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Accession order fixes #330

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merged 5 commits into from
Sep 27, 2024
Merged

Accession order fixes #330

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3ff504a
fix script: detect unsorted accessions; feature: report gap size
cbielow Sep 16, 2024
d789b71
re-establish ordered accessions
cbielow Sep 16, 2024
4bc2d59
Update version
cbielow Sep 17, 2024
18df105
Update psi-ms.obo
mobiusklein Sep 27, 2024
ea5162e
Merge branch 'master' into next_acc
mobiusklein Sep 27, 2024
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34 changes: 17 additions & 17 deletions psi-ms.obo
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
format-version: 1.2
data-version: 4.1.176
date: 17:09:2024 15:26
saved-by: Michael Hoopmann
data-version: 4.1.177
date: 27:09:2024 07:15
saved-by: Chris Bielow
auto-generated-by: OBO-Edit 2.3.1
default-namespace: MS
namespace-id-rule: * MS:$sequence(7,0,9999999)$
Expand Down Expand Up @@ -22522,6 +22522,20 @@ name: spectrum clustering software
def: "Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte." [PSI:MS]
is_a: MS:1000531 ! software

[Term]
id: MS:1003407
name: Scout
def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003408
name: Scout score
def: "Scout identification search engine score" [PSI:MS]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1003407 ! higher score better
relationship: has_value_type xsd:double ! The allowed value-type for this CV term

[Term]
id: MS:1003409
name: Stellar
Expand Down Expand Up @@ -24306,20 +24320,6 @@ synonym: "RT-MSMS-Q2" RELATED [PMID:24494671]
synonym: "RT-MSMS-Q3" RELATED [PMID:24494671]
synonym: "RT-MSMS-Q4" RELATED [PMID:24494671]

[Term]
id: MS:1003407
name: Scout
def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS]
is_a: MS:1001456 ! analysis software

[Term]
id: MS:1003408
name: Scout score
def: "Scout identification search engine score" [PSI:MS]
is_a: MS:1001143 ! PSM-level search engine specific statistic
relationship: has_order MS:1003407 ! higher score better
relationship: has_value_type xsd:double ! The allowed value-type for this CV term

[Term]
id: PEFF:0000001
name: PEFF CV term
Expand Down
4 changes: 3 additions & 1 deletion scripts/find_next_available_number.py
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Original file line number Diff line number Diff line change
Expand Up @@ -22,10 +22,12 @@ def collect_gaps(stream, min_value=1000300):
last_seen[cv] = acc
continue
diff = acc - last_in_cv
if diff < 1:
sys.stderr.write(f"CV is not sorted! {cv}:{acc} found after {cv}:{last_in_cv}\n")
if diff > 1 and acc > min_value:
for i in range(1, diff):
gaps.append((cv, last_in_cv + i))
sys.stderr.write(f"Found gap {gaps[-diff + 1]} to {gaps[-1]}\n")
sys.stderr.write(f"Found gap of size {diff-1}: {gaps[-diff + 1]} to {gaps[-1]}\n")
last_seen[cv] = acc
return gaps, last_seen
except UnicodeDecodeError:
Expand Down
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