set)
full_peptide_set.add_variant_set(peptide_set)
if filter_by_length:
full_peptide_set.filter_to_fdr_by_length(fdr)
else:
full_peptide_set.filter_to_fdr(fdr)
return full_peptide_set
def create_library_merged_psm_list_separate_fdr_peptide_length(
psm_set, fdr=0.01):
full_peptide_set = ming_psm_library.PeptideVariantSet("Combined")
peptide_length_map = {}
for psm in psm_set.psms:
peptide_length = len(psm.get_stripped_sequence())
if not peptide_length in peptide_length_map:
peptide_length_map[peptide_length] = ming_psm_library.PSMset(
"length" + str(peptide_length))
peptide_length_map[peptide_length].psms.append(psm)
#Lets do FDR on each length
for peptide_length in peptide_length_map:
#print peptide_length_map[peptide_length]
peptide_set = ming_psm_library.PeptideVariantSet("Test")
peptide_set.add_psms_set(peptide_length_map[peptide_length])
peptide_set.filter_to_fdr(fdr)
full_peptide_set.add_variant_set(peptide_set)
#print full_peptide_set.peptide_list
return full_peptide_set