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Change default function to resolve GSM ids
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bin/sra_ids_to_runinfo.py

Lines changed: 7 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -193,9 +193,11 @@ def is_valid(cls, identifier):
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class DatabaseResolver:
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"""Define a service class for resolving various identifiers to experiments."""
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196-
_GEO_PREFIXES = {"GSE"}
196+
_GEO_PREFIXES = {
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"GSE",
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"GSM"
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}
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_SRA_PREFIXES = {
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"GSM",
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"PRJNA",
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"SAMN",
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"SRR",
@@ -207,7 +209,9 @@ class DatabaseResolver:
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"PRJDB",
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"SAMD",
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}
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_ENA_PREFIXES = {"ERR"}
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_ENA_PREFIXES = {
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"ERR"
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}
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@classmethod
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def expand_identifier(cls, identifier):

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